Fix for the CI

Feature/clover

.gitignore

@@ -93,6 +93,7 @@ build*/*
 *.xcodeproj/*
 build.sh
 .vscode
+*.code-workspace
 
 # Eigen source #
 ################
@@ -123,3 +124,8 @@ make-bin-BUCK.sh
 lib/qcd/spin/gamma-gen/*.h
 lib/qcd/spin/gamma-gen/*.cc
 
+# vs code editor files #
+########################
+.vscode/
+.vscode/settings.json
+settings.json

.travis.yml

@@ -9,68 +9,6 @@ matrix:
     - os:        osx
       osx_image: xcode8.3
       compiler: clang
-    - compiler: gcc
-      dist: trusty
-      sudo: required
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.9
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: VERSION=-4.9
-    - compiler: gcc
-      dist: trusty
-      sudo: required
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-5
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: VERSION=-5
-    - compiler: clang
-      dist: trusty
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.8
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: CLANG_LINK=http://llvm.org/releases/3.8.0/clang+llvm-3.8.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
-    - compiler: clang
-      dist: trusty
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.8
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: CLANG_LINK=http://llvm.org/releases/3.7.0/clang+llvm-3.7.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
       
 before_install:
     - export GRIDDIR=`pwd`
@@ -106,9 +44,4 @@ script:
     - make -j4
     - ./benchmarks/Benchmark_dwf --threads 1 --debug-signals
     - make check
-    - echo make clean
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then ../configure --enable-precision=single --enable-simd=SSE4 --enable-comms=mpi-auto ; fi
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then make -j4; fi
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then mpirun.openmpi -n 2 ./benchmarks/Benchmark_dwf --threads 1 --mpi 2.1.1.1; fi
-
 

README.md

@@ -1,27 +1,44 @@
-# Grid
-<table>
-<tr>
-    <td>Last stable release</td>
-    <td><a href="https://travis-ci.org/paboyle/Grid">
-    <img src="https://travis-ci.org/paboyle/Grid.svg?branch=master"></a>
-    </td>
-</tr>
-<tr>
-    <td>Development branch</td>
-    <td><a href="https://travis-ci.org/paboyle/Grid">
-    <img src="https://travis-ci.org/paboyle/Grid.svg?branch=develop"></a>
-    </td>
-</tr>
-</table>
+# Grid [![Teamcity status](http://ci.cliath.ph.ed.ac.uk/app/rest/builds/aggregated/strob:(buildType:(affectedProject(id:Grid)),branch:name:develop)/statusIcon.svg)](http://ci.cliath.ph.ed.ac.uk/project.html?projectId=Grid&tab=projectOverview) [![Travis status](https://travis-ci.org/paboyle/Grid.svg?branch=develop)](https://travis-ci.org/paboyle/Grid)
 
 **Data parallel C++ mathematical object library.**
 
 License: GPL v2.
 
-Last update Nov 2016.
+Last update June 2017.
 
 _Please do not send pull requests to the `master` branch which is reserved for releases._
 
+
+
+### Description
+This library provides data parallel C++ container classes with internal memory layout
+that is transformed to map efficiently to SIMD architectures. CSHIFT facilities
+are provided, similar to HPF and cmfortran, and user control is given over the mapping of
+array indices to both MPI tasks and SIMD processing elements.
+
+* Identically shaped arrays then be processed with perfect data parallelisation.
+* Such identically shaped arrays are called conformable arrays.
+
+The transformation is based on the observation that Cartesian array processing involves
+identical processing to be performed on different regions of the Cartesian array.
+
+The library will both geometrically decompose into MPI tasks and across SIMD lanes.
+Local vector loops are parallelised with OpenMP pragmas.
+
+Data parallel array operations can then be specified with a SINGLE data parallel paradigm, but
+optimally use MPI, OpenMP and SIMD parallelism under the hood. This is a significant simplification
+for most programmers.
+
+The layout transformations are parametrised by the SIMD vector length. This adapts according to the architecture.
+Presently SSE4, ARM NEON (128 bits) AVX, AVX2, QPX (256 bits), IMCI and AVX512 (512 bits) targets are supported.
+
+These are presented as `vRealF`, `vRealD`, `vComplexF`, and `vComplexD` internal vector data types. 
+The corresponding scalar types are named `RealF`, `RealD`, `ComplexF` and `ComplexD`.
+
+MPI, OpenMP, and SIMD parallelism are present in the library.
+Please see [this paper](https://arxiv.org/abs/1512.03487) for more detail.
+
+
 ### Compilers
 
 Intel ICPC v16.0.3 and later
@@ -56,35 +73,25 @@ When you file an issue, please go though the following checklist:
 6. Attach the output of `make V=1`.
 7. Describe the issue and any previous attempt to solve it. If relevant, show how to reproduce the issue using a minimal working example.
 
+### Required libraries
+Grid requires:
 
+[GMP](https://gmplib.org/), 
 
-### Description
-This library provides data parallel C++ container classes with internal memory layout
-that is transformed to map efficiently to SIMD architectures. CSHIFT facilities
-are provided, similar to HPF and cmfortran, and user control is given over the mapping of
-array indices to both MPI tasks and SIMD processing elements.
+[MPFR](http://www.mpfr.org/) 
 
-* Identically shaped arrays then be processed with perfect data parallelisation.
-* Such identically shaped arrays are called conformable arrays.
+Bootstrapping grid downloads and uses for internal dense matrix (non-QCD operations) the Eigen library.
 
-The transformation is based on the observation that Cartesian array processing involves
-identical processing to be performed on different regions of the Cartesian array.
+Grid optionally uses:
 
-The library will both geometrically decompose into MPI tasks and across SIMD lanes.
-Local vector loops are parallelised with OpenMP pragmas.
+[HDF5](https://support.hdfgroup.org/HDF5/)  
 
-Data parallel array operations can then be specified with a SINGLE data parallel paradigm, but
-optimally use MPI, OpenMP and SIMD parallelism under the hood. This is a significant simplification
-for most programmers.
+[LIME](http://usqcd-software.github.io/c-lime/) for ILDG and SciDAC file format support. 
 
-The layout transformations are parametrised by the SIMD vector length. This adapts according to the architecture.
-Presently SSE4 (128 bit) AVX, AVX2, QPX (256 bit), IMCI, and AVX512 (512 bit) targets are supported (ARM NEON on the way).
+[FFTW](http://www.fftw.org) either generic version or via the Intel MKL library.
 
-These are presented as `vRealF`, `vRealD`, `vComplexF`, and `vComplexD` internal vector data types. These may be useful in themselves for other programmers.
-The corresponding scalar types are named `RealF`, `RealD`, `ComplexF` and `ComplexD`.
+LAPACK either generic version or Intel MKL library.
 
-MPI, OpenMP, and SIMD parallelism are present in the library.
-Please see https://arxiv.org/abs/1512.03487 for more detail.
 
 ### Quick start
 First, start by cloning the repository:
@@ -155,7 +162,6 @@ The following options can be use with the `--enable-comms=` option to target dif
 | `none`         | no communications                                             |
 | `mpi[-auto]`   | MPI communications                                            |
 | `mpi3[-auto]`  | MPI communications using MPI 3 shared memory                  |
-| `mpi3l[-auto]` | MPI communications using MPI 3 shared memory and leader model |
 | `shmem `       | Cray SHMEM communications                                     |
 
 For the MPI interfaces the optional `-auto` suffix instructs the `configure` scripts to determine all the necessary compilation and linking flags. This is done by extracting the informations from the MPI wrapper specified in the environment variable `MPICXX` (if not specified `configure` will scan though a list of default names). The `-auto` suffix is not supported by the Cray environment wrapper scripts. Use the standard versions instead.  
@@ -173,7 +179,8 @@ The following options can be use with the `--enable-simd=` option to target diff
 | `AVXFMA4`   | AVX (256 bit) + FMA4                   |
 | `AVX2`      | AVX 2 (256 bit)                        |
 | `AVX512`    | AVX 512 bit                            |
-| `QPX`       | QPX (256 bit)                          |
+| `NEONv8`    | [ARM NEON](http://infocenter.arm.com/help/index.jsp?topic=/com.arm.doc.den0024a/ch07s03.html) (128 bit)                     |
+| `QPX`       | IBM QPX (256 bit)                      |
 
 Alternatively, some CPU codenames can be directly used:
 
@@ -195,21 +202,205 @@ The following configuration is recommended for the Intel Knights Landing platfor
 ``` bash
 ../configure --enable-precision=double\
              --enable-simd=KNL        \
-             --enable-comms=mpi-auto \
-             --with-gmp=<path>        \
-             --with-mpfr=<path>       \
+             --enable-comms=mpi-auto  \
              --enable-mkl             \
              CXX=icpc MPICXX=mpiicpc
 ```
+The MKL flag enables use of BLAS and FFTW from the Intel Math Kernels Library.
 
-where `<path>` is the UNIX prefix where GMP and MPFR are installed. If you are working on a Cray machine that does not use the `mpiicpc` wrapper, please use:
+If you are working on a Cray machine that does not use the `mpiicpc` wrapper, please use:
 
 ``` bash
 ../configure --enable-precision=double\
              --enable-simd=KNL        \
              --enable-comms=mpi       \
-             --with-gmp=<path>        \
-             --with-mpfr=<path>       \
              --enable-mkl             \
              CXX=CC CC=cc
-```
+```
+
+If gmp and mpfr are NOT in standard places (/usr/) these flags may be needed:
+``` bash
+               --with-gmp=<path>        \
+               --with-mpfr=<path>       \
+```
+where `<path>` is the UNIX prefix where GMP and MPFR are installed. 
+
+Knight's Landing with Intel Omnipath adapters with two adapters per node 
+presently performs better with use of more than one rank per node, using shared memory 
+for interior communication. This is the mpi3 communications implementation. 
+We recommend four ranks per node for best performance, but optimum is local volume dependent.
+
+``` bash
+../configure --enable-precision=double\
+             --enable-simd=KNL        \
+             --enable-comms=mpi3-auto \
+             --enable-mkl             \
+             CC=icpc MPICXX=mpiicpc 
+```
+
+### Build setup for Intel Haswell Xeon platform
+
+The following configuration is recommended for the Intel Haswell platform:
+
+``` bash
+../configure --enable-precision=double\
+             --enable-simd=AVX2       \
+             --enable-comms=mpi3-auto \
+             --enable-mkl             \
+             CXX=icpc MPICXX=mpiicpc
+```
+The MKL flag enables use of BLAS and FFTW from the Intel Math Kernels Library.
+
+If gmp and mpfr are NOT in standard places (/usr/) these flags may be needed:
+``` bash
+               --with-gmp=<path>        \
+               --with-mpfr=<path>       \
+```
+where `<path>` is the UNIX prefix where GMP and MPFR are installed. 
+
+If you are working on a Cray machine that does not use the `mpiicpc` wrapper, please use:
+
+``` bash
+../configure --enable-precision=double\
+             --enable-simd=AVX2       \
+             --enable-comms=mpi3      \
+             --enable-mkl             \
+             CXX=CC CC=cc
+```
+Since Dual socket nodes are commonplace, we recommend MPI-3 as the default with the use of 
+one rank per socket. If using the Intel MPI library, threads should be pinned to NUMA domains using
+```
+        export I_MPI_PIN=1
+```
+This is the default.
+
+### Build setup for Intel Skylake Xeon platform
+
+The following configuration is recommended for the Intel Skylake platform:
+
+``` bash
+../configure --enable-precision=double\
+             --enable-simd=AVX512     \
+             --enable-comms=mpi3      \
+             --enable-mkl             \
+             CXX=mpiicpc
+```
+The MKL flag enables use of BLAS and FFTW from the Intel Math Kernels Library.
+
+If gmp and mpfr are NOT in standard places (/usr/) these flags may be needed:
+``` bash
+               --with-gmp=<path>        \
+               --with-mpfr=<path>       \
+```
+where `<path>` is the UNIX prefix where GMP and MPFR are installed. 
+
+If you are working on a Cray machine that does not use the `mpiicpc` wrapper, please use:
+
+``` bash
+../configure --enable-precision=double\
+             --enable-simd=AVX512     \
+             --enable-comms=mpi3      \
+             --enable-mkl             \
+             CXX=CC CC=cc
+```
+Since Dual socket nodes are commonplace, we recommend MPI-3 as the default with the use of 
+one rank per socket. If using the Intel MPI library, threads should be pinned to NUMA domains using
+``` 
+        export I_MPI_PIN=1
+```
+This is the default. 
+
+#### Expected Skylake Gold 6148 dual socket (single prec, single node 20+20 cores) performance using NUMA MPI mapping): 
+
+mpirun -n 2 benchmarks/Benchmark_dwf --grid 16.16.16.16 --mpi 2.1.1.1 --cacheblocking 2.2.2.2 --dslash-asm --shm 1024 --threads 18 
+
+TBA
+
+
+### Build setup for AMD EPYC / RYZEN
+
+The AMD EPYC is a multichip module comprising 32 cores spread over four distinct chips each with 8 cores.
+So, even with a single socket node there is a quad-chip module. Dual socket nodes with 64 cores total
+are common. Each chip within the module exposes a separate NUMA domain.
+There are four NUMA domains per socket and we recommend one MPI rank per NUMA domain.
+MPI-3 is recommended with the use of four ranks per socket,
+and 8 threads per rank. 
+
+The following configuration is recommended for the AMD EPYC platform.
+
+``` bash
+../configure --enable-precision=double\
+             --enable-simd=AVX2       \
+             --enable-comms=mpi3 \
+             CXX=mpicxx 
+```
+
+If gmp and mpfr are NOT in standard places (/usr/) these flags may be needed:
+``` bash
+               --with-gmp=<path>        \
+               --with-mpfr=<path>       \
+```
+where `<path>` is the UNIX prefix where GMP and MPFR are installed. 
+
+Using MPICH and g++ v4.9.2, best performance can be obtained using explicit GOMP_CPU_AFFINITY flags for each MPI rank.
+This can be done by invoking MPI on a wrapper script omp_bind.sh to handle this. 
+
+It is recommended to run 8 MPI ranks on a single dual socket AMD EPYC, with 8 threads per rank using MPI3 and
+shared memory to communicate within this node:
+
+mpirun -np 8 ./omp_bind.sh ./Benchmark_dwf --mpi 2.2.2.1 --dslash-unroll --threads 8 --grid 16.16.16.16 --cacheblocking 4.4.4.4 
+
+Where omp_bind.sh does the following:
+```
+#!/bin/bash
+
+numanode=` expr $PMI_RANK % 8 `
+basecore=`expr $numanode \* 16`
+core0=`expr $basecore + 0 `
+core1=`expr $basecore + 2 `
+core2=`expr $basecore + 4 `
+core3=`expr $basecore + 6 `
+core4=`expr $basecore + 8 `
+core5=`expr $basecore + 10 `
+core6=`expr $basecore + 12 `
+core7=`expr $basecore + 14 `
+
+export GOMP_CPU_AFFINITY="$core0 $core1 $core2 $core3 $core4 $core5 $core6 $core7"
+echo GOMP_CUP_AFFINITY $GOMP_CPU_AFFINITY
+
+$@
+```
+
+Performance:
+
+#### Expected AMD EPYC 7601 dual socket (single prec, single node 32+32 cores) performance using NUMA MPI mapping): 
+
+mpirun  -np 8 ./omp_bind.sh ./Benchmark_dwf --threads 8 --mpi 2.2.2.1 --dslash-unroll --grid 16.16.16.16 --cacheblocking 4.4.4.4
+
+TBA
+
+### Build setup for BlueGene/Q
+
+To be written...
+
+### Build setup for ARM Neon
+
+To be written...
+
+### Build setup for laptops, other compilers, non-cluster builds
+
+Many versions of g++ and clang++ work with Grid, and involve merely replacing CXX (and MPICXX),
+and omit the enable-mkl flag. 
+
+Single node builds are enabled with 
+```
+            --enable-comms=none
+```
+
+FFTW support that is not in the default search path may then enabled with
+```
+    --with-fftw=<installpath>
+```
+
+BLAS will not be compiled in by default, and Lanczos will default to Eigen diagonalisation.
+

TODO

@@ -1,23 +1,48 @@
 TODO:
 ---------------
 
-Peter's work list:
-2)- Precision conversion and sort out localConvert      <-- 
-3)- Remove DenseVector, DenseMatrix; Use Eigen instead. <-- started 
-4)- Binary I/O speed up & x-strips
--- Profile CG, BlockCG, etc... Flop count/rate -- PARTIAL, time but no flop/s yet
--- Physical propagator interface
--- Conserved currents
--- GaugeFix into central location
--- Multigrid Wilson and DWF, compare to other Multigrid implementations
--- HDCR resume
+Code item work list
 
+a) namespaces & indentation
+ GRID_BEGIN_NAMESPACE();
+ GRID_END_NAMESPACE();
+-- delete QCD namespace
+
+b) GPU branch
+- start branch
+- Increase Macro use in core library support; prepare for change
+- Audit volume of "device" code
+- Virtual function audit
+- Start port once Nvidia box is up
+- Cut down volume of code for first port? How?
+
+Physics item work list:
+
+1)- BG/Q port and check ; Andrew says ok.
+2)- Consistent linear solver flop count/rate -- PARTIAL, time but no flop/s yet
+3)- Physical propagator interface
+4)- Multigrid Wilson and DWF, compare to other Multigrid implementations
+5)- HDCR resume
+
+----------------------------
 Recent DONE 
+-- RNG I/O in ILDG/SciDAC (minor) 
+-- Precision conversion and sort out localConvert      <-- partial/easy
+-- Conserved currents (Andrew)
+-- Split grid
+-- Christoph's local basis expansion Lanczos
+-- MultiRHS with spread out extra dim -- Go through filesystem with SciDAC I/O ; <-- DONE ; bmark cori
+-- Lanczos Remove DenseVector, DenseMatrix; Use Eigen instead. <-- DONE
+-- GaugeFix into central location                      <-- DONE
+-- Scidac and Ildg metadata handling                   <-- DONE
+-- Binary I/O MPI2 IO                                  <-- DONE
+-- Binary I/O speed up & x-strips                      <-- DONE
 -- Cut down the exterior overhead                      <-- DONE
 -- Interior legs from SHM comms                        <-- DONE
 -- Half-precision comms                                <-- DONE
--- Merge high precision reduction into develop        
--- multiRHS DWF; benchmark on Cori/BNL for comms elimination
+-- Merge high precision reduction into develop         <-- DONE
+-- BlockCG, BCGrQ                                      <-- DONE
+-- multiRHS DWF; benchmark on Cori/BNL for comms elimination <-- DONE
    -- slice* linalg routines for multiRHS, BlockCG    
 
 -----

benchmarks/Benchmark_ITT.cc

@@ -0,0 +1,800 @@
+    /*************************************************************************************
+
+    Grid physics library, www.github.com/paboyle/Grid 
+
+    Source file: ./benchmarks/Benchmark_memory_bandwidth.cc
+
+    Copyright (C) 2015
+
+Author: Peter Boyle <paboyle@ph.ed.ac.uk>
+Author: paboyle <paboyle@ph.ed.ac.uk>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+    See the full license in the file "LICENSE" in the top level distribution directory
+    *************************************************************************************/
+    /*  END LEGAL */
+#include <Grid/Grid.h>
+
+using namespace std;
+using namespace Grid;
+using namespace Grid::QCD;
+
+typedef WilsonFermion5D<DomainWallVec5dImplR> WilsonFermion5DR;
+typedef WilsonFermion5D<DomainWallVec5dImplF> WilsonFermion5DF;
+typedef WilsonFermion5D<DomainWallVec5dImplD> WilsonFermion5DD;
+
+
+std::vector<int> L_list;
+std::vector<int> Ls_list;
+std::vector<double> mflop_list;
+
+double mflop_ref;
+double mflop_ref_err;
+
+int NN_global;
+
+struct time_statistics{
+  double mean;
+  double err;
+  double min;
+  double max;
+
+  void statistics(std::vector<double> v){
+      double sum = std::accumulate(v.begin(), v.end(), 0.0);
+      mean = sum / v.size();
+
+      std::vector<double> diff(v.size());
+      std::transform(v.begin(), v.end(), diff.begin(), [=](double x) { return x - mean; });
+      double sq_sum = std::inner_product(diff.begin(), diff.end(), diff.begin(), 0.0);
+      err = std::sqrt(sq_sum / (v.size()*(v.size() - 1)));
+
+      auto result = std::minmax_element(v.begin(), v.end());
+      min = *result.first;
+      max = *result.second;
+}
+};
+
+void comms_header(){
+  std::cout <<GridLogMessage << " L  "<<"\t"<<" Ls  "<<"\t"
+            <<std::setw(11)<<"bytes"<<"MB/s uni (err/min/max)"<<"\t\t"<<"MB/s bidi (err/min/max)"<<std::endl;
+};
+
+Gamma::Algebra Gmu [] = {
+  Gamma::Algebra::GammaX,
+  Gamma::Algebra::GammaY,
+  Gamma::Algebra::GammaZ,
+  Gamma::Algebra::GammaT
+};
+struct controls {
+  int Opt;
+  int CommsOverlap;
+  Grid::CartesianCommunicator::CommunicatorPolicy_t CommsAsynch;
+  //  int HugePages;
+};
+
+class Benchmark {
+public:
+  static void Decomposition (void ) {
+
+    int threads = GridThread::GetThreads();
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "= Grid is setup to use "<<threads<<" threads"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage<<"Grid Default Decomposition patterns\n";
+    std::cout<<GridLogMessage<<"\tOpenMP threads : "<<GridThread::GetThreads()<<std::endl;
+    std::cout<<GridLogMessage<<"\tMPI tasks      : "<<GridCmdVectorIntToString(GridDefaultMpi())<<std::endl;
+    std::cout<<GridLogMessage<<"\tvReal          : "<<sizeof(vReal )*8    <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vReal::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvRealF         : "<<sizeof(vRealF)*8    <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vRealF::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvRealD         : "<<sizeof(vRealD)*8    <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vRealD::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvComplex       : "<<sizeof(vComplex )*8 <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vComplex::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvComplexF      : "<<sizeof(vComplexF)*8 <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vComplexF::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvComplexD      : "<<sizeof(vComplexD)*8 <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vComplexD::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+  }
+
+  static void Comms(void)
+  {
+    int Nloop=200;
+    int nmu=0;
+    int maxlat=32;
+
+    std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplexD::Nsimd());
+    std::vector<int> mpi_layout  = GridDefaultMpi();
+
+    for(int mu=0;mu<Nd;mu++) if (mpi_layout[mu]>1) nmu++;
+
+    std::vector<double> t_time(Nloop);
+    time_statistics timestat;
+
+    std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "= Benchmarking threaded STENCIL halo exchange in "<<nmu<<" dimensions"<<std::endl;
+    std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+    comms_header();
+
+    for(int lat=4;lat<=maxlat;lat+=4){
+      for(int Ls=8;Ls<=8;Ls*=2){
+
+	std::vector<int> latt_size  ({lat*mpi_layout[0],
+	      lat*mpi_layout[1],
+	      lat*mpi_layout[2],
+	      lat*mpi_layout[3]});
+
+	GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+	RealD Nrank = Grid._Nprocessors;
+	RealD Nnode = Grid.NodeCount();
+	RealD ppn = Nrank/Nnode;
+
+	std::vector<HalfSpinColourVectorD *> xbuf(8);
+	std::vector<HalfSpinColourVectorD *> rbuf(8);
+	Grid.ShmBufferFreeAll();
+	for(int d=0;d<8;d++){
+	  xbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	  rbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	  bzero((void *)xbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	  bzero((void *)rbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	}
+
+	int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
+	int ncomm;
+	double dbytes;
+	std::vector<double> times(Nloop);
+	for(int i=0;i<Nloop;i++){
+
+	  double start=usecond();
+
+	  dbytes=0;
+	  ncomm=0;
+
+	  parallel_for(int dir=0;dir<8;dir++){
+
+	    double tbytes;
+	    int mu =dir % 4;
+
+	    if (mpi_layout[mu]>1 ) {
+	        
+	      int xmit_to_rank;
+	      int recv_from_rank;
+	      if ( dir == mu ) { 
+		int comm_proc=1;
+		Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	      } else { 
+		int comm_proc = mpi_layout[mu]-1;
+		Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	      }
+	      tbytes= Grid.StencilSendToRecvFrom((void *)&xbuf[dir][0], xmit_to_rank,
+						 (void *)&rbuf[dir][0], recv_from_rank,
+						 bytes,dir);
+	  
+#ifdef GRID_OMP
+#pragma omp atomic
+#endif
+	      ncomm++;
+
+#ifdef GRID_OMP
+#pragma omp atomic
+#endif
+	      dbytes+=tbytes;
+	    }
+	  }
+	  Grid.Barrier();
+	  double stop=usecond();
+	  t_time[i] = stop-start; // microseconds
+	}
+
+	timestat.statistics(t_time);
+	//	for(int i=0;i<t_time.size();i++){
+	//	  std::cout << i<<" "<<t_time[i]<<std::endl;
+	//	}
+
+	dbytes=dbytes*ppn;
+	double xbytes    = dbytes*0.5;
+	double rbytes    = dbytes*0.5;
+	double bidibytes = dbytes;
+
+	std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+		 <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+		 <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+		 <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+		 << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+		 << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
+
+ 
+	
+	    }
+    }    
+
+    return;
+  }
+
+  static void Memory(void)
+  {
+    const int Nvec=8;
+    typedef Lattice< iVector< vReal,Nvec> > LatticeVec;
+    typedef iVector<vReal,Nvec> Vec;
+
+    std::vector<int> simd_layout = GridDefaultSimd(Nd,vReal::Nsimd());
+    std::vector<int> mpi_layout  = GridDefaultMpi();
+
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "= Benchmarking a*x + y bandwidth"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "  L  "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<< "\t\tGB/s / node"<<std::endl;
+    std::cout<<GridLogMessage << "----------------------------------------------------------"<<std::endl;
+  
+    uint64_t NP;
+    uint64_t NN;
+
+
+  uint64_t lmax=48;
+#define NLOOP (100*lmax*lmax*lmax*lmax/lat/lat/lat/lat)
+
+    GridSerialRNG          sRNG;      sRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
+    for(int lat=8;lat<=lmax;lat+=4){
+
+      std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
+      int64_t vol= latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+
+      NP= Grid.RankCount();
+      NN =Grid.NodeCount();
+
+      Vec rn ; random(sRNG,rn);
+
+      LatticeVec z(&Grid); z=rn;
+      LatticeVec x(&Grid); x=rn;
+      LatticeVec y(&Grid); y=rn;
+      double a=2.0;
+
+      uint64_t Nloop=NLOOP;
+
+      double start=usecond();
+      for(int i=0;i<Nloop;i++){
+	z=a*x-y;
+        x._odata[0]=z._odata[0]; // force serial dependency to prevent optimise away
+        y._odata[4]=z._odata[4];
+      }
+      double stop=usecond();
+      double time = (stop-start)/Nloop*1000;
+     
+      double flops=vol*Nvec*2;// mul,add
+      double bytes=3.0*vol*Nvec*sizeof(Real);
+      std::cout<<GridLogMessage<<std::setprecision(3) 
+	       << lat<<"\t\t"<<bytes<<"   \t\t"<<bytes/time<<"\t\t"<<flops/time<<"\t\t"<<(stop-start)/1000./1000.
+	       << "\t\t"<< bytes/time/NN <<std::endl;
+
+    }
+  };
+
+  static double DWF5(int Ls,int L)
+  {
+    RealD mass=0.1;
+    RealD M5  =1.8;
+
+    double mflops;
+    double mflops_best = 0;
+    double mflops_worst= 0;
+    std::vector<double> mflops_all;
+
+    ///////////////////////////////////////////////////////
+    // Set/Get the layout & grid size
+    ///////////////////////////////////////////////////////
+    int threads = GridThread::GetThreads();
+    std::vector<int> mpi = GridDefaultMpi(); assert(mpi.size()==4);
+    std::vector<int> local({L,L,L,L});
+
+    GridCartesian         * TmpGrid   = SpaceTimeGrid::makeFourDimGrid(std::vector<int>({64,64,64,64}), 
+								       GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    uint64_t NP = TmpGrid->RankCount();
+    uint64_t NN = TmpGrid->NodeCount();
+    NN_global=NN;
+    uint64_t SHM=NP/NN;
+
+    std::vector<int> internal;
+    if      ( SHM == 1 )   internal = std::vector<int>({1,1,1,1});
+    else if ( SHM == 2 )   internal = std::vector<int>({2,1,1,1});
+    else if ( SHM == 4 )   internal = std::vector<int>({2,2,1,1});
+    else if ( SHM == 8 )   internal = std::vector<int>({2,2,2,1});
+    else assert(0);
+
+    std::vector<int> nodes({mpi[0]/internal[0],mpi[1]/internal[1],mpi[2]/internal[2],mpi[3]/internal[3]});
+    std::vector<int> latt4({local[0]*nodes[0],local[1]*nodes[1],local[2]*nodes[2],local[3]*nodes[3]});
+
+    ///////// Welcome message ////////////
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "Benchmark DWF Ls vec on "<<L<<"^4 local volume "<<std::endl;
+    std::cout<<GridLogMessage << "* Global volume  : "<<GridCmdVectorIntToString(latt4)<<std::endl;
+    std::cout<<GridLogMessage << "* Ls             : "<<Ls<<std::endl;
+    std::cout<<GridLogMessage << "* MPI ranks      : "<<GridCmdVectorIntToString(mpi)<<std::endl;
+    std::cout<<GridLogMessage << "* Intranode      : "<<GridCmdVectorIntToString(internal)<<std::endl;
+    std::cout<<GridLogMessage << "* nodes          : "<<GridCmdVectorIntToString(nodes)<<std::endl;
+    std::cout<<GridLogMessage << "* Using "<<threads<<" threads"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+    ///////// Lattice Init ////////////
+    GridCartesian         * UGrid    = SpaceTimeGrid::makeFourDimGrid(latt4, GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    GridRedBlackCartesian * UrbGrid  = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
+    GridCartesian         * sUGrid   = SpaceTimeGrid::makeFourDimDWFGrid(latt4,GridDefaultMpi());
+    GridRedBlackCartesian * sUrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(sUGrid);
+    GridCartesian         * sFGrid   = SpaceTimeGrid::makeFiveDimDWFGrid(Ls,UGrid);
+    GridRedBlackCartesian * sFrbGrid = SpaceTimeGrid::makeFiveDimDWFRedBlackGrid(Ls,UGrid);
+
+    ///////// RNG Init ////////////
+    std::vector<int> seeds4({1,2,3,4});
+    std::vector<int> seeds5({5,6,7,8});
+    GridParallelRNG          RNG4(UGrid);  RNG4.SeedFixedIntegers(seeds4);
+    GridParallelRNG          RNG5(sFGrid);  RNG5.SeedFixedIntegers(seeds5);
+    std::cout << GridLogMessage << "Initialised RNGs" << std::endl;
+
+    ///////// Source preparation ////////////
+    LatticeFermion src   (sFGrid); random(RNG5,src);
+    LatticeFermion tmp   (sFGrid);
+
+    RealD N2 = 1.0/::sqrt(norm2(src));
+    src = src*N2;
+    
+    LatticeGaugeField Umu(UGrid);  SU3::HotConfiguration(RNG4,Umu); 
+
+    WilsonFermion5DR sDw(Umu,*sFGrid,*sFrbGrid,*sUGrid,*sUrbGrid,M5);
+    LatticeFermion src_e (sFrbGrid);
+    LatticeFermion src_o (sFrbGrid);
+    LatticeFermion r_e   (sFrbGrid);
+    LatticeFermion r_o   (sFrbGrid);
+    LatticeFermion r_eo  (sFGrid);
+    LatticeFermion err   (sFGrid);
+    {
+
+      pickCheckerboard(Even,src_e,src);
+      pickCheckerboard(Odd,src_o,src);
+
+#if defined(AVX512) 
+      const int num_cases = 6;
+      std::string fmt("A/S ; A/O ; U/S ; U/O ; G/S ; G/O ");
+#else
+      const int num_cases = 4;
+      std::string fmt("U/S ; U/O ; G/S ; G/O ");
+#endif
+      controls Cases [] = {
+#ifdef AVX512
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+#endif
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  }
+      }; 
+
+      for(int c=0;c<num_cases;c++) {
+
+	QCD::WilsonKernelsStatic::Comms = Cases[c].CommsOverlap;
+	QCD::WilsonKernelsStatic::Opt   = Cases[c].Opt;
+	CartesianCommunicator::SetCommunicatorPolicy(Cases[c].CommsAsynch);
+
+	std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+	if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptGeneric   ) std::cout << GridLogMessage<< "* Using GENERIC Nc WilsonKernels" <<std::endl;
+	if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptHandUnroll) std::cout << GridLogMessage<< "* Using Nc=3       WilsonKernels" <<std::endl;
+	if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptInlineAsm ) std::cout << GridLogMessage<< "* Using Asm Nc=3   WilsonKernels" <<std::endl;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsAndCompute ) std::cout << GridLogMessage<< "* Using Overlapped Comms/Compute" <<std::endl;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsThenCompute) std::cout << GridLogMessage<< "* Using sequential comms compute" <<std::endl;
+	if ( sizeof(Real)==4 )   std::cout << GridLogMessage<< "* SINGLE precision "<<std::endl;
+	if ( sizeof(Real)==8 )   std::cout << GridLogMessage<< "* DOUBLE precision "<<std::endl;
+	std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+	int nwarm = 100;
+	uint64_t ncall = 1000;
+
+	double t0=usecond();
+	sFGrid->Barrier();
+	for(int i=0;i<nwarm;i++){
+	  sDw.DhopEO(src_o,r_e,DaggerNo);
+	}
+	sFGrid->Barrier();
+	double t1=usecond();
+
+	sDw.ZeroCounters();
+	time_statistics timestat;
+	std::vector<double> t_time(ncall);
+	for(uint64_t i=0;i<ncall;i++){
+	  t0=usecond();
+	  sDw.DhopEO(src_o,r_e,DaggerNo);
+	  t1=usecond();
+	  t_time[i] = t1-t0;
+	}
+	sFGrid->Barrier();
+	
+	double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+	double flops=(1344.0*volume)/2;
+	double mf_hi, mf_lo, mf_err;
+
+	timestat.statistics(t_time);
+	mf_hi = flops/timestat.min;
+	mf_lo = flops/timestat.max;
+	mf_err= flops/timestat.min * timestat.err/timestat.mean;
+
+	mflops = flops/timestat.mean;
+	mflops_all.push_back(mflops);
+	if ( mflops_best == 0   ) mflops_best = mflops;
+	if ( mflops_worst== 0   ) mflops_worst= mflops;
+	if ( mflops>mflops_best ) mflops_best = mflops;
+	if ( mflops<mflops_worst) mflops_worst= mflops;
+
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"sDeo mflop/s =   "<< mflops << " ("<<mf_err<<") " << mf_lo<<"-"<<mf_hi <<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"sDeo mflop/s per rank   "<< mflops/NP<<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"sDeo mflop/s per node   "<< mflops/NN<<std::endl;
+
+	sDw.Report();
+
+      }
+      double robust = mflops_worst/mflops_best;;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " sDeo Best  mflop/s        =   "<< mflops_best << " ; " << mflops_best/NN<<" per node " <<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " sDeo Worst mflop/s        =   "<< mflops_worst<< " ; " << mflops_worst/NN<<" per node " <<std::endl;
+
+      std::cout<<GridLogMessage <<std::setprecision(3)<< L<<"^4 x "<<Ls<< " Performance Robustness   =   "<< robust <<std::endl;
+      std::cout<<GridLogMessage <<fmt << std::endl;
+      std::cout<<GridLogMessage;
+
+      for(int i=0;i<mflops_all.size();i++){
+	std::cout<<mflops_all[i]/NN<<" ; " ;
+      }
+      std::cout<<std::endl;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+    }
+    return mflops_best;
+  }
+
+  static double DWF(int Ls,int L, double & robust)
+  {
+    RealD mass=0.1;
+    RealD M5  =1.8;
+
+    double mflops;
+    double mflops_best = 0;
+    double mflops_worst= 0;
+    std::vector<double> mflops_all;
+
+    ///////////////////////////////////////////////////////
+    // Set/Get the layout & grid size
+    ///////////////////////////////////////////////////////
+    int threads = GridThread::GetThreads();
+    std::vector<int> mpi = GridDefaultMpi(); assert(mpi.size()==4);
+    std::vector<int> local({L,L,L,L});
+
+    GridCartesian         * TmpGrid   = SpaceTimeGrid::makeFourDimGrid(std::vector<int>({64,64,64,64}), 
+								       GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    uint64_t NP = TmpGrid->RankCount();
+    uint64_t NN = TmpGrid->NodeCount();
+    NN_global=NN;
+    uint64_t SHM=NP/NN;
+
+    std::vector<int> internal;
+    if      ( SHM == 1 )   internal = std::vector<int>({1,1,1,1});
+    else if ( SHM == 2 )   internal = std::vector<int>({2,1,1,1});
+    else if ( SHM == 4 )   internal = std::vector<int>({2,2,1,1});
+    else if ( SHM == 8 )   internal = std::vector<int>({2,2,2,1});
+    else assert(0);
+
+    std::vector<int> nodes({mpi[0]/internal[0],mpi[1]/internal[1],mpi[2]/internal[2],mpi[3]/internal[3]});
+    std::vector<int> latt4({local[0]*nodes[0],local[1]*nodes[1],local[2]*nodes[2],local[3]*nodes[3]});
+
+    ///////// Welcome message ////////////
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "Benchmark DWF on "<<L<<"^4 local volume "<<std::endl;
+    std::cout<<GridLogMessage << "* Global volume  : "<<GridCmdVectorIntToString(latt4)<<std::endl;
+    std::cout<<GridLogMessage << "* Ls             : "<<Ls<<std::endl;
+    std::cout<<GridLogMessage << "* MPI ranks      : "<<GridCmdVectorIntToString(mpi)<<std::endl;
+    std::cout<<GridLogMessage << "* Intranode      : "<<GridCmdVectorIntToString(internal)<<std::endl;
+    std::cout<<GridLogMessage << "* nodes          : "<<GridCmdVectorIntToString(nodes)<<std::endl;
+    std::cout<<GridLogMessage << "* Using "<<threads<<" threads"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+
+    ///////// Lattice Init ////////////
+    GridCartesian         * UGrid   = SpaceTimeGrid::makeFourDimGrid(latt4, GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    GridRedBlackCartesian * UrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
+    GridCartesian         * FGrid   = SpaceTimeGrid::makeFiveDimGrid(Ls,UGrid);
+    GridRedBlackCartesian * FrbGrid = SpaceTimeGrid::makeFiveDimRedBlackGrid(Ls,UGrid);
+
+    
+    ///////// RNG Init ////////////
+    std::vector<int> seeds4({1,2,3,4});
+    std::vector<int> seeds5({5,6,7,8});
+    GridParallelRNG          RNG4(UGrid);  RNG4.SeedFixedIntegers(seeds4);
+    GridParallelRNG          RNG5(FGrid);  RNG5.SeedFixedIntegers(seeds5);
+    std::cout << GridLogMessage << "Initialised RNGs" << std::endl;
+
+    ///////// Source preparation ////////////
+    LatticeFermion src   (FGrid); random(RNG5,src);
+    LatticeFermion ref   (FGrid);
+    LatticeFermion tmp   (FGrid);
+
+    RealD N2 = 1.0/::sqrt(norm2(src));
+    src = src*N2;
+    
+    LatticeGaugeField Umu(UGrid);  SU3::HotConfiguration(RNG4,Umu); 
+
+    DomainWallFermionR Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
+
+    ////////////////////////////////////
+    // Naive wilson implementation
+    ////////////////////////////////////
+    {
+      LatticeGaugeField Umu5d(FGrid); 
+      std::vector<LatticeColourMatrix> U(4,FGrid);
+      for(int ss=0;ss<Umu._grid->oSites();ss++){
+	for(int s=0;s<Ls;s++){
+	  Umu5d._odata[Ls*ss+s] = Umu._odata[ss];
+	}
+      }
+      ref = zero;
+      for(int mu=0;mu<Nd;mu++){
+	U[mu] = PeekIndex<LorentzIndex>(Umu5d,mu);
+      }
+      for(int mu=0;mu<Nd;mu++){
+	
+	tmp = U[mu]*Cshift(src,mu+1,1);
+	ref=ref + tmp - Gamma(Gmu[mu])*tmp;
+	
+	tmp =adj(U[mu])*src;
+	tmp =Cshift(tmp,mu+1,-1);
+	ref=ref + tmp + Gamma(Gmu[mu])*tmp;
+      }
+      ref = -0.5*ref;
+    }
+
+    LatticeFermion src_e (FrbGrid);
+    LatticeFermion src_o (FrbGrid);
+    LatticeFermion r_e   (FrbGrid);
+    LatticeFermion r_o   (FrbGrid);
+    LatticeFermion r_eo  (FGrid);
+    LatticeFermion err   (FGrid);
+    {
+
+      pickCheckerboard(Even,src_e,src);
+      pickCheckerboard(Odd,src_o,src);
+
+#if defined(AVX512) 
+      const int num_cases = 6;
+      std::string fmt("A/S ; A/O ; U/S ; U/O ; G/S ; G/O ");
+#else
+      const int num_cases = 4;
+      std::string fmt("U/S ; U/O ; G/S ; G/O ");
+#endif
+      controls Cases [] = {
+#ifdef AVX512
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+#endif
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  }
+      }; 
+
+      for(int c=0;c<num_cases;c++) {
+
+	QCD::WilsonKernelsStatic::Comms = Cases[c].CommsOverlap;
+	QCD::WilsonKernelsStatic::Opt   = Cases[c].Opt;
+	CartesianCommunicator::SetCommunicatorPolicy(Cases[c].CommsAsynch);
+
+	std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+	if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptGeneric   ) std::cout << GridLogMessage<< "* Using GENERIC Nc WilsonKernels" <<std::endl;
+	if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptHandUnroll) std::cout << GridLogMessage<< "* Using Nc=3       WilsonKernels" <<std::endl;
+	if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptInlineAsm ) std::cout << GridLogMessage<< "* Using Asm Nc=3   WilsonKernels" <<std::endl;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsAndCompute ) std::cout << GridLogMessage<< "* Using Overlapped Comms/Compute" <<std::endl;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsThenCompute) std::cout << GridLogMessage<< "* Using sequential comms compute" <<std::endl;
+	if ( sizeof(Real)==4 )   std::cout << GridLogMessage<< "* SINGLE precision "<<std::endl;
+	if ( sizeof(Real)==8 )   std::cout << GridLogMessage<< "* DOUBLE precision "<<std::endl;
+	std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+	int nwarm = 200;
+	double t0=usecond();
+	FGrid->Barrier();
+	for(int i=0;i<nwarm;i++){
+	  Dw.DhopEO(src_o,r_e,DaggerNo);
+	}
+	FGrid->Barrier();
+	double t1=usecond();
+	//	uint64_t ncall = (uint64_t) 2.5*1000.0*1000.0*nwarm/(t1-t0);
+	//	if (ncall < 500) ncall = 500;
+	uint64_t ncall = 1000;
+
+	FGrid->Broadcast(0,&ncall,sizeof(ncall));
+
+	//	std::cout << GridLogMessage << " Estimate " << ncall << " calls per second"<<std::endl;
+	Dw.ZeroCounters();
+
+	time_statistics timestat;
+	std::vector<double> t_time(ncall);
+	for(uint64_t i=0;i<ncall;i++){
+	  t0=usecond();
+	  Dw.DhopEO(src_o,r_e,DaggerNo);
+	  t1=usecond();
+	  t_time[i] = t1-t0;
+	}
+	FGrid->Barrier();
+	
+	double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+	double flops=(1344.0*volume)/2;
+	double mf_hi, mf_lo, mf_err;
+
+	timestat.statistics(t_time);
+	mf_hi = flops/timestat.min;
+	mf_lo = flops/timestat.max;
+	mf_err= flops/timestat.min * timestat.err/timestat.mean;
+
+	mflops = flops/timestat.mean;
+	mflops_all.push_back(mflops);
+	if ( mflops_best == 0   ) mflops_best = mflops;
+	if ( mflops_worst== 0   ) mflops_worst= mflops;
+	if ( mflops>mflops_best ) mflops_best = mflops;
+	if ( mflops<mflops_worst) mflops_worst= mflops;
+
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"Deo mflop/s =   "<< mflops << " ("<<mf_err<<") " << mf_lo<<"-"<<mf_hi <<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"Deo mflop/s per rank   "<< mflops/NP<<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"Deo mflop/s per node   "<< mflops/NN<<std::endl;
+
+	Dw.Report();
+
+	Dw.DhopEO(src_o,r_e,DaggerNo);
+	Dw.DhopOE(src_e,r_o,DaggerNo);
+	setCheckerboard(r_eo,r_o);
+	setCheckerboard(r_eo,r_e);
+	err = r_eo-ref; 
+	std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
+	assert((norm2(err)<1.0e-4));
+
+      }
+      robust = mflops_worst/mflops_best;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " Deo Best  mflop/s        =   "<< mflops_best << " ; " << mflops_best/NN<<" per node " <<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " Deo Worst mflop/s        =   "<< mflops_worst<< " ; " << mflops_worst/NN<<" per node " <<std::endl;
+      std::cout<<GridLogMessage << std::fixed<<std::setprecision(3)<< L<<"^4 x "<<Ls<< " Performance Robustness   =   "<< robust  <<std::endl;
+      std::cout<<GridLogMessage <<fmt << std::endl;
+      std::cout<<GridLogMessage ;
+
+      for(int i=0;i<mflops_all.size();i++){
+	std::cout<<mflops_all[i]/NN<<" ; " ;
+      }
+      std::cout<<std::endl;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+    }
+    return mflops_best;
+  }
+
+};
+
+int main (int argc, char ** argv)
+{
+  Grid_init(&argc,&argv);
+
+  CartesianCommunicator::SetCommunicatorPolicy(CartesianCommunicator::CommunicatorPolicySequential);
+#ifdef KNL
+  LebesgueOrder::Block = std::vector<int>({8,2,2,2});
+#else
+  LebesgueOrder::Block = std::vector<int>({2,2,2,2});
+#endif
+  Benchmark::Decomposition();
+
+  int do_memory=1;
+  int do_comms =1;
+  int do_su3   =0;
+  int do_wilson=1;
+  int do_dwf   =1;
+
+  if ( do_su3 ) {
+    // empty for now
+  }
+#if 1
+  int sel=2;
+  std::vector<int> L_list({8,12,16,24});
+#else
+  int sel=1;
+  std::vector<int> L_list({8,12});
+#endif
+  int selm1=sel-1;
+  std::vector<double> robust_list;
+
+  std::vector<double> wilson;
+  std::vector<double> dwf4;
+  std::vector<double> dwf5;
+
+  if ( do_wilson ) {
+    int Ls=1;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Wilson dslash 4D vectorised" <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    for(int l=0;l<L_list.size();l++){
+      double robust;
+      wilson.push_back(Benchmark::DWF(1,L_list[l],robust));
+    }
+  }
+
+  int Ls=16;
+  if ( do_dwf ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Domain wall dslash 4D vectorised" <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    for(int l=0;l<L_list.size();l++){
+      double robust;
+      double result = Benchmark::DWF(Ls,L_list[l],robust) ;
+      dwf4.push_back(result);
+      robust_list.push_back(robust);
+    }
+  }
+
+  if ( do_dwf ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Domain wall dslash 4D vectorised" <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    for(int l=0;l<L_list.size();l++){
+      dwf5.push_back(Benchmark::DWF5(Ls,L_list[l]));
+    }
+
+  }
+
+  if ( do_dwf ) {
+
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " Summary table Ls="<<Ls <<std::endl;
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << "L \t\t Wilson \t DWF4 \t DWF5 " <<std::endl;
+  for(int l=0;l<L_list.size();l++){
+    std::cout<<GridLogMessage << L_list[l] <<" \t\t "<< wilson[l]<<" \t "<<dwf4[l]<<" \t "<<dwf5[l] <<std::endl;
+  }
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  }
+
+  int NN=NN_global;
+  if ( do_memory ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Memory benchmark " <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    Benchmark::Memory();
+  }
+
+  if ( do_comms && (NN>1) ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Communications benchmark " <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    Benchmark::Comms();
+  }
+
+  if ( do_dwf ) {
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " Per Node Summary table Ls="<<Ls <<std::endl;
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " L \t\t Wilson\t\t DWF4  \t\t DWF5 " <<std::endl;
+  for(int l=0;l<L_list.size();l++){
+    std::cout<<GridLogMessage << L_list[l] <<" \t\t "<< wilson[l]/NN<<" \t "<<dwf4[l]/NN<<" \t "<<dwf5[l] /NN<<std::endl;
+  }
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " Comparison point     result: "  << 0.5*(dwf4[sel]+dwf4[selm1])/NN << " Mflop/s per node"<<std::endl;
+  std::cout<<GridLogMessage << " Comparison point is 0.5*("<<dwf4[sel]/NN<<"+"<<dwf4[selm1]/NN << ") "<<std::endl;
+  std::cout<<std::setprecision(3);
+  std::cout<<GridLogMessage << " Comparison point robustness: "  << robust_list[sel] <<std::endl;
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+  }
+
+
+  Grid_finalize();
+}

benchmarks/Benchmark_comms.cc

@@ -31,6 +31,32 @@ using namespace std;
 using namespace Grid;
 using namespace Grid::QCD;
 
+struct time_statistics{
+  double mean;
+  double err;
+  double min;
+  double max;
+
+  void statistics(std::vector<double> v){
+      double sum = std::accumulate(v.begin(), v.end(), 0.0);
+      mean = sum / v.size();
+
+      std::vector<double> diff(v.size());
+      std::transform(v.begin(), v.end(), diff.begin(), [=](double x) { return x - mean; });
+      double sq_sum = std::inner_product(diff.begin(), diff.end(), diff.begin(), 0.0);
+      err = std::sqrt(sq_sum / (v.size()*(v.size() - 1)));
+
+      auto result = std::minmax_element(v.begin(), v.end());
+      min = *result.first;
+      max = *result.second;
+}
+};
+
+void header(){
+  std::cout <<GridLogMessage << " L  "<<"\t"<<" Ls  "<<"\t"
+            <<std::setw(11)<<"bytes"<<"MB/s uni (err/min/max)"<<"\t\t"<<"MB/s bidi (err/min/max)"<<std::endl;
+};
+
 int main (int argc, char ** argv)
 {
   Grid_init(&argc,&argv);
@@ -40,17 +66,21 @@ int main (int argc, char ** argv)
   int threads = GridThread::GetThreads();
   std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;
 
-  int Nloop=10;
+  int Nloop=100;
   int nmu=0;
+  int maxlat=32;
   for(int mu=0;mu<Nd;mu++) if (mpi_layout[mu]>1) nmu++;
 
+  std::cout << GridLogMessage << "Number of iterations to average: "<< Nloop << std::endl;
+  std::vector<double> t_time(Nloop);
+  time_statistics timestat;
+
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "= Benchmarking concurrent halo exchange in "<<nmu<<" dimensions"<<std::endl;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
-  std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
-  int maxlat=24;
+  header();
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -58,17 +88,25 @@ int main (int argc, char ** argv)
       				    lat*mpi_layout[3]});
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+      RealD Nrank = Grid._Nprocessors;
+      RealD Nnode = Grid.NodeCount();
+      RealD ppn = Nrank/Nnode;
 
-      std::vector<std::vector<HalfSpinColourVectorD> > xbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
-      std::vector<std::vector<HalfSpinColourVectorD> > rbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
+      std::vector<Vector<HalfSpinColourVectorD> > xbuf(8);	
+      std::vector<Vector<HalfSpinColourVectorD> > rbuf(8);
 
       int ncomm;
       int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
+      for(int mu=0;mu<8;mu++){
+	xbuf[mu].resize(lat*lat*lat*Ls);
+	rbuf[mu].resize(lat*lat*lat*Ls);
+	//	std::cout << " buffers " << std::hex << (uint64_t)&xbuf[mu][0] <<" " << (uint64_t)&rbuf[mu][0] <<std::endl;
+      }
 
-      double start=usecond();
       for(int i=0;i<Nloop;i++){
+      double start=usecond();
 
-	std::vector<CartesianCommunicator::CommsRequest_t> requests;
+	std::vector<CommsRequest_t> requests;
 
 	ncomm=0;
 	for(int mu=0;mu<4;mu++){
@@ -79,7 +117,6 @@ int main (int argc, char ** argv)
 	    int comm_proc=1;
 	    int xmit_to_rank;
 	    int recv_from_rank;
-	    
 	    Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
 	    Grid.SendToRecvFromBegin(requests,
 				   (void *)&xbuf[mu][0],
@@ -102,18 +139,24 @@ int main (int argc, char ** argv)
 	}
 	Grid.SendToRecvFromComplete(requests);
 	Grid.Barrier();
-
+	double stop=usecond();
+	t_time[i] = stop-start; // microseconds
       }
-      double stop=usecond();
 
-      double dbytes    = bytes;
-      double xbytes    = Nloop*dbytes*2.0*ncomm;
+      timestat.statistics(t_time);
+
+      double dbytes    = bytes*ppn;
+      double xbytes    = dbytes*2.0*ncomm;
       double rbytes    = xbytes;
       double bidibytes = xbytes+rbytes;
 
-      double time = stop-start; // microseconds
+      std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+               <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+               <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+               <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+               << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+               << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
 
-      std::cout<<GridLogMessage << lat<<"\t\t"<<Ls<<"\t\t"<<bytes<<"\t\t"<<xbytes/time<<"\t\t"<<bidibytes/time<<std::endl;
     }
   }    
 
@@ -121,25 +164,32 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "= Benchmarking sequential halo exchange in "<<nmu<<" dimensions"<<std::endl;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
-  std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
-
+  header();
 
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat,lat,lat,lat});
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+      RealD Nrank = Grid._Nprocessors;
+      RealD Nnode = Grid.NodeCount();
+      RealD ppn = Nrank/Nnode;
 
-      std::vector<std::vector<HalfSpinColourVectorD> > xbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
-      std::vector<std::vector<HalfSpinColourVectorD> > rbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
+      std::vector<Vector<HalfSpinColourVectorD> > xbuf(8);
+      std::vector<Vector<HalfSpinColourVectorD> > rbuf(8);
 
+      for(int mu=0;mu<8;mu++){
+	xbuf[mu].resize(lat*lat*lat*Ls);
+	rbuf[mu].resize(lat*lat*lat*Ls);
+	//	std::cout << " buffers " << std::hex << (uint64_t)&xbuf[mu][0] <<" " << (uint64_t)&rbuf[mu][0] <<std::endl;
+      }
 
       int ncomm;
       int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
 
-      double start=usecond();
       for(int i=0;i<Nloop;i++){
+      double start=usecond();
     
 	ncomm=0;
 	for(int mu=0;mu<4;mu++){
@@ -152,7 +202,7 @@ int main (int argc, char ** argv)
 	    int recv_from_rank;
 	    
 	    {
-	      std::vector<CartesianCommunicator::CommsRequest_t> requests;
+	      std::vector<CommsRequest_t> requests;
 	      Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
 	      Grid.SendToRecvFromBegin(requests,
 				       (void *)&xbuf[mu][0],
@@ -165,7 +215,7 @@ int main (int argc, char ** argv)
 
 	    comm_proc = mpi_layout[mu]-1;
 	    {
-	      std::vector<CartesianCommunicator::CommsRequest_t> requests;
+	      std::vector<CommsRequest_t> requests;
 	      Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
 	      Grid.SendToRecvFromBegin(requests,
 				       (void *)&xbuf[mu+4][0],
@@ -178,30 +228,37 @@ int main (int argc, char ** argv)
 	  }
 	}
 	Grid.Barrier();
+	double stop=usecond();
+	t_time[i] = stop-start; // microseconds
+
       }
 
-      double stop=usecond();
+      timestat.statistics(t_time);
       
-      double dbytes    = bytes;
-      double xbytes    = Nloop*dbytes*2.0*ncomm;
+      double dbytes    = bytes*ppn;
+      double xbytes    = dbytes*2.0*ncomm;
       double rbytes    = xbytes;
       double bidibytes = xbytes+rbytes;
 
-      double time = stop-start;
+    std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+               <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+               <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+               <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+               << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+               << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
 
-      std::cout<<GridLogMessage << lat<<"\t\t"<<Ls<<"\t\t"<<bytes<<"\t\t"<<xbytes/time<<"\t\t"<<bidibytes/time<<std::endl;
+      
     }
   }  
 
 
-  Nloop=10;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "= Benchmarking concurrent STENCIL halo exchange in "<<nmu<<" dimensions"<<std::endl;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
-  std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
+  header();
 
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -209,6 +266,9 @@ int main (int argc, char ** argv)
       				    lat*mpi_layout[3]});
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+      RealD Nrank = Grid._Nprocessors;
+      RealD Nnode = Grid.NodeCount();
+      RealD ppn = Nrank/Nnode;
 
       std::vector<HalfSpinColourVectorD *> xbuf(8);
       std::vector<HalfSpinColourVectorD *> rbuf(8);
@@ -216,73 +276,86 @@ int main (int argc, char ** argv)
       for(int d=0;d<8;d++){
 	xbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
 	rbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)xbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)rbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
       }
 
       int ncomm;
       int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
 
-      double start=usecond();
+      double dbytes;
       for(int i=0;i<Nloop;i++){
+	double start=usecond();
 
-	std::vector<CartesianCommunicator::CommsRequest_t> requests;
-
+	dbytes=0;
 	ncomm=0;
+
+	std::vector<CommsRequest_t> requests;
+
 	for(int mu=0;mu<4;mu++){
 	
+
 	  if (mpi_layout[mu]>1 ) {
 	  
 	    ncomm++;
 	    int comm_proc=1;
 	    int xmit_to_rank;
 	    int recv_from_rank;
-	    
 	    Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
-	    Grid.StencilSendToRecvFromBegin(requests,
-					    (void *)&xbuf[mu][0],
-					    xmit_to_rank,
-					    (void *)&rbuf[mu][0],
-					    recv_from_rank,
-					    bytes);
+	    dbytes+=
+	      Grid.StencilSendToRecvFromBegin(requests,
+					      (void *)&xbuf[mu][0],
+					      xmit_to_rank,
+					      (void *)&rbuf[mu][0],
+					      recv_from_rank,
+					      bytes,mu);
 	
 	    comm_proc = mpi_layout[mu]-1;
 	  
 	    Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
-	    Grid.StencilSendToRecvFromBegin(requests,
-					    (void *)&xbuf[mu+4][0],
-					    xmit_to_rank,
-					    (void *)&rbuf[mu+4][0],
-					    recv_from_rank,
-					    bytes);
+	    dbytes+=
+	      Grid.StencilSendToRecvFromBegin(requests,
+					      (void *)&xbuf[mu+4][0],
+					      xmit_to_rank,
+					      (void *)&rbuf[mu+4][0],
+					      recv_from_rank,
+					      bytes,mu+4);
 	  
 	  }
 	}
-	Grid.StencilSendToRecvFromComplete(requests);
+	Grid.StencilSendToRecvFromComplete(requests,0);
 	Grid.Barrier();
-
+	double stop=usecond();
+	t_time[i] = stop-start; // microseconds
+	
       }
-      double stop=usecond();
 
-      double dbytes    = bytes;
-      double xbytes    = Nloop*dbytes*2.0*ncomm;
-      double rbytes    = xbytes;
-      double bidibytes = xbytes+rbytes;
+      timestat.statistics(t_time);
+
+      dbytes=dbytes*ppn;
+      double xbytes    = dbytes*0.5;
+      double rbytes    = dbytes*0.5;
+      double bidibytes = dbytes;
+
+      std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+               <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+               <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+               <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+               << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+               << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
 
-      double time = stop-start; // microseconds
 
-      std::cout<<GridLogMessage << lat<<"\t\t"<<Ls<<"\t\t"<<bytes<<"\t\t"<<xbytes/time<<"\t\t"<<bidibytes/time<<std::endl;
     }
   }    
 
 
-
-  Nloop=100;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "= Benchmarking sequential STENCIL halo exchange in "<<nmu<<" dimensions"<<std::endl;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
-  std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
+  header();
 
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -290,6 +363,9 @@ int main (int argc, char ** argv)
       				    lat*mpi_layout[3]});
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+      RealD Nrank = Grid._Nprocessors;
+      RealD Nnode = Grid.NodeCount();
+      RealD ppn = Nrank/Nnode;
 
       std::vector<HalfSpinColourVectorD *> xbuf(8);
       std::vector<HalfSpinColourVectorD *> rbuf(8);
@@ -297,16 +373,18 @@ int main (int argc, char ** argv)
       for(int d=0;d<8;d++){
 	xbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
 	rbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)xbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)rbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
       }
 
       int ncomm;
       int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
-
-      double start=usecond();
+      double dbytes;
       for(int i=0;i<Nloop;i++){
+	double start=usecond();
 
-	std::vector<CartesianCommunicator::CommsRequest_t> requests;
-
+	std::vector<CommsRequest_t> requests;
+	dbytes=0;
 	ncomm=0;
 	for(int mu=0;mu<4;mu++){
 	
@@ -318,44 +396,146 @@ int main (int argc, char ** argv)
 	    int recv_from_rank;
 	    
 	    Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
-	    Grid.StencilSendToRecvFromBegin(requests,
-					    (void *)&xbuf[mu][0],
-					    xmit_to_rank,
-					    (void *)&rbuf[mu][0],
-					    recv_from_rank,
-					    bytes);
-	    Grid.StencilSendToRecvFromComplete(requests);
+	    dbytes+=
+	      Grid.StencilSendToRecvFromBegin(requests,
+					      (void *)&xbuf[mu][0],
+					      xmit_to_rank,
+					      (void *)&rbuf[mu][0],
+					      recv_from_rank,
+					      bytes,mu);
+	    Grid.StencilSendToRecvFromComplete(requests,mu);
 	    requests.resize(0);
 
 	    comm_proc = mpi_layout[mu]-1;
 	  
 	    Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
-	    Grid.StencilSendToRecvFromBegin(requests,
-					    (void *)&xbuf[mu+4][0],
-					    xmit_to_rank,
-					    (void *)&rbuf[mu+4][0],
-					    recv_from_rank,
-					    bytes);
-	    Grid.StencilSendToRecvFromComplete(requests);
+	    dbytes+=
+	      Grid.StencilSendToRecvFromBegin(requests,
+					      (void *)&xbuf[mu+4][0],
+					      xmit_to_rank,
+					      (void *)&rbuf[mu+4][0],
+					      recv_from_rank,
+					      bytes,mu+4);
+	    Grid.StencilSendToRecvFromComplete(requests,mu+4);
 	    requests.resize(0);
 	  
 	  }
 	}
 	Grid.Barrier();
-
+	double stop=usecond();
+	t_time[i] = stop-start; // microseconds
+	
       }
-      double stop=usecond();
 
-      double dbytes    = bytes;
-      double xbytes    = Nloop*dbytes*2.0*ncomm;
-      double rbytes    = xbytes;
-      double bidibytes = xbytes+rbytes;
+      timestat.statistics(t_time);
 
-      double time = stop-start; // microseconds
+      dbytes=dbytes*ppn;
+      double xbytes    = dbytes*0.5;
+      double rbytes    = dbytes*0.5;
+      double bidibytes = dbytes;
 
-      std::cout<<GridLogMessage << lat<<"\t\t"<<Ls<<"\t\t"<<bytes<<"\t\t"<<xbytes/time<<"\t\t"<<bidibytes/time<<std::endl;
+
+      std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+               <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+               <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+               <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+               << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+               << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
+ 
     }
   }    
 
+
+
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << "= Benchmarking threaded STENCIL halo exchange in "<<nmu<<" dimensions"<<std::endl;
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+  header();
+
+  for(int lat=4;lat<=maxlat;lat+=4){
+    for(int Ls=8;Ls<=8;Ls*=2){
+
+      std::vector<int> latt_size  ({lat*mpi_layout[0],
+      				    lat*mpi_layout[1],
+      				    lat*mpi_layout[2],
+      				    lat*mpi_layout[3]});
+
+      GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+      RealD Nrank = Grid._Nprocessors;
+      RealD Nnode = Grid.NodeCount();
+      RealD ppn = Nrank/Nnode;
+
+      std::vector<HalfSpinColourVectorD *> xbuf(8);
+      std::vector<HalfSpinColourVectorD *> rbuf(8);
+      Grid.ShmBufferFreeAll();
+      for(int d=0;d<8;d++){
+	xbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	rbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)xbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)rbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+      }
+
+      int ncomm;
+      int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
+      double dbytes;
+      for(int i=0;i<Nloop;i++){
+	double start=usecond();
+
+	std::vector<CommsRequest_t> requests;
+	dbytes=0;
+	ncomm=0;
+
+	parallel_for(int dir=0;dir<8;dir++){
+
+	  double tbytes;
+	  int mu =dir % 4;
+
+	  if (mpi_layout[mu]>1 ) {
+	  
+	    ncomm++;
+	    int xmit_to_rank;
+	    int recv_from_rank;
+	    if ( dir == mu ) { 
+	      int comm_proc=1;
+	      Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	    } else { 
+	      int comm_proc = mpi_layout[mu]-1;
+	      Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	    }
+
+	    tbytes= Grid.StencilSendToRecvFrom((void *)&xbuf[dir][0], xmit_to_rank,
+					       (void *)&rbuf[dir][0], recv_from_rank, bytes,dir);
+
+#pragma omp atomic
+	    dbytes+=tbytes;
+	  }
+	}
+	Grid.Barrier();
+	double stop=usecond();
+	t_time[i] = stop-start; // microseconds
+      }
+
+      timestat.statistics(t_time);
+
+      dbytes=dbytes*ppn;
+      double xbytes    = dbytes*0.5;
+      double rbytes    = dbytes*0.5;
+      double bidibytes = dbytes;
+
+
+      std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+               <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+               <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+               <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+               << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+               << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
+ 
+    }
+  }    
+
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << "= All done; Bye Bye"<<std::endl;
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+
   Grid_finalize();
 }

benchmarks/Benchmark_dwf.cc

@@ -51,7 +51,13 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;
 
   std::vector<int> latt4 = GridDefaultLatt();
-  const int Ls=16;
+  int Ls=16;
+  for(int i=0;i<argc;i++)
+    if(std::string(argv[i]) == "-Ls"){
+      std::stringstream ss(argv[i+1]); ss >> Ls;
+    }
+
+
   GridCartesian         * UGrid   = SpaceTimeGrid::makeFourDimGrid(GridDefaultLatt(), GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
   GridRedBlackCartesian * UrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
   GridCartesian         * FGrid   = SpaceTimeGrid::makeFiveDimGrid(Ls,UGrid);
@@ -165,7 +171,7 @@ int main (int argc, char ** argv)
   std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
 
   DomainWallFermionR Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
-  int ncall =1000;
+  int ncall =500;
   if (1) {
     FGrid->Barrier();
     Dw.ZeroCounters();
@@ -302,6 +308,7 @@ int main (int argc, char ** argv)
       std::cout<< "sD ERR   \n " << err  <<std::endl;
     }
     assert(sum < 1.0e-4);
+
     
     if(1){
       std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
@@ -381,8 +388,23 @@ int main (int argc, char ** argv)
       }
       assert(error<1.0e-4);
     }
+
+  if(0){
+    std::cout << "Single cache warm call to sDw.Dhop " <<std::endl;
+    for(int i=0;i< PerformanceCounter::NumTypes(); i++ ){
+      sDw.Dhop(ssrc,sresult,0);
+      PerformanceCounter Counter(i);
+      Counter.Start();
+      sDw.Dhop(ssrc,sresult,0);
+      Counter.Stop();
+      Counter.Report();
+    }
   }
 
+  }
+
+
+
   if (1)
   { // Naive wilson dag implementation
     ref = zero;
@@ -487,9 +509,9 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "norm diff even  "<< norm2(src_e)<<std::endl;
   std::cout<<GridLogMessage << "norm diff odd   "<< norm2(src_o)<<std::endl;
 
-  //assert(norm2(src_e)<1.0e-4);
-  //assert(norm2(src_o)<1.0e-4);
-
+  assert(norm2(src_e)<1.0e-4);
+  assert(norm2(src_o)<1.0e-4);
   Grid_finalize();
+  exit(0);
 }
 

benchmarks/Benchmark_gparity.cc

@@ -0,0 +1,190 @@
+#include <Grid/Grid.h>
+#include <sstream>
+using namespace std;
+using namespace Grid;
+using namespace Grid::QCD;
+
+template<class d>
+struct scal {
+  d internal;
+};
+
+  Gamma::Algebra Gmu [] = {
+    Gamma::Algebra::GammaX,
+    Gamma::Algebra::GammaY,
+    Gamma::Algebra::GammaZ,
+    Gamma::Algebra::GammaT
+  };
+
+typedef typename GparityDomainWallFermionF::FermionField GparityLatticeFermionF;
+typedef typename GparityDomainWallFermionD::FermionField GparityLatticeFermionD;
+
+
+
+int main (int argc, char ** argv)
+{
+  Grid_init(&argc,&argv);
+
+  int Ls=16;
+  for(int i=0;i<argc;i++)
+    if(std::string(argv[i]) == "-Ls"){
+      std::stringstream ss(argv[i+1]); ss >> Ls;
+    }
+
+
+  int threads = GridThread::GetThreads();
+  std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;
+  std::cout<<GridLogMessage << "Ls = " << Ls << std::endl;
+
+  std::vector<int> latt4 = GridDefaultLatt();
+
+  GridCartesian         * UGrid   = SpaceTimeGrid::makeFourDimGrid(GridDefaultLatt(), GridDefaultSimd(Nd,vComplexF::Nsimd()),GridDefaultMpi());
+  GridRedBlackCartesian * UrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
+  GridCartesian         * FGrid   = SpaceTimeGrid::makeFiveDimGrid(Ls,UGrid);
+  GridRedBlackCartesian * FrbGrid = SpaceTimeGrid::makeFiveDimRedBlackGrid(Ls,UGrid);
+
+  std::vector<int> seeds4({1,2,3,4});
+  std::vector<int> seeds5({5,6,7,8});
+  
+  std::cout << GridLogMessage << "Initialising 4d RNG" << std::endl;
+  GridParallelRNG          RNG4(UGrid);  RNG4.SeedFixedIntegers(seeds4);
+  std::cout << GridLogMessage << "Initialising 5d RNG" << std::endl;
+  GridParallelRNG          RNG5(FGrid);  RNG5.SeedFixedIntegers(seeds5);
+  std::cout << GridLogMessage << "Initialised RNGs" << std::endl;
+
+  GparityLatticeFermionF src   (FGrid); random(RNG5,src);
+  RealD N2 = 1.0/::sqrt(norm2(src));
+  src = src*N2;
+
+  GparityLatticeFermionF result(FGrid); result=zero;
+  GparityLatticeFermionF    ref(FGrid);    ref=zero;
+  GparityLatticeFermionF    tmp(FGrid);
+  GparityLatticeFermionF    err(FGrid);
+
+  std::cout << GridLogMessage << "Drawing gauge field" << std::endl;
+  LatticeGaugeFieldF Umu(UGrid); 
+  SU3::HotConfiguration(RNG4,Umu); 
+  std::cout << GridLogMessage << "Random gauge initialised " << std::endl;
+
+  RealD mass=0.1;
+  RealD M5  =1.8;
+
+  RealD NP = UGrid->_Nprocessors;
+  RealD NN = UGrid->NodeCount();
+
+  std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
+  std::cout << GridLogMessage<< "* Kernel options --dslash-generic, --dslash-unroll, --dslash-asm" <<std::endl;
+  std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
+  std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
+  std::cout << GridLogMessage<< "* Benchmarking DomainWallFermion::Dhop                  "<<std::endl;
+  std::cout << GridLogMessage<< "* Vectorising space-time by "<<vComplexF::Nsimd()<<std::endl;
+#ifdef GRID_OMP
+  if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsAndCompute ) std::cout << GridLogMessage<< "* Using Overlapped Comms/Compute" <<std::endl;
+  if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsThenCompute) std::cout << GridLogMessage<< "* Using sequential comms compute" <<std::endl;
+#endif
+  if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptGeneric   ) std::cout << GridLogMessage<< "* Using GENERIC Nc WilsonKernels" <<std::endl;
+  if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptHandUnroll) std::cout << GridLogMessage<< "* Using Nc=3       WilsonKernels" <<std::endl;
+  if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptInlineAsm ) std::cout << GridLogMessage<< "* Using Asm Nc=3   WilsonKernels" <<std::endl;
+  std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
+
+
+
+  std::cout << GridLogMessage<< "* SINGLE/SINGLE"<<std::endl;
+  GparityDomainWallFermionF Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
+  int ncall =1000;
+  if (1) {
+    FGrid->Barrier();
+    Dw.ZeroCounters();
+    Dw.Dhop(src,result,0);
+    std::cout<<GridLogMessage<<"Called warmup"<<std::endl;
+    double t0=usecond();
+    for(int i=0;i<ncall;i++){
+      __SSC_START;
+      Dw.Dhop(src,result,0);
+      __SSC_STOP;
+    }
+    double t1=usecond();
+    FGrid->Barrier();
+    
+    double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+    double flops=2*1344*volume*ncall;
+
+    std::cout<<GridLogMessage << "Called Dw "<<ncall<<" times in "<<t1-t0<<" us"<<std::endl;
+    //    std::cout<<GridLogMessage << "norm result "<< norm2(result)<<std::endl;
+    //    std::cout<<GridLogMessage << "norm ref    "<< norm2(ref)<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s =   "<< flops/(t1-t0)<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s per rank =  "<< flops/(t1-t0)/NP<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s per node =  "<< flops/(t1-t0)/NN<<std::endl;
+    Dw.Report();
+  }
+
+  std::cout << GridLogMessage<< "* SINGLE/HALF"<<std::endl;
+  GparityDomainWallFermionFH DwH(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
+  if (1) {
+    FGrid->Barrier();
+    DwH.ZeroCounters();
+    DwH.Dhop(src,result,0);
+    double t0=usecond();
+    for(int i=0;i<ncall;i++){
+      __SSC_START;
+      DwH.Dhop(src,result,0);
+      __SSC_STOP;
+    }
+    double t1=usecond();
+    FGrid->Barrier();
+    
+    double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+    double flops=2*1344*volume*ncall;
+
+    std::cout<<GridLogMessage << "Called half prec comms Dw "<<ncall<<" times in "<<t1-t0<<" us"<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s =   "<< flops/(t1-t0)<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s per rank =  "<< flops/(t1-t0)/NP<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s per node =  "<< flops/(t1-t0)/NN<<std::endl;
+    DwH.Report();
+  }
+
+  GridCartesian         * UGrid_d   = SpaceTimeGrid::makeFourDimGrid(GridDefaultLatt(), GridDefaultSimd(Nd,vComplexD::Nsimd()),GridDefaultMpi());
+  GridRedBlackCartesian * UrbGrid_d = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid_d);
+  GridCartesian         * FGrid_d   = SpaceTimeGrid::makeFiveDimGrid(Ls,UGrid_d);
+  GridRedBlackCartesian * FrbGrid_d = SpaceTimeGrid::makeFiveDimRedBlackGrid(Ls,UGrid_d);
+
+  
+  std::cout << GridLogMessage<< "* DOUBLE/DOUBLE"<<std::endl;
+  GparityLatticeFermionD src_d(FGrid_d);
+  precisionChange(src_d,src);
+
+  LatticeGaugeFieldD Umu_d(UGrid_d); 
+  precisionChange(Umu_d,Umu);
+
+  GparityLatticeFermionD result_d(FGrid_d);
+
+  GparityDomainWallFermionD DwD(Umu_d,*FGrid_d,*FrbGrid_d,*UGrid_d,*UrbGrid_d,mass,M5);
+  if (1) {
+    FGrid_d->Barrier();
+    DwD.ZeroCounters();
+    DwD.Dhop(src_d,result_d,0);
+    std::cout<<GridLogMessage<<"Called warmup"<<std::endl;
+    double t0=usecond();
+    for(int i=0;i<ncall;i++){
+      __SSC_START;
+      DwD.Dhop(src_d,result_d,0);
+      __SSC_STOP;
+    }
+    double t1=usecond();
+    FGrid_d->Barrier();
+    
+    double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+    double flops=2*1344*volume*ncall;
+
+    std::cout<<GridLogMessage << "Called Dw "<<ncall<<" times in "<<t1-t0<<" us"<<std::endl;
+    //    std::cout<<GridLogMessage << "norm result "<< norm2(result)<<std::endl;
+    //    std::cout<<GridLogMessage << "norm ref    "<< norm2(ref)<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s =   "<< flops/(t1-t0)<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s per rank =  "<< flops/(t1-t0)/NP<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s per node =  "<< flops/(t1-t0)/NN<<std::endl;
+    DwD.Report();
+  }
+
+  Grid_finalize();
+}
+

benchmarks/Benchmark_memory_bandwidth.cc

@@ -55,21 +55,21 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<<std::endl;
   std::cout<<GridLogMessage << "----------------------------------------------------------"<<std::endl;
-  uint64_t lmax=44;
-#define NLOOP (1*lmax*lmax*lmax*lmax/vol)
-  for(int lat=4;lat<=lmax;lat+=4){
+  uint64_t lmax=96;
+#define NLOOP (10*lmax*lmax*lmax*lmax/vol)
+  for(int lat=8;lat<=lmax;lat+=8){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol= latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
 
       uint64_t Nloop=NLOOP;
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
 
-      LatticeVec z(&Grid); //random(pRNG,z);
-      LatticeVec x(&Grid); //random(pRNG,x);
-      LatticeVec y(&Grid); //random(pRNG,y);
+      LatticeVec z(&Grid);// random(pRNG,z);
+      LatticeVec x(&Grid);// random(pRNG,x);
+      LatticeVec y(&Grid);// random(pRNG,y);
       double a=2.0;
 
 
@@ -83,7 +83,7 @@ int main (int argc, char ** argv)
       double time = (stop-start)/Nloop*1000;
       
       double flops=vol*Nvec*2;// mul,add
-      double bytes=3*vol*Nvec*sizeof(Real);
+      double bytes=3.0*vol*Nvec*sizeof(Real);
       std::cout<<GridLogMessage<<std::setprecision(3) << lat<<"\t\t"<<bytes<<"   \t\t"<<bytes/time<<"\t\t"<<flops/time<<"\t\t"<<(stop-start)/1000./1000.<<std::endl;
 
     }
@@ -94,17 +94,17 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<<std::endl;
   std::cout<<GridLogMessage << "----------------------------------------------------------"<<std::endl;
   
-  for(int lat=4;lat<=lmax;lat+=4){
+  for(int lat=8;lat<=lmax;lat+=8){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol= latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
 
-      LatticeVec z(&Grid); //random(pRNG,z);
-      LatticeVec x(&Grid); //random(pRNG,x);
-      LatticeVec y(&Grid); //random(pRNG,y);
+      LatticeVec z(&Grid);// random(pRNG,z);
+      LatticeVec x(&Grid);// random(pRNG,x);
+      LatticeVec y(&Grid);// random(pRNG,y);
       double a=2.0;
 
       uint64_t Nloop=NLOOP;
@@ -119,7 +119,7 @@ int main (int argc, char ** argv)
       double time = (stop-start)/Nloop*1000;
      
       double flops=vol*Nvec*2;// mul,add
-      double bytes=3*vol*Nvec*sizeof(Real);
+      double bytes=3.0*vol*Nvec*sizeof(Real);
       std::cout<<GridLogMessage<<std::setprecision(3) << lat<<"\t\t"<<bytes<<"   \t\t"<<bytes/time<<"\t\t"<<flops/time<<"\t\t"<<(stop-start)/1000./1000.<<std::endl;
 
     }
@@ -129,20 +129,20 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<<std::endl;
 
-  for(int lat=4;lat<=lmax;lat+=4){
+  for(int lat=8;lat<=lmax;lat+=8){
 
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol= latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
       uint64_t Nloop=NLOOP;
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
 
-      LatticeVec z(&Grid); //random(pRNG,z);
-      LatticeVec x(&Grid); //random(pRNG,x);
-      LatticeVec y(&Grid); //random(pRNG,y);
+      LatticeVec z(&Grid);// random(pRNG,z);
+      LatticeVec x(&Grid);// random(pRNG,x);
+      LatticeVec y(&Grid);// random(pRNG,y);
       RealD a=2.0;
 
 
@@ -154,7 +154,7 @@ int main (int argc, char ** argv)
       double stop=usecond();
       double time = (stop-start)/Nloop*1000;
       
-      double bytes=2*vol*Nvec*sizeof(Real);
+      double bytes=2.0*vol*Nvec*sizeof(Real);
       double flops=vol*Nvec*1;// mul
       std::cout<<GridLogMessage <<std::setprecision(3) << lat<<"\t\t"<<bytes<<"   \t\t"<<bytes/time<<"\t\t"<<flops/time<<"\t\t"<<(stop-start)/1000./1000.<<std::endl;
 
@@ -166,17 +166,17 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<<std::endl;
   std::cout<<GridLogMessage << "----------------------------------------------------------"<<std::endl;
 
-  for(int lat=4;lat<=lmax;lat+=4){
+  for(int lat=8;lat<=lmax;lat+=8){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol= latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
       uint64_t Nloop=NLOOP;
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
-      LatticeVec z(&Grid); //random(pRNG,z);
-      LatticeVec x(&Grid); //random(pRNG,x);
-      LatticeVec y(&Grid); //random(pRNG,y);
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
+      LatticeVec z(&Grid);// random(pRNG,z);
+      LatticeVec x(&Grid);// random(pRNG,x);
+      LatticeVec y(&Grid);// random(pRNG,y);
       RealD a=2.0;
       Real nn;      
       double start=usecond();
@@ -187,7 +187,7 @@ int main (int argc, char ** argv)
       double stop=usecond();
       double time = (stop-start)/Nloop*1000;
       
-      double bytes=vol*Nvec*sizeof(Real);
+      double bytes=1.0*vol*Nvec*sizeof(Real);
       double flops=vol*Nvec*2;// mul,add
       std::cout<<GridLogMessage<<std::setprecision(3) << lat<<"\t\t"<<bytes<<"  \t\t"<<bytes/time<<"\t\t"<<flops/time<< "\t\t"<<(stop-start)/1000./1000.<< "\t\t " <<std::endl;
 

benchmarks/Benchmark_staggered.cc

@@ -40,7 +40,7 @@ int main (int argc, char ** argv)
   std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplex::Nsimd());
   std::vector<int> mpi_layout  = GridDefaultMpi();
   GridCartesian               Grid(latt_size,simd_layout,mpi_layout);
-  GridRedBlackCartesian     RBGrid(latt_size,simd_layout,mpi_layout);
+  GridRedBlackCartesian     RBGrid(&Grid);
 
   int threads = GridThread::GetThreads();
   std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;

benchmarks/Benchmark_su3.cc

@@ -35,14 +35,14 @@ using namespace Grid::QCD;
 int main (int argc, char ** argv)
 {
   Grid_init(&argc,&argv);
-#define LMAX (32)
+#define LMAX (64)
 
-  int Nloop=200;
+  int64_t Nloop=20;
 
   std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplex::Nsimd());
   std::vector<int> mpi_layout  = GridDefaultMpi();
 
-  int threads = GridThread::GetThreads();
+  int64_t threads = GridThread::GetThreads();
   std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;
 
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
@@ -54,16 +54,16 @@ int main (int argc, char ** argv)
   for(int lat=2;lat<=LMAX;lat+=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
 
-      LatticeColourMatrix z(&Grid);// random(pRNG,z);
-      LatticeColourMatrix x(&Grid);// random(pRNG,x);
-      LatticeColourMatrix y(&Grid);// random(pRNG,y);
+      LatticeColourMatrix z(&Grid); random(pRNG,z);
+      LatticeColourMatrix x(&Grid); random(pRNG,x);
+      LatticeColourMatrix y(&Grid); random(pRNG,y);
 
       double start=usecond();
-      for(int i=0;i<Nloop;i++){
+      for(int64_t i=0;i<Nloop;i++){
 	x=x*y;
       }
       double stop=usecond();
@@ -86,17 +86,17 @@ int main (int argc, char ** argv)
   for(int lat=2;lat<=LMAX;lat+=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
 
-      LatticeColourMatrix z(&Grid); //random(pRNG,z);
-      LatticeColourMatrix x(&Grid); //random(pRNG,x);
-      LatticeColourMatrix y(&Grid); //random(pRNG,y);
+      LatticeColourMatrix z(&Grid); random(pRNG,z);
+      LatticeColourMatrix x(&Grid); random(pRNG,x);
+      LatticeColourMatrix y(&Grid); random(pRNG,y);
 
       double start=usecond();
-      for(int i=0;i<Nloop;i++){
+      for(int64_t i=0;i<Nloop;i++){
 	z=x*y;
       }
       double stop=usecond();
@@ -117,17 +117,17 @@ int main (int argc, char ** argv)
   for(int lat=2;lat<=LMAX;lat+=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
 
-      LatticeColourMatrix z(&Grid); //random(pRNG,z);
-      LatticeColourMatrix x(&Grid); //random(pRNG,x);
-      LatticeColourMatrix y(&Grid); //random(pRNG,y);
+      LatticeColourMatrix z(&Grid); random(pRNG,z);
+      LatticeColourMatrix x(&Grid); random(pRNG,x);
+      LatticeColourMatrix y(&Grid); random(pRNG,y);
 
       double start=usecond();
-      for(int i=0;i<Nloop;i++){
+      for(int64_t i=0;i<Nloop;i++){
 	mult(z,x,y);
       }
       double stop=usecond();
@@ -148,17 +148,17 @@ int main (int argc, char ** argv)
   for(int lat=2;lat<=LMAX;lat+=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
-      int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      int64_t vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
 
-      LatticeColourMatrix z(&Grid); //random(pRNG,z);
-      LatticeColourMatrix x(&Grid); //random(pRNG,x);
-      LatticeColourMatrix y(&Grid); //random(pRNG,y);
+      LatticeColourMatrix z(&Grid); random(pRNG,z);
+      LatticeColourMatrix x(&Grid); random(pRNG,x);
+      LatticeColourMatrix y(&Grid); random(pRNG,y);
 
       double start=usecond();
-      for(int i=0;i<Nloop;i++){
+      for(int64_t i=0;i<Nloop;i++){
 	mac(z,x,y);
       }
       double stop=usecond();

benchmarks/Benchmark_wilson.cc

@@ -58,7 +58,7 @@ int main (int argc, char ** argv)
   std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplex::Nsimd());
   std::vector<int> mpi_layout  = GridDefaultMpi();
   GridCartesian               Grid(latt_size,simd_layout,mpi_layout);
-  GridRedBlackCartesian     RBGrid(latt_size,simd_layout,mpi_layout);
+  GridRedBlackCartesian     RBGrid(&Grid);
 
   int threads = GridThread::GetThreads();
   std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;

benchmarks/Benchmark_wilson_sweep.cc

@@ -93,7 +93,7 @@ int main (int argc, char ** argv)
 	  std::cout << latt_size.back() << "\t\t";
 
 	  GridCartesian           Grid(latt_size,simd_layout,mpi_layout);
-	  GridRedBlackCartesian RBGrid(latt_size,simd_layout,mpi_layout);
+	  GridRedBlackCartesian RBGrid(&Grid);
 
 	  GridParallelRNG  pRNG(&Grid); pRNG.SeedFixedIntegers(seeds);
 	  LatticeGaugeField Umu(&Grid); random(pRNG,Umu);

bootstrap.sh

@@ -1,11 +1,9 @@
-]#!/usr/bin/env bash
+#!/usr/bin/env bash
 
 EIGEN_URL='http://bitbucket.org/eigen/eigen/get/3.3.3.tar.bz2'
 
 echo "-- deploying Eigen source..."
-wget ${EIGEN_URL} --no-check-certificate
-./scripts/update_eigen.sh `basename ${EIGEN_URL}`
-rm `basename ${EIGEN_URL}`
+wget ${EIGEN_URL} --no-check-certificate && ./scripts/update_eigen.sh `basename ${EIGEN_URL}` && rm `basename ${EIGEN_URL}`
 
 echo '-- generating Make.inc files...'
 ./scripts/filelist

configure.ac

@@ -13,6 +13,10 @@ m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])])
 ################ Get git info
 #AC_REVISION([m4_esyscmd_s([./scripts/configure.commit])])
 
+################ Set flags
+# do not move!
+CXXFLAGS="-O3 $CXXFLAGS"
+
 ############### Checks for programs
 AC_PROG_CXX
 AC_PROG_RANLIB
@@ -27,7 +31,6 @@ AX_GXX_VERSION
 AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"],
       [version of g++ that will compile the code])
 
-CXXFLAGS="-O3 $CXXFLAGS"
 
 
 ############### Checks for typedefs, structures, and compiler characteristics
@@ -51,9 +54,14 @@ AC_CHECK_HEADERS(malloc/malloc.h)
 AC_CHECK_HEADERS(malloc.h)
 AC_CHECK_HEADERS(endian.h)
 AC_CHECK_HEADERS(execinfo.h)
+AC_CHECK_HEADERS(numaif.h)
 AC_CHECK_DECLS([ntohll],[], [], [[#include <arpa/inet.h>]])
 AC_CHECK_DECLS([be64toh],[], [], [[#include <arpa/inet.h>]])
 
+############## Standard libraries
+AC_CHECK_LIB([m],[cos])
+AC_CHECK_LIB([stdc++],[abort])
+
 ############### GMP and MPFR
 AC_ARG_WITH([gmp],
     [AS_HELP_STRING([--with-gmp=prefix],
@@ -184,6 +192,15 @@ AC_SEARCH_LIBS([limeCreateReader], [lime],
 In order to use ILGG file format please install or provide the correct path to your installation
 Info at: http://usqcd.jlab.org/usqcd-docs/c-lime/)])
 
+AC_SEARCH_LIBS([crc32], [z],
+               [AC_DEFINE([HAVE_ZLIB], [1], [Define to 1 if you have the `LIBZ' library])]
+               [have_zlib=true] [LIBS="${LIBS} -lz"],
+	       [AC_MSG_ERROR(zlib library was not found in your system.)])
+
+AC_SEARCH_LIBS([move_pages], [numa],
+               [AC_DEFINE([HAVE_LIBNUMA], [1], [Define to 1 if you have the `LIBNUMA' library])]
+               [have_libnuma=true] [LIBS="${LIBS} -lnuma"],
+	       [AC_MSG_WARN(libnuma library was not found in your system. Some optimisations will not apply)])
 
 AC_SEARCH_LIBS([H5Fopen], [hdf5_cpp],
                [AC_DEFINE([HAVE_HDF5], [1], [Define to 1 if you have the `HDF5' library])]
@@ -237,6 +254,7 @@ case ${ax_cv_cxx_compiler_vendor} in
         SIMD_FLAGS='';;
       KNL)
         AC_DEFINE([AVX512],[1],[AVX512 intrinsics])
+        AC_DEFINE([KNL],[1],[Knights landing processor])
         SIMD_FLAGS='-march=knl';;
       GEN)
         AC_DEFINE([GEN],[1],[generic vector code])
@@ -244,6 +262,9 @@ case ${ax_cv_cxx_compiler_vendor} in
                            [generic SIMD vector width (in bytes)])
         SIMD_GEN_WIDTH_MSG=" (width= $ac_gen_simd_width)"
         SIMD_FLAGS='';;
+      NEONv8)
+        AC_DEFINE([NEONV8],[1],[ARMv8 NEON])
+        SIMD_FLAGS='-march=armv8-a';;
       QPX|BGQ)
         AC_DEFINE([QPX],[1],[QPX intrinsics for BG/Q])
         SIMD_FLAGS='';;
@@ -272,6 +293,7 @@ case ${ax_cv_cxx_compiler_vendor} in
         SIMD_FLAGS='';;
       KNL)
         AC_DEFINE([AVX512],[1],[AVX512 intrinsics for Knights Landing])
+        AC_DEFINE([KNL],[1],[Knights landing processor])
         SIMD_FLAGS='-xmic-avx512';;
       GEN)
         AC_DEFINE([GEN],[1],[generic vector code])
@@ -309,10 +331,39 @@ case ${ac_PRECISION} in
      double)
        AC_DEFINE([GRID_DEFAULT_PRECISION_DOUBLE],[1],[GRID_DEFAULT_PRECISION is DOUBLE] )
      ;;
+     *)
+     AC_MSG_ERROR([${ac_PRECISION} unsupported --enable-precision option]);
+     ;;
 esac
 
+######################  Shared memory allocation technique under MPI3
+AC_ARG_ENABLE([shm],[AC_HELP_STRING([--enable-shm=shmopen|hugetlbfs],
+              [Select SHM allocation technique])],[ac_SHM=${enable_shm}],[ac_SHM=shmopen])
+
+case ${ac_SHM} in
+
+     shmopen)
+     AC_DEFINE([GRID_MPI3_SHMOPEN],[1],[GRID_MPI3_SHMOPEN] )
+     ;;
+
+     hugetlbfs)
+     AC_DEFINE([GRID_MPI3_SHMMMAP],[1],[GRID_MPI3_SHMMMAP] )
+     ;;
+
+     *)
+     AC_MSG_ERROR([${ac_SHM} unsupported --enable-shm option]);
+     ;;
+esac
+
+######################  Shared base path for SHMMMAP
+AC_ARG_ENABLE([shmpath],[AC_HELP_STRING([--enable-shmpath=path],
+              [Select SHM mmap base path for hugetlbfs])],
+	      [ac_SHMPATH=${enable_shmpath}],
+	      [ac_SHMPATH=/var/lib/hugetlbfs/pagesize-2MB/])
+AC_DEFINE_UNQUOTED([GRID_SHM_PATH],["$ac_SHMPATH"],[Path to a hugetlbfs filesystem for MMAPing])
+
 ############### communication type selection
-AC_ARG_ENABLE([comms],[AC_HELP_STRING([--enable-comms=none|mpi|mpi-auto|mpi3|mpi3-auto|shmem],
+AC_ARG_ENABLE([comms],[AC_HELP_STRING([--enable-comms=none|mpi|mpi-auto],
               [Select communications])],[ac_COMMS=${enable_comms}],[ac_COMMS=none])
 
 case ${ac_COMMS} in
@@ -320,22 +371,10 @@ case ${ac_COMMS} in
         AC_DEFINE([GRID_COMMS_NONE],[1],[GRID_COMMS_NONE] )
         comms_type='none'
      ;;
-     mpi3l*)
-       AC_DEFINE([GRID_COMMS_MPI3L],[1],[GRID_COMMS_MPI3L] )
-       comms_type='mpi3l'
-     ;;
-     mpi3*)
+     mpi*)
         AC_DEFINE([GRID_COMMS_MPI3],[1],[GRID_COMMS_MPI3] )
         comms_type='mpi3'
      ;;
-     mpi*)
-        AC_DEFINE([GRID_COMMS_MPI],[1],[GRID_COMMS_MPI] )
-        comms_type='mpi'
-     ;;
-     shmem)
-        AC_DEFINE([GRID_COMMS_SHMEM],[1],[GRID_COMMS_SHMEM] )
-        comms_type='shmem'
-     ;;
      *)
         AC_MSG_ERROR([${ac_COMMS} unsupported --enable-comms option]);
      ;;
@@ -355,7 +394,7 @@ esac
 AM_CONDITIONAL(BUILD_COMMS_SHMEM, [ test "${comms_type}X" == "shmemX" ])
 AM_CONDITIONAL(BUILD_COMMS_MPI,   [ test "${comms_type}X" == "mpiX" ])
 AM_CONDITIONAL(BUILD_COMMS_MPI3,  [ test "${comms_type}X" == "mpi3X" ] )
-AM_CONDITIONAL(BUILD_COMMS_MPI3L, [ test "${comms_type}X" == "mpi3lX" ] )
+AM_CONDITIONAL(BUILD_COMMS_MPIT,  [ test "${comms_type}X" == "mpitX" ] )
 AM_CONDITIONAL(BUILD_COMMS_NONE,  [ test "${comms_type}X" == "noneX" ])
 
 ############### RNG selection
@@ -460,6 +499,8 @@ compiler version            : ${ax_cv_gxx_version}
 SIMD                        : ${ac_SIMD}${SIMD_GEN_WIDTH_MSG}
 Threading                   : ${ac_openmp}
 Communications type         : ${comms_type}
+Shared memory allocator     : ${ac_SHM}
+Shared memory mmap path     : ${ac_SHMPATH}
 Default precision           : ${ac_PRECISION}
 Software FP16 conversion    : ${ac_SFW_FP16}
 RNG choice                  : ${ac_RNG}
@@ -493,6 +534,7 @@ AC_CONFIG_FILES(tests/forces/Makefile)
 AC_CONFIG_FILES(tests/hadrons/Makefile)
 AC_CONFIG_FILES(tests/hmc/Makefile)
 AC_CONFIG_FILES(tests/solver/Makefile)
+AC_CONFIG_FILES(tests/lanczos/Makefile)
 AC_CONFIG_FILES(tests/smearing/Makefile)
 AC_CONFIG_FILES(tests/qdpxx/Makefile)
 AC_CONFIG_FILES(tests/testu01/Makefile)

extras/Hadrons/Application.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Application.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -43,6 +42,7 @@ using namespace Hadrons;
 // constructors ////////////////////////////////////////////////////////////////
 Application::Application(void)
 {
+    initLogger();
     LOG(Message) << "Modules available:" << std::endl;
     auto list = ModuleFactory::getInstance().getBuilderList();
     for (auto &m: list)
@@ -73,12 +73,6 @@ Application::Application(const std::string parameterFileName)
     parameterFileName_ = parameterFileName;
 }
 
-// environment shortcut ////////////////////////////////////////////////////////
-Environment & Application::env(void) const
-{
-    return Environment::getInstance();
-}
-
 // access //////////////////////////////////////////////////////////////////////
 void Application::setPar(const Application::GlobalPar &par)
 {
@@ -94,14 +88,13 @@ const Application::GlobalPar & Application::getPar(void)
 // execute /////////////////////////////////////////////////////////////////////
 void Application::run(void)
 {
-    if (!parameterFileName_.empty() and (env().getNModule() == 0))
+    if (!parameterFileName_.empty() and (vm().getNModule() == 0))
     {
         parseParameterFile(parameterFileName_);
     }
-    if (!scheduled_)
-    {
-        schedule();
-    }
+    vm().printContent();
+    env().printContent();
+    schedule();
     printSchedule();
     configLoop();
 }
@@ -124,12 +117,20 @@ void Application::parseParameterFile(const std::string parameterFileName)
     LOG(Message) << "Building application from '" << parameterFileName << "'..." << std::endl;
     read(reader, "parameters", par);
     setPar(par);
-    push(reader, "modules");
-    push(reader, "module");
+    if (!push(reader, "modules"))
+    {
+        HADRON_ERROR(Parsing, "Cannot open node 'modules' in parameter file '" 
+                              + parameterFileName + "'");
+    }
+    if (!push(reader, "module"))
+    {
+        HADRON_ERROR(Parsing, "Cannot open node 'modules/module' in parameter file '" 
+                              + parameterFileName + "'");
+    }
     do
     {
         read(reader, "id", id);
-        env().createModule(id.name, id.type, reader);
+        vm().createModule(id.name, id.type, reader);
     } while (reader.nextElement("module"));
     pop(reader);
     pop(reader);
@@ -139,7 +140,7 @@ void Application::saveParameterFile(const std::string parameterFileName)
 {
     XmlWriter          writer(parameterFileName);
     ObjectId           id;
-    const unsigned int nMod = env().getNModule();
+    const unsigned int nMod = vm().getNModule();
     
     LOG(Message) << "Saving application to '" << parameterFileName << "'..." << std::endl;
     write(writer, "parameters", getPar());
@@ -147,10 +148,10 @@ void Application::saveParameterFile(const std::string parameterFileName)
     for (unsigned int i = 0; i < nMod; ++i)
     {
         push(writer, "module");
-        id.name = env().getModuleName(i);
-        id.type = env().getModule(i)->getRegisteredName();
+        id.name = vm().getModuleName(i);
+        id.type = vm().getModule(i)->getRegisteredName();
         write(writer, "id", id);
-        env().getModule(i)->saveParameters(writer, "options");
+        vm().getModule(i)->saveParameters(writer, "options");
         pop(writer);
     }
     pop(writer);
@@ -158,95 +159,13 @@ void Application::saveParameterFile(const std::string parameterFileName)
 }
 
 // schedule computation ////////////////////////////////////////////////////////
-#define MEM_MSG(size)\
-sizeString((size)*locVol_) << " (" << sizeString(size)  << "/site)"
-
-#define DEFINE_MEMPEAK \
-GeneticScheduler<unsigned int>::ObjFunc memPeak = \
-[this](const std::vector<unsigned int> &program)\
-{\
-    unsigned int memPeak;\
-    bool         msg;\
-    \
-    msg = HadronsLogMessage.isActive();\
-    HadronsLogMessage.Active(false);\
-    env().dryRun(true);\
-    memPeak = env().executeProgram(program);\
-    env().dryRun(false);\
-    env().freeAll();\
-    HadronsLogMessage.Active(true);\
-    \
-    return memPeak;\
-}
-
 void Application::schedule(void)
 {
-    DEFINE_MEMPEAK;
-    
-    // build module dependency graph
-    LOG(Message) << "Building module graph..." << std::endl;
-    auto graph = env().makeModuleGraph();
-    auto con = graph.getConnectedComponents();
-    
-    // constrained topological sort using a genetic algorithm
-    LOG(Message) << "Scheduling computation..." << std::endl;
-    LOG(Message) << "               #module= " << graph.size() << std::endl;
-    LOG(Message) << "       population size= " << par_.genetic.popSize << std::endl;
-    LOG(Message) << "       max. generation= " << par_.genetic.maxGen << std::endl;
-    LOG(Message) << "  max. cst. generation= " << par_.genetic.maxCstGen << std::endl;
-    LOG(Message) << "         mutation rate= " << par_.genetic.mutationRate << std::endl;
-    
-    unsigned int                               k = 0, gen, prevPeak, nCstPeak = 0;
-    std::random_device                         rd;
-    GeneticScheduler<unsigned int>::Parameters par;
-    
-    par.popSize      = par_.genetic.popSize;
-    par.mutationRate = par_.genetic.mutationRate;
-    par.seed         = rd();
-    memPeak_         = 0;
-    CartesianCommunicator::BroadcastWorld(0, &(par.seed), sizeof(par.seed));
-    for (unsigned int i = 0; i < con.size(); ++i)
+    if (!scheduled_ and !loadedSchedule_)
     {
-        GeneticScheduler<unsigned int> scheduler(con[i], memPeak, par);
-        
-        gen = 0;
-        do
-        {
-            LOG(Debug) << "Generation " << gen << ":" << std::endl;
-            scheduler.nextGeneration();
-            if (gen != 0)
-            {
-                if (prevPeak == scheduler.getMinValue())
-                {
-                    nCstPeak++;
-                }
-                else
-                {
-                    nCstPeak = 0;
-                }
-            }
-            
-            prevPeak = scheduler.getMinValue();
-            if (gen % 10 == 0)
-            {
-                LOG(Iterative) << "Generation " << gen << ": "
-                               << MEM_MSG(scheduler.getMinValue()) << std::endl;
-            }
-            
-            gen++;
-        } while ((gen < par_.genetic.maxGen)
-                 and (nCstPeak < par_.genetic.maxCstGen));
-        auto &t = scheduler.getMinSchedule();
-        if (scheduler.getMinValue() > memPeak_)
-        {
-            memPeak_ = scheduler.getMinValue();
-        }
-        for (unsigned int j = 0; j < t.size(); ++j)
-        {
-            program_.push_back(t[j]);
-        }
+        program_   = vm().schedule(par_.genetic);
+        scheduled_ = true;
     }
-    scheduled_ = true;
 }
 
 void Application::saveSchedule(const std::string filename)
@@ -256,21 +175,19 @@ void Application::saveSchedule(const std::string filename)
     
     if (!scheduled_)
     {
-        HADRON_ERROR("Computation not scheduled");
+        HADRON_ERROR(Definition, "Computation not scheduled");
     }
     LOG(Message) << "Saving current schedule to '" << filename << "'..."
                  << std::endl;
     for (auto address: program_)
     {
-        program.push_back(env().getModuleName(address));
+        program.push_back(vm().getModuleName(address));
     }
     write(writer, "schedule", program);
 }
 
 void Application::loadSchedule(const std::string filename)
 {
-    DEFINE_MEMPEAK;
-    
     TextReader               reader(filename);
     std::vector<std::string> program;
     
@@ -280,24 +197,24 @@ void Application::loadSchedule(const std::string filename)
     program_.clear();
     for (auto &name: program)
     {
-        program_.push_back(env().getModuleAddress(name));
+        program_.push_back(vm().getModuleAddress(name));
     }
-    scheduled_ = true;
-    memPeak_   = memPeak(program_);
+    loadedSchedule_ = true;
 }
 
 void Application::printSchedule(void)
 {
     if (!scheduled_)
     {
-        HADRON_ERROR("Computation not scheduled");
+        HADRON_ERROR(Definition, "Computation not scheduled");
     }
-    LOG(Message) << "Schedule (memory peak: " << MEM_MSG(memPeak_) << "):"
+    auto peak = vm().memoryNeeded(program_);
+    LOG(Message) << "Schedule (memory needed: " << sizeString(peak) << "):"
                  << std::endl;
     for (unsigned int i = 0; i < program_.size(); ++i)
     {
         LOG(Message) << std::setw(4) << i + 1 << ": "
-                     << env().getModuleName(program_[i]) << std::endl;
+                     << vm().getModuleName(program_[i]) << std::endl;
     }
 }
 
@@ -310,8 +227,8 @@ void Application::configLoop(void)
     {
         LOG(Message) << BIG_SEP << " Starting measurement for trajectory " << t
                      << " " << BIG_SEP << std::endl;
-        env().setTrajectory(t);
-        env().executeProgram(program_);
+        vm().setTrajectory(t);
+        vm().executeProgram(program_);
     }
     LOG(Message) << BIG_SEP << " End of measurement " << BIG_SEP << std::endl;
     env().freeAll();

extras/Hadrons/Application.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Application.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -31,8 +30,7 @@ See the full license in the file "LICENSE" in the top level distribution directo
 #define Hadrons_Application_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
-#include <Grid/Hadrons/Environment.hpp>
-#include <Grid/Hadrons/ModuleFactory.hpp>
+#include <Grid/Hadrons/VirtualMachine.hpp>
 #include <Grid/Hadrons/Modules.hpp>
 
 BEGIN_HADRONS_NAMESPACE
@@ -51,25 +49,13 @@ public:
                                         unsigned int, end,
                                         unsigned int, step);
     };
-    class GeneticPar: Serializable
-    {
-    public:
-        GeneticPar(void):
-            popSize{20}, maxGen{1000}, maxCstGen{100}, mutationRate{.1} {};
-    public:
-        GRID_SERIALIZABLE_CLASS_MEMBERS(GeneticPar,
-                                        unsigned int, popSize,
-                                        unsigned int, maxGen,
-                                        unsigned int, maxCstGen,
-                                        double      , mutationRate);
-    };
     class GlobalPar: Serializable
     {
     public:
         GRID_SERIALIZABLE_CLASS_MEMBERS(GlobalPar,
-                                        TrajRange,   trajCounter,
-                                        GeneticPar,  genetic,
-                                        std::string, seed);
+                                        TrajRange,                  trajCounter,
+                                        VirtualMachine::GeneticPar, genetic,
+                                        std::string,                seed);
     };
 public:
     // constructors
@@ -100,14 +86,15 @@ public:
     void configLoop(void);
 private:
     // environment shortcut
-    Environment & env(void) const;
+    DEFINE_ENV_ALIAS;
+    // virtual machine shortcut
+    DEFINE_VM_ALIAS;
 private:
-    long unsigned int         locVol_;
-    std::string               parameterFileName_{""};
-    GlobalPar                 par_;
-    std::vector<unsigned int> program_;
-    Environment::Size         memPeak_;
-    bool                      scheduled_{false};
+    long unsigned int       locVol_;
+    std::string             parameterFileName_{""};
+    GlobalPar               par_;
+    VirtualMachine::Program program_;
+    bool                    scheduled_{false}, loadedSchedule_{false};
 };
 
 /******************************************************************************
@@ -117,14 +104,16 @@ private:
 template <typename M>
 void Application::createModule(const std::string name)
 {
-    env().createModule<M>(name);
+    vm().createModule<M>(name);
+    scheduled_ = false;
 }
 
 template <typename M>
 void Application::createModule(const std::string name,
                                const typename M::Par &par)
 {
-    env().createModule<M>(name, par);
+    vm().createModule<M>(name, par);
+    scheduled_ = false;
 }
 
 END_HADRONS_NAMESPACE

extras/Hadrons/Environment.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Environment.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -35,15 +34,19 @@ using namespace Grid;
 using namespace QCD;
 using namespace Hadrons;
 
+#define ERROR_NO_ADDRESS(address)\
+HADRON_ERROR(Definition, "no object with address " + std::to_string(address));
+
 /******************************************************************************
  *                       Environment implementation                           *
  ******************************************************************************/
 // constructor /////////////////////////////////////////////////////////////////
 Environment::Environment(void)
 {
-    nd_ = GridDefaultLatt().size();
+    dim_ = GridDefaultLatt();
+    nd_  = dim_.size();
     grid4d_.reset(SpaceTimeGrid::makeFourDimGrid(
-        GridDefaultLatt(), GridDefaultSimd(nd_, vComplex::Nsimd()),
+        dim_, GridDefaultSimd(nd_, vComplex::Nsimd()),
         GridDefaultMpi()));
     gridRb4d_.reset(SpaceTimeGrid::makeFourDimRedBlackGrid(grid4d_.get()));
     auto loc = getGrid()->LocalDimensions();
@@ -55,28 +58,6 @@ Environment::Environment(void)
     rng4d_.reset(new GridParallelRNG(grid4d_.get()));
 }
 
-// dry run /////////////////////////////////////////////////////////////////////
-void Environment::dryRun(const bool isDry)
-{
-    dryRun_ = isDry;
-}
-
-bool Environment::isDryRun(void) const
-{
-    return dryRun_;
-}
-
-// trajectory number ///////////////////////////////////////////////////////////
-void Environment::setTrajectory(const unsigned int traj)
-{
-    traj_ = traj;
-}
-
-unsigned int Environment::getTrajectory(void) const
-{
-    return traj_;
-}
-
 // grids ///////////////////////////////////////////////////////////////////////
 void Environment::createGrid(const unsigned int Ls)
 {
@@ -104,7 +85,7 @@ GridCartesian * Environment::getGrid(const unsigned int Ls) const
     }
     catch(std::out_of_range &)
     {
-        HADRON_ERROR("no grid with Ls= " << Ls);
+        HADRON_ERROR(Definition, "no grid with Ls= " + std::to_string(Ls));
     }
 }
 
@@ -123,7 +104,7 @@ GridRedBlackCartesian * Environment::getRbGrid(const unsigned int Ls) const
     }
     catch(std::out_of_range &)
     {
-        HADRON_ERROR("no red-black 5D grid with Ls= " << Ls);
+        HADRON_ERROR(Definition, "no red-black 5D grid with Ls= " + std::to_string(Ls));
     }
 }
 
@@ -132,6 +113,21 @@ unsigned int Environment::getNd(void) const
     return nd_;
 }
 
+std::vector<int> Environment::getDim(void) const
+{
+    return dim_;
+}
+
+int Environment::getDim(const unsigned int mu) const
+{
+    return dim_[mu];
+}
+
+unsigned long int Environment::getLocalVolume(void) const
+{
+    return locVol_;
+}
+
 // random number generator /////////////////////////////////////////////////////
 void Environment::setSeed(const std::vector<int> &seed)
 {
@@ -143,276 +139,6 @@ GridParallelRNG * Environment::get4dRng(void) const
     return rng4d_.get();
 }
 
-// module management ///////////////////////////////////////////////////////////
-void Environment::pushModule(Environment::ModPt &pt)
-{
-    std::string name = pt->getName();
-    
-    if (!hasModule(name))
-    {
-        std::vector<unsigned int> inputAddress;
-        unsigned int              address;
-        ModuleInfo                m;
-        
-        m.data = std::move(pt);
-        m.type = typeIdPt(*m.data.get());
-        m.name = name;
-        auto input  = m.data->getInput();
-        for (auto &in: input)
-        {
-            if (!hasObject(in))
-            {
-                addObject(in , -1);
-            }
-            m.input.push_back(objectAddress_[in]);
-        }
-        auto output = m.data->getOutput();
-        module_.push_back(std::move(m));
-        address              = static_cast<unsigned int>(module_.size() - 1);
-        moduleAddress_[name] = address;
-        for (auto &out: output)
-        {
-            if (!hasObject(out))
-            {
-                addObject(out, address);
-            }
-            else
-            {
-                if (object_[objectAddress_[out]].module < 0)
-                {
-                    object_[objectAddress_[out]].module = address;
-                }
-                else
-                {
-                    HADRON_ERROR("object '" + out
-                                 + "' is already produced by module '"
-                                 + module_[object_[getObjectAddress(out)].module].name
-                                 + "' (while pushing module '" + name + "')");
-                }
-            }
-        }
-    }
-    else
-    {
-        HADRON_ERROR("module '" + name + "' already exists");
-    }
-}
-
-unsigned int Environment::getNModule(void) const
-{
-    return module_.size();
-}
-
-void Environment::createModule(const std::string name, const std::string type,
-                               XmlReader &reader)
-{
-    auto &factory = ModuleFactory::getInstance();
-    auto pt       = factory.create(type, name);
-    
-    pt->parseParameters(reader, "options");
-    pushModule(pt);
-}
-
-ModuleBase * Environment::getModule(const unsigned int address) const
-{
-    if (hasModule(address))
-    {
-        return module_[address].data.get();
-    }
-    else
-    {
-        HADRON_ERROR("no module with address " + std::to_string(address));
-    }
-}
-
-ModuleBase * Environment::getModule(const std::string name) const
-{
-    return getModule(getModuleAddress(name));
-}
-
-unsigned int Environment::getModuleAddress(const std::string name) const
-{
-    if (hasModule(name))
-    {
-        return moduleAddress_.at(name);
-    }
-    else
-    {
-        HADRON_ERROR("no module with name '" + name + "'");
-    }
-}
-
-std::string Environment::getModuleName(const unsigned int address) const
-{
-    if (hasModule(address))
-    {
-        return module_[address].name;
-    }
-    else
-    {
-        HADRON_ERROR("no module with address " + std::to_string(address));
-    }
-}
-
-std::string Environment::getModuleType(const unsigned int address) const
-{
-    if (hasModule(address))
-    {
-        return typeName(module_[address].type);
-    }
-    else
-    {
-        HADRON_ERROR("no module with address " + std::to_string(address));
-    }
-}
-
-std::string Environment::getModuleType(const std::string name) const
-{
-    return getModuleType(getModuleAddress(name));
-}
-
-bool Environment::hasModule(const unsigned int address) const
-{
-    return (address < module_.size());
-}
-
-bool Environment::hasModule(const std::string name) const
-{
-    return (moduleAddress_.find(name) != moduleAddress_.end());
-}
-
-Graph<unsigned int> Environment::makeModuleGraph(void) const
-{
-    Graph<unsigned int> moduleGraph;
-    
-    for (unsigned int i = 0; i < module_.size(); ++i)
-    {
-        moduleGraph.addVertex(i);
-        for (auto &j: module_[i].input)
-        {
-            moduleGraph.addEdge(object_[j].module, i);
-        }
-    }
-    
-    return moduleGraph;
-}
-
-#define BIG_SEP "==============="
-#define SEP     "---------------"
-#define MEM_MSG(size)\
-sizeString((size)*locVol_) << " (" << sizeString(size)  << "/site)"
-
-Environment::Size
-Environment::executeProgram(const std::vector<unsigned int> &p)
-{
-    Size                                memPeak = 0, sizeBefore, sizeAfter;
-    std::vector<std::set<unsigned int>> freeProg;
-    bool                                continueCollect, nothingFreed;
-    
-    // build garbage collection schedule
-    freeProg.resize(p.size());
-    for (unsigned int i = 0; i < object_.size(); ++i)
-    {
-        auto pred = [i, this](const unsigned int j)
-        {
-            auto &in = module_[j].input;
-            auto it  = std::find(in.begin(), in.end(), i);
-            
-            return (it != in.end()) or (j == object_[i].module);
-        };
-        auto it = std::find_if(p.rbegin(), p.rend(), pred);
-        if (it != p.rend())
-        {
-            freeProg[p.rend() - it - 1].insert(i);
-        }
-    }
-    
-    // program execution
-    for (unsigned int i = 0; i < p.size(); ++i)
-    {
-        // execute module
-        if (!isDryRun())
-        {
-            LOG(Message) << SEP << " Measurement step " << i+1 << "/"
-                         << p.size() << " (module '" << module_[p[i]].name
-                         << "') " << SEP << std::endl;
-        }
-        (*module_[p[i]].data)();
-        sizeBefore = getTotalSize();
-        // print used memory after execution
-        if (!isDryRun())
-        {
-            LOG(Message) << "Allocated objects: " << MEM_MSG(sizeBefore)
-                         << std::endl;
-        }
-        if (sizeBefore > memPeak)
-        {
-            memPeak = sizeBefore;
-        }
-        // garbage collection for step i
-        if (!isDryRun())
-        {
-            LOG(Message) << "Garbage collection..." << std::endl;
-        }
-        nothingFreed = true;
-        do
-        {
-            continueCollect = false;
-            auto toFree = freeProg[i];
-            for (auto &j: toFree)
-            {
-                // continue garbage collection while there are still
-                // objects without owners
-                continueCollect = continueCollect or !hasOwners(j);
-                if(freeObject(j))
-                {
-                    // if an object has been freed, remove it from
-                    // the garbage collection schedule
-                    freeProg[i].erase(j);
-                    nothingFreed = false;
-                }
-            }
-        } while (continueCollect);
-        // any remaining objects in step i garbage collection schedule
-        // is scheduled for step i + 1
-        if (i + 1 < p.size())
-        {
-            for (auto &j: freeProg[i])
-            {
-                freeProg[i + 1].insert(j);
-            }
-        }
-        // print used memory after garbage collection if necessary
-        if (!isDryRun())
-        {
-            sizeAfter = getTotalSize();
-            if (sizeBefore != sizeAfter)
-            {
-                LOG(Message) << "Allocated objects: " << MEM_MSG(sizeAfter)
-                             << std::endl;
-            }
-            else
-            {
-                LOG(Message) << "Nothing to free" << std::endl;
-            }
-        }
-    }
-    
-    return memPeak;
-}
-
-Environment::Size Environment::executeProgram(const std::vector<std::string> &p)
-{
-    std::vector<unsigned int> pAddress;
-    
-    for (auto &n: p)
-    {
-        pAddress.push_back(getModuleAddress(n));
-    }
-    
-    return executeProgram(pAddress);
-}
-
 // general memory management ///////////////////////////////////////////////////
 void Environment::addObject(const std::string name, const int moduleAddress)
 {
@@ -422,46 +148,25 @@ void Environment::addObject(const std::string name, const int moduleAddress)
         
         info.name   = name;
         info.module = moduleAddress;
+        info.data   = nullptr;
         object_.push_back(std::move(info));
         objectAddress_[name] = static_cast<unsigned int>(object_.size() - 1);
     }
     else
     {
-        HADRON_ERROR("object '" + name + "' already exists");
+        HADRON_ERROR(Definition, "object '" + name + "' already exists");
     }
 }
 
-void Environment::registerObject(const unsigned int address,
-                                 const unsigned int size, const unsigned int Ls)
+void Environment::setObjectModule(const unsigned int objAddress,
+                                  const int modAddress)
 {
-    if (!hasRegisteredObject(address))
-    {
-        if (hasObject(address))
-        {
-            object_[address].size         = size;
-            object_[address].Ls           = Ls;
-            object_[address].isRegistered = true;
-        }
-        else
-        {
-            HADRON_ERROR("no object with address " + std::to_string(address));
-        }
-    }
-    else
-    {
-        HADRON_ERROR("object with address " + std::to_string(address)
-                     + " already registered");
-    }
+    object_[objAddress].module = modAddress;
 }
 
-void Environment::registerObject(const std::string name,
-                                 const unsigned int size, const unsigned int Ls)
+unsigned int Environment::getMaxAddress(void) const
 {
-    if (!hasObject(name))
-    {
-        addObject(name);
-    }
-    registerObject(getObjectAddress(name), size, Ls);
+    return object_.size();
 }
 
 unsigned int Environment::getObjectAddress(const std::string name) const
@@ -472,7 +177,7 @@ unsigned int Environment::getObjectAddress(const std::string name) const
     }
     else
     {
-        HADRON_ERROR("no object with name '" + name + "'");
+        HADRON_ERROR(Definition, "no object with name '" + name + "'");
     }
 }
 
@@ -484,24 +189,26 @@ std::string Environment::getObjectName(const unsigned int address) const
     }
     else
     {
-        HADRON_ERROR("no object with address " + std::to_string(address));
+        ERROR_NO_ADDRESS(address);
     }
 }
 
 std::string Environment::getObjectType(const unsigned int address) const
 {
-    if (hasRegisteredObject(address))
+    if (hasObject(address))
     {
-        return typeName(object_[address].type);
-    }
-    else if (hasObject(address))
-    {
-        HADRON_ERROR("object with address " + std::to_string(address)
-                     + " exists but is not registered");
+        if (object_[address].type)
+        {
+            return typeName(object_[address].type);
+        }
+        else
+        {
+            return "<no type>";
+        }
     }
     else
     {
-        HADRON_ERROR("no object with address " + std::to_string(address));
+        ERROR_NO_ADDRESS(address);
     }
 }
 
@@ -512,18 +219,13 @@ std::string Environment::getObjectType(const std::string name) const
 
 Environment::Size Environment::getObjectSize(const unsigned int address) const
 {
-    if (hasRegisteredObject(address))
+    if (hasObject(address))
     {
         return object_[address].size;
     }
-    else if (hasObject(address))
-    {
-        HADRON_ERROR("object with address " + std::to_string(address)
-                     + " exists but is not registered");
-    }
     else
     {
-        HADRON_ERROR("no object with address " + std::to_string(address));
+        ERROR_NO_ADDRESS(address);
     }
 }
 
@@ -532,20 +234,49 @@ Environment::Size Environment::getObjectSize(const std::string name) const
     return getObjectSize(getObjectAddress(name));
 }
 
-unsigned int Environment::getObjectLs(const unsigned int address) const
+Environment::Storage Environment::getObjectStorage(const unsigned int address) const
 {
-    if (hasRegisteredObject(address))
+    if (hasObject(address))
     {
-        return object_[address].Ls;
-    }
-    else if (hasObject(address))
-    {
-        HADRON_ERROR("object with address " + std::to_string(address)
-                     + " exists but is not registered");
+        return object_[address].storage;
     }
     else
     {
-        HADRON_ERROR("no object with address " + std::to_string(address));
+        ERROR_NO_ADDRESS(address);
+    }
+}
+
+Environment::Storage Environment::getObjectStorage(const std::string name) const
+{
+    return getObjectStorage(getObjectAddress(name));
+}
+
+int Environment::getObjectModule(const unsigned int address) const
+{
+    if (hasObject(address))
+    {
+        return object_[address].module;
+    }
+    else
+    {
+        ERROR_NO_ADDRESS(address);
+    }
+}
+
+int Environment::getObjectModule(const std::string name) const
+{
+    return getObjectModule(getObjectAddress(name));
+}
+
+unsigned int Environment::getObjectLs(const unsigned int address) const
+{
+    if (hasObject(address))
+    {
+        return object_[address].Ls;
+    }
+    else
+    {
+        ERROR_NO_ADDRESS(address);
     }
 }
 
@@ -566,30 +297,6 @@ bool Environment::hasObject(const std::string name) const
     return ((it != objectAddress_.end()) and hasObject(it->second));
 }
 
-bool Environment::hasRegisteredObject(const unsigned int address) const
-{
-    if (hasObject(address))
-    {
-        return object_[address].isRegistered;
-    }
-    else
-    {
-        return false;
-    }
-}
-
-bool Environment::hasRegisteredObject(const std::string name) const
-{
-    if (hasObject(name))
-    {
-        return hasRegisteredObject(getObjectAddress(name));
-    }
-    else
-    {
-        return false;
-    }
-}
-
 bool Environment::hasCreatedObject(const unsigned int address) const
 {
     if (hasObject(address))
@@ -630,92 +337,27 @@ Environment::Size Environment::getTotalSize(void) const
     
     for (auto &o: object_)
     {
-        if (o.isRegistered)
-        {
-            size += o.size;
-        }
+        size += o.size;
     }
     
     return size;
 }
 
-void Environment::addOwnership(const unsigned int owner,
-                               const unsigned int property)
+void Environment::freeObject(const unsigned int address)
 {
-    if (hasObject(property))
+    if (hasCreatedObject(address))
     {
-        object_[property].owners.insert(owner);
-    }
-    else
-    {
-        HADRON_ERROR("no object with address " + std::to_string(property));
-    }
-    if (hasObject(owner))
-    {
-        object_[owner].properties.insert(property);
-    }
-    else
-    {
-        HADRON_ERROR("no object with address " + std::to_string(owner));
+        LOG(Message) << "Destroying object '" << object_[address].name
+                     << "'" << std::endl;
     }
+    object_[address].size = 0;
+    object_[address].type = nullptr;
+    object_[address].data.reset(nullptr);
 }
 
-void Environment::addOwnership(const std::string owner,
-                               const std::string property)
+void Environment::freeObject(const std::string name)
 {
-    addOwnership(getObjectAddress(owner), getObjectAddress(property));
-}
-
-bool Environment::hasOwners(const unsigned int address) const
-{
-    
-    if (hasObject(address))
-    {
-        return (!object_[address].owners.empty());
-    }
-    else
-    {
-        HADRON_ERROR("no object with address " + std::to_string(address));
-    }
-}
-
-bool Environment::hasOwners(const std::string name) const
-{
-    return hasOwners(getObjectAddress(name));
-}
-
-bool Environment::freeObject(const unsigned int address)
-{
-    if (!hasOwners(address))
-    {
-        if (!isDryRun() and object_[address].isRegistered)
-        {
-            LOG(Message) << "Destroying object '" << object_[address].name
-                         << "'" << std::endl;
-        }
-        for (auto &p: object_[address].properties)
-        {
-            object_[p].owners.erase(address);
-        }
-        object_[address].size         = 0;
-        object_[address].Ls           = 0;
-        object_[address].isRegistered = false;
-        object_[address].type         = nullptr;
-        object_[address].owners.clear();
-        object_[address].properties.clear();
-        object_[address].data.reset(nullptr);
-        
-        return true;
-    }
-    else
-    {
-        return false;
-    }
-}
-
-bool Environment::freeObject(const std::string name)
-{
-    return freeObject(getObjectAddress(name));
+    freeObject(getObjectAddress(name));
 }
 
 void Environment::freeAll(void)
@@ -726,18 +368,24 @@ void Environment::freeAll(void)
     }
 }
 
-void Environment::printContent(void)
+void Environment::protectObjects(const bool protect)
 {
-    LOG(Message) << "Modules: " << std::endl;
-    for (unsigned int i = 0; i < module_.size(); ++i)
-    {
-        LOG(Message) << std::setw(4) << i << ": "
-                     << getModuleName(i) << std::endl;
-    }
-    LOG(Message) << "Objects: " << std::endl;
+    protect_ = protect;
+}
+
+bool Environment::objectsProtected(void) const
+{
+    return protect_;
+}
+
+// print environment content ///////////////////////////////////////////////////
+void Environment::printContent(void) const
+{
+    LOG(Debug) << "Objects: " << std::endl;
     for (unsigned int i = 0; i < object_.size(); ++i)
     {
-        LOG(Message) << std::setw(4) << i << ": "
-                     << getObjectName(i) << std::endl;
+        LOG(Debug) << std::setw(4) << i << ": "
+                   << getObjectName(i) << " ("
+                   << sizeString(getObjectSize(i)) << ")" << std::endl;
     }
 }

extras/Hadrons/Environment.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Environment.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -31,20 +30,12 @@ See the full license in the file "LICENSE" in the top level distribution directo
 #define Hadrons_Environment_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
-#include <Grid/Hadrons/Graph.hpp>
-
-#ifndef SITE_SIZE_TYPE
-#define SITE_SIZE_TYPE unsigned int
-#endif
 
 BEGIN_HADRONS_NAMESPACE
 
 /******************************************************************************
  *                         Global environment                                 *
  ******************************************************************************/
-// forward declaration of Module
-class ModuleBase;
-
 class Object
 {
 public:
@@ -66,137 +57,100 @@ private:
     std::unique_ptr<T> objPt_{nullptr};
 };
 
+#define DEFINE_ENV_ALIAS \
+inline Environment & env(void) const\
+{\
+    return Environment::getInstance();\
+}
+
 class Environment
 {
     SINGLETON(Environment);
 public:
     typedef SITE_SIZE_TYPE                         Size;
-    typedef std::unique_ptr<ModuleBase>            ModPt;
     typedef std::unique_ptr<GridCartesian>         GridPt;
     typedef std::unique_ptr<GridRedBlackCartesian> GridRbPt;
     typedef std::unique_ptr<GridParallelRNG>       RngPt;
-    typedef std::unique_ptr<LatticeBase>           LatticePt;
+    enum class Storage {object, cache, temporary};
 private:
-    struct ModuleInfo
-    {
-        const std::type_info      *type{nullptr};
-        std::string               name;
-        ModPt                     data{nullptr};
-        std::vector<unsigned int> input;
-    };
     struct ObjInfo
     {
         Size                    size{0};
+        Storage                 storage{Storage::object};
         unsigned int            Ls{0};
-        bool                    isRegistered{false};
         const std::type_info    *type{nullptr};
         std::string             name;
         int                     module{-1};
-        std::set<unsigned int>  owners, properties;
         std::unique_ptr<Object> data{nullptr};
     };
 public:
-    // dry run
-    void                    dryRun(const bool isDry);
-    bool                    isDryRun(void) const;
-    // trajectory number
-    void                    setTrajectory(const unsigned int traj);
-    unsigned int            getTrajectory(void) const;
     // grids
     void                    createGrid(const unsigned int Ls);
     GridCartesian *         getGrid(const unsigned int Ls = 1) const;
     GridRedBlackCartesian * getRbGrid(const unsigned int Ls = 1) const;
+    std::vector<int>        getDim(void) const;
+    int                     getDim(const unsigned int mu) const;
+    unsigned long int       getLocalVolume(void) const;
     unsigned int            getNd(void) const;
     // random number generator
     void                    setSeed(const std::vector<int> &seed);
     GridParallelRNG *       get4dRng(void) const;
-    // module management
-    void                    pushModule(ModPt &pt);
-    template <typename M>
-    void                    createModule(const std::string name);
-    template <typename M>
-    void                    createModule(const std::string name,
-                                         const typename M::Par &par);
-    void                    createModule(const std::string name,
-                                         const std::string type,
-                                         XmlReader &reader);
-    unsigned int            getNModule(void) const;
-    ModuleBase *            getModule(const unsigned int address) const;
-    ModuleBase *            getModule(const std::string name) const;
-    template <typename M>
-    M *                     getModule(const unsigned int address) const;
-    template <typename M>
-    M *                     getModule(const std::string name) const;
-    unsigned int            getModuleAddress(const std::string name) const;
-    std::string             getModuleName(const unsigned int address) const;
-    std::string             getModuleType(const unsigned int address) const;
-    std::string             getModuleType(const std::string name) const;
-    bool                    hasModule(const unsigned int address) const;
-    bool                    hasModule(const std::string name) const;
-    Graph<unsigned int>     makeModuleGraph(void) const;
-    Size                    executeProgram(const std::vector<unsigned int> &p);
-    Size                    executeProgram(const std::vector<std::string> &p);
     // general memory management
     void                    addObject(const std::string name,
                                       const int moduleAddress = -1);
-    void                    registerObject(const unsigned int address,
-                                           const unsigned int size,
-                                           const unsigned int Ls = 1);
-    void                    registerObject(const std::string name,
-                                           const unsigned int size,
-                                           const unsigned int Ls = 1);
-    template <typename T>
-    unsigned int            lattice4dSize(void) const;
-    template <typename T>
-    void                    registerLattice(const unsigned int address,
-                                            const unsigned int Ls = 1);
-    template <typename T>
-    void                    registerLattice(const std::string name,
-                                            const unsigned int Ls = 1);
-    template <typename T>
-    void                    setObject(const unsigned int address, T *object);
-    template <typename T>
-    void                    setObject(const std::string name, T *object);
+    template <typename B, typename T, typename ... Ts>
+    void                    createDerivedObject(const std::string name,
+                                                const Environment::Storage storage,
+                                                const unsigned int Ls,
+                                                Ts && ... args);
+    template <typename T, typename ... Ts>
+    void                    createObject(const std::string name,
+                                         const Environment::Storage storage,
+                                         const unsigned int Ls,
+                                         Ts && ... args);
+    void                    setObjectModule(const unsigned int objAddress,
+                                            const int modAddress);
     template <typename T>
     T *                     getObject(const unsigned int address) const;
     template <typename T>
     T *                     getObject(const std::string name) const;
-    template <typename T>
-    T *                     createLattice(const unsigned int address);
-    template <typename T>
-    T *                     createLattice(const std::string name);
+    unsigned int            getMaxAddress(void) const;
     unsigned int            getObjectAddress(const std::string name) const;
     std::string             getObjectName(const unsigned int address) const;
     std::string             getObjectType(const unsigned int address) const;
     std::string             getObjectType(const std::string name) const;
     Size                    getObjectSize(const unsigned int address) const;
     Size                    getObjectSize(const std::string name) const;
+    Storage                 getObjectStorage(const unsigned int address) const;
+    Storage                 getObjectStorage(const std::string name) const;
+    int                     getObjectModule(const unsigned int address) const;
+    int                     getObjectModule(const std::string name) const;
     unsigned int            getObjectLs(const unsigned int address) const;
     unsigned int            getObjectLs(const std::string name) const;
     bool                    hasObject(const unsigned int address) const;
     bool                    hasObject(const std::string name) const;
-    bool                    hasRegisteredObject(const unsigned int address) const;
-    bool                    hasRegisteredObject(const std::string name) const;
     bool                    hasCreatedObject(const unsigned int address) const;
     bool                    hasCreatedObject(const std::string name) const;
     bool                    isObject5d(const unsigned int address) const;
     bool                    isObject5d(const std::string name) const;
+    template <typename T>
+    bool                    isObjectOfType(const unsigned int address) const;
+    template <typename T>
+    bool                    isObjectOfType(const std::string name) const;
     Environment::Size       getTotalSize(void) const;
-    void                    addOwnership(const unsigned int owner,
-                                         const unsigned int property);
-    void                    addOwnership(const std::string owner,
-                                         const std::string property);
-    bool                    hasOwners(const unsigned int address) const;
-    bool                    hasOwners(const std::string name) const;
-    bool                    freeObject(const unsigned int address);
-    bool                    freeObject(const std::string name);
+    void                    freeObject(const unsigned int address);
+    void                    freeObject(const std::string name);
     void                    freeAll(void);
-    void                    printContent(void);
+    void                    protectObjects(const bool protect);
+    bool                    objectsProtected(void) const;
+    // print environment content
+    void                    printContent(void) const;
 private:
     // general
-    bool                                   dryRun_{false};
-    unsigned int                           traj_, locVol_;
+    unsigned long int                      locVol_;
+    bool                                   protect_{true};
     // grids
+    std::vector<int>                       dim_;
     GridPt                                 grid4d_;
     std::map<unsigned int, GridPt>         grid5d_;
     GridRbPt                               gridRb4d_;
@@ -204,11 +158,6 @@ private:
     unsigned int                           nd_;
     // random number generator
     RngPt                                  rng4d_;
-    // module and related maps
-    std::vector<ModuleInfo>                module_;
-    std::map<std::string, unsigned int>    moduleAddress_;
-    // lattice store
-    std::map<unsigned int, LatticePt>      lattice_;
     // object store
     std::vector<ObjInfo>                   object_;
     std::map<std::string, unsigned int>    objectAddress_;
@@ -245,116 +194,85 @@ void Holder<T>::reset(T *pt)
 /******************************************************************************
  *                     Environment template implementation                    *
  ******************************************************************************/
-// module management ///////////////////////////////////////////////////////////
-template <typename M>
-void Environment::createModule(const std::string name)
+// general memory management ///////////////////////////////////////////////////
+template <typename B, typename T, typename ... Ts>
+void Environment::createDerivedObject(const std::string name,
+                                      const Environment::Storage storage,
+                                      const unsigned int Ls,
+                                      Ts && ... args)
 {
-    ModPt pt(new M(name));
+    if (!hasObject(name))
+    {
+        addObject(name);
+    }
     
-    pushModule(pt);
-}
-
-template <typename M>
-void Environment::createModule(const std::string name,
-                               const typename M::Par &par)
-{
-    ModPt pt(new M(name));
+    unsigned int address = getObjectAddress(name);
     
-    static_cast<M *>(pt.get())->setPar(par);
-    pushModule(pt);
-}
-
-template <typename M>
-M * Environment::getModule(const unsigned int address) const
-{
-    if (auto *pt = dynamic_cast<M *>(getModule(address)))
+    if (!object_[address].data or !objectsProtected())
     {
-        return pt;
+        MemoryStats memStats;
+    
+        if (!MemoryProfiler::stats)
+        {
+            MemoryProfiler::stats = &memStats;
+        }
+        size_t initMem           = MemoryProfiler::stats->currentlyAllocated;
+        object_[address].storage = storage;
+        object_[address].Ls      = Ls;
+        object_[address].data.reset(new Holder<B>(new T(std::forward<Ts>(args)...)));
+        object_[address].size    = MemoryProfiler::stats->maxAllocated - initMem;
+        object_[address].type    = &typeid(T);
+        if (MemoryProfiler::stats == &memStats)
+        {
+            MemoryProfiler::stats = nullptr;
+        }
     }
-    else
+    // object already exists, no error if it is a cache, error otherwise
+    else if ((object_[address].storage != Storage::cache) or 
+             (object_[address].storage != storage)        or
+             (object_[address].name    != name)           or
+             (object_[address].type    != &typeid(T)))
     {
-        HADRON_ERROR("module '" + module_[address].name
-                     + "' does not have type " + typeid(M).name()
-                     + "(object type: " + getModuleType(address) + ")");
+        HADRON_ERROR(Definition, "object '" + name + "' already allocated");
     }
 }
 
-template <typename M>
-M * Environment::getModule(const std::string name) const
+template <typename T, typename ... Ts>
+void Environment::createObject(const std::string name, 
+                               const Environment::Storage storage,
+                               const unsigned int Ls,
+                               Ts && ... args)
 {
-    return getModule<M>(getModuleAddress(name));
-}
-
-template <typename T>
-unsigned int Environment::lattice4dSize(void) const
-{
-    return sizeof(typename T::vector_object)/getGrid()->Nsimd();
-}
-
-template <typename T>
-void Environment::registerLattice(const unsigned int address,
-                                  const unsigned int Ls)
-{
-    createGrid(Ls);
-    registerObject(address, Ls*lattice4dSize<T>(), Ls);
-}
-
-template <typename T>
-void Environment::registerLattice(const std::string name, const unsigned int Ls)
-{
-    createGrid(Ls);
-    registerObject(name, Ls*lattice4dSize<T>(), Ls);
-}
-
-template <typename T>
-void Environment::setObject(const unsigned int address, T *object)
-{
-    if (hasRegisteredObject(address))
-    {
-        object_[address].data.reset(new Holder<T>(object));
-        object_[address].type = &typeid(T);
-    }
-    else if (hasObject(address))
-    {
-        HADRON_ERROR("object with address " + std::to_string(address) +
-                     " exists but is not registered");
-    }
-    else
-    {
-        HADRON_ERROR("no object with address " + std::to_string(address));
-    }
-}
-
-template <typename T>
-void Environment::setObject(const std::string name, T *object)
-{
-    setObject(getObjectAddress(name), object);
+    createDerivedObject<T, T>(name, storage, Ls, std::forward<Ts>(args)...);
 }
 
 template <typename T>
 T * Environment::getObject(const unsigned int address) const
 {
-    if (hasRegisteredObject(address))
+    if (hasObject(address))
     {
-        if (auto h = dynamic_cast<Holder<T> *>(object_[address].data.get()))
+        if (hasCreatedObject(address))
         {
-            return h->getPt();
+            if (auto h = dynamic_cast<Holder<T> *>(object_[address].data.get()))
+            {
+                return h->getPt();
+            }
+            else
+            {
+                HADRON_ERROR(Definition, "object with address " + std::to_string(address) +
+                            " does not have type '" + typeName(&typeid(T)) +
+                            "' (has type '" + getObjectType(address) + "')");
+            }
         }
         else
         {
-            HADRON_ERROR("object with address " + std::to_string(address) +
-                         " does not have type '" + typeid(T).name() +
-                         "' (has type '" + getObjectType(address) + "')");
+            HADRON_ERROR(Definition, "object with address " + std::to_string(address) +
+                         " is empty");
         }
     }
-    else if (hasObject(address))
-    {
-        HADRON_ERROR("object with address " + std::to_string(address) +
-                     " exists but is not registered");
-    }
     else
     {
-        HADRON_ERROR("no object with address " + std::to_string(address));
+        HADRON_ERROR(Definition, "no object with address " + std::to_string(address));
     }
 }
 
@@ -365,19 +283,29 @@ T * Environment::getObject(const std::string name) const
 }
 
 template <typename T>
-T * Environment::createLattice(const unsigned int address)
+bool Environment::isObjectOfType(const unsigned int address) const
 {
-    GridCartesian *g = getGrid(getObjectLs(address));
-    
-    setObject(address, new T(g));
-    
-    return getObject<T>(address);
+    if (hasObject(address))
+    {
+        if (auto h = dynamic_cast<Holder<T> *>(object_[address].data.get()))
+        {
+            return true;
+        }
+        else
+        {
+            return false;
+        }
+    }
+    else
+    {
+        HADRON_ERROR(Definition, "no object with address " + std::to_string(address));
+    }
 }
 
 template <typename T>
-T * Environment::createLattice(const std::string name)
+bool Environment::isObjectOfType(const std::string name) const
 {
-    return createLattice<T>(getObjectAddress(name));
+    return isObjectOfType<T>(getObjectAddress(name));
 }
 
 END_HADRONS_NAMESPACE

extras/Hadrons/Exceptions.cc

@@ -0,0 +1,57 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Exceptions.cc
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Exceptions.hpp>
+
+#ifndef ERR_SUFF
+#define ERR_SUFF " (" + loc + ")"
+#endif
+
+#define CONST_EXC(name, init) \
+name::name(std::string msg, std::string loc)\
+:init\
+{}
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace Exceptions;
+
+// logic errors
+CONST_EXC(Logic, logic_error(msg + ERR_SUFF))
+CONST_EXC(Definition, Logic("definition error: " + msg, loc))
+CONST_EXC(Implementation, Logic("implementation error: " + msg, loc))
+CONST_EXC(Range, Logic("range error: " + msg, loc))
+CONST_EXC(Size, Logic("size error: " + msg, loc))
+// runtime errors
+CONST_EXC(Runtime, runtime_error(msg + ERR_SUFF))
+CONST_EXC(Argument, Runtime("argument error: " + msg, loc))
+CONST_EXC(Io, Runtime("IO error: " + msg, loc))
+CONST_EXC(Memory, Runtime("memory error: " + msg, loc))
+CONST_EXC(Parsing, Runtime("parsing error: " + msg, loc))
+CONST_EXC(Program, Runtime("program error: " + msg, loc))
+CONST_EXC(System, Runtime("system error: " + msg, loc))

extras/Hadrons/Exceptions.hpp

@@ -0,0 +1,72 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Exceptions.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Exceptions_hpp_
+#define Hadrons_Exceptions_hpp_
+
+#include <stdexcept>
+#ifndef Hadrons_Global_hpp_
+#include <Grid/Hadrons/Global.hpp>
+#endif
+
+#define SRC_LOC std::string(__FUNCTION__) + " at " + std::string(__FILE__) + ":"\
+                + std::to_string(__LINE__)
+#define HADRON_ERROR(exc, msg)\
+LOG(Error) << msg << std::endl;\
+throw(Exceptions::exc(msg, SRC_LOC));
+
+#define DECL_EXC(name, base) \
+class name: public base\
+{\
+public:\
+    name(std::string msg, std::string loc);\
+}
+
+BEGIN_HADRONS_NAMESPACE
+
+namespace Exceptions
+{
+    // logic errors
+    DECL_EXC(Logic, std::logic_error);
+    DECL_EXC(Definition, Logic);
+    DECL_EXC(Implementation, Logic);
+    DECL_EXC(Range, Logic);
+    DECL_EXC(Size, Logic);
+    // runtime errors
+    DECL_EXC(Runtime, std::runtime_error);
+    DECL_EXC(Argument, Runtime);
+    DECL_EXC(Io, Runtime);
+    DECL_EXC(Memory, Runtime);
+    DECL_EXC(Parsing, Runtime);
+    DECL_EXC(Program, Runtime);
+    DECL_EXC(System, Runtime);
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Exceptions_hpp_

extras/Hadrons/Factory.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Factory.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -95,7 +94,7 @@ std::unique_ptr<T> Factory<T>::create(const std::string type,
     }
     catch (std::out_of_range &)
     {
-        HADRON_ERROR("object of type '" + type + "' unknown");
+        HADRON_ERROR(Argument, "object of type '" + type + "' unknown");
     }
     
     return func(name);

extras/Hadrons/GeneticScheduler.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/GeneticScheduler.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -38,13 +37,13 @@ BEGIN_HADRONS_NAMESPACE
 /******************************************************************************
  *                   Scheduler based on a genetic algorithm                   *
  ******************************************************************************/
-template <typename T>
+template <typename V, typename T>
 class GeneticScheduler
 {
 public:
-    typedef std::vector<T>                   Gene;
-    typedef std::pair<Gene *, Gene *>        GenePair;
-    typedef std::function<int(const Gene &)> ObjFunc;
+    typedef std::vector<T>                 Gene;
+    typedef std::pair<Gene *, Gene *>      GenePair;
+    typedef std::function<V(const Gene &)> ObjFunc;
     struct Parameters
     {
         double       mutationRate;
@@ -65,7 +64,7 @@ public:
     void benchmarkCrossover(const unsigned int nIt);
     // print population
     friend std::ostream & operator<<(std::ostream &out,
-                                     const GeneticScheduler<T> &s)
+                                     const GeneticScheduler<V, T> &s)
     {
         out << "[";
         for (auto &p: s.population_)
@@ -87,19 +86,19 @@ private:
     void     mutation(Gene &m, const Gene &c);
     
 private:
-    Graph<T>                 &graph_;
-    const ObjFunc            &func_;
-    const Parameters         par_;
-    std::multimap<int, Gene> population_;
-    std::mt19937             gen_;
+    Graph<T>               &graph_;
+    const ObjFunc          &func_;
+    const Parameters       par_;
+    std::multimap<V, Gene> population_;
+    std::mt19937           gen_;
 };
 
 /******************************************************************************
  *                       template implementation                              *
  ******************************************************************************/
 // constructor /////////////////////////////////////////////////////////////////
-template <typename T>
-GeneticScheduler<T>::GeneticScheduler(Graph<T> &graph, const ObjFunc &func,
+template <typename V, typename T>
+GeneticScheduler<V, T>::GeneticScheduler(Graph<T> &graph, const ObjFunc &func,
                                       const Parameters &par)
 : graph_(graph)
 , func_(func)
@@ -109,22 +108,22 @@ GeneticScheduler<T>::GeneticScheduler(Graph<T> &graph, const ObjFunc &func,
 }
 
 // access //////////////////////////////////////////////////////////////////////
-template <typename T>
-const typename GeneticScheduler<T>::Gene &
-GeneticScheduler<T>::getMinSchedule(void)
+template <typename V, typename T>
+const typename GeneticScheduler<V, T>::Gene &
+GeneticScheduler<V, T>::getMinSchedule(void)
 {
     return population_.begin()->second;
 }
 
-template <typename T>
-int GeneticScheduler<T>::getMinValue(void)
+template <typename V, typename T>
+int GeneticScheduler<V, T>::getMinValue(void)
 {
     return population_.begin()->first;
 }
 
 // breed a new generation //////////////////////////////////////////////////////
-template <typename T>
-void GeneticScheduler<T>::nextGeneration(void)
+template <typename V, typename T>
+void GeneticScheduler<V, T>::nextGeneration(void)
 {
     // random initialization of the population if necessary
     if (population_.size() != par_.popSize)
@@ -158,8 +157,8 @@ void GeneticScheduler<T>::nextGeneration(void)
 }
 
 // evolution steps /////////////////////////////////////////////////////////////
-template <typename T>
-void GeneticScheduler<T>::initPopulation(void)
+template <typename V, typename T>
+void GeneticScheduler<V, T>::initPopulation(void)
 {
     population_.clear();
     for (unsigned int i = 0; i < par_.popSize; ++i)
@@ -170,8 +169,8 @@ void GeneticScheduler<T>::initPopulation(void)
     }
 }
 
-template <typename T>
-void GeneticScheduler<T>::doCrossover(void)
+template <typename V, typename T>
+void GeneticScheduler<V, T>::doCrossover(void)
 {
     auto p = selectPair();
     Gene &p1 = *(p.first), &p2 = *(p.second);
@@ -185,8 +184,8 @@ void GeneticScheduler<T>::doCrossover(void)
     }
 }
 
-template <typename T>
-void GeneticScheduler<T>::doMutation(void)
+template <typename V, typename T>
+void GeneticScheduler<V, T>::doMutation(void)
 {
     std::uniform_real_distribution<double>      mdis(0., 1.);
     std::uniform_int_distribution<unsigned int> pdis(0, population_.size() - 1);
@@ -206,40 +205,35 @@ void GeneticScheduler<T>::doMutation(void)
 }
 
 // genetic operators ///////////////////////////////////////////////////////////
-template <typename T>
-typename GeneticScheduler<T>::GenePair GeneticScheduler<T>::selectPair(void)
+template <typename V, typename T>
+typename GeneticScheduler<V, T>::GenePair GeneticScheduler<V, T>::selectPair(void)
 {
     std::vector<double> prob;
     unsigned int        ind;
     Gene                *p1, *p2;
+    const double        max = population_.rbegin()->first;
     
+
     for (auto &c: population_)
     {
-        prob.push_back(1./c.first);
-    }
-    do
-    {
-        double probCpy;
-        
-        std::discrete_distribution<unsigned int> dis1(prob.begin(), prob.end());
-        auto rIt = population_.begin();
-        ind = dis1(gen_);
-        std::advance(rIt, ind);
-        p1 = &(rIt->second);
-        probCpy   = prob[ind];
-        prob[ind] = 0.;
-        std::discrete_distribution<unsigned int> dis2(prob.begin(), prob.end());
-        rIt = population_.begin();
-        std::advance(rIt, dis2(gen_));
-        p2 = &(rIt->second);
-        prob[ind] = probCpy;
-    } while (p1 == p2);
+        prob.push_back(std::exp((c.first-1.)/max));
+    }        
+    std::discrete_distribution<unsigned int> dis1(prob.begin(), prob.end());
+    auto rIt = population_.begin();
+    ind = dis1(gen_);
+    std::advance(rIt, ind);
+    p1 = &(rIt->second);
+    prob[ind] = 0.;
+    std::discrete_distribution<unsigned int> dis2(prob.begin(), prob.end());
+    rIt = population_.begin();
+    std::advance(rIt, dis2(gen_));
+    p2 = &(rIt->second);
     
     return std::make_pair(p1, p2);
 }
 
-template <typename T>
-void GeneticScheduler<T>::crossover(Gene &c1, Gene &c2, const Gene &p1,
+template <typename V, typename T>
+void GeneticScheduler<V, T>::crossover(Gene &c1, Gene &c2, const Gene &p1,
                                     const Gene &p2)
 {
     Gene                                        buf;
@@ -273,8 +267,8 @@ void GeneticScheduler<T>::crossover(Gene &c1, Gene &c2, const Gene &p1,
     }
 }
 
-template <typename T>
-void GeneticScheduler<T>::mutation(Gene &m, const Gene &c)
+template <typename V, typename T>
+void GeneticScheduler<V, T>::mutation(Gene &m, const Gene &c)
 {
     Gene                                        buf;
     std::uniform_int_distribution<unsigned int> dis(0, c.size() - 1);
@@ -303,8 +297,8 @@ void GeneticScheduler<T>::mutation(Gene &m, const Gene &c)
     }
 }
 
-template <typename T>
-void GeneticScheduler<T>::benchmarkCrossover(const unsigned int nIt)
+template <typename V, typename T>
+void GeneticScheduler<V, T>::benchmarkCrossover(const unsigned int nIt)
 {
     Gene   p1, p2, c1, c2;
     double neg = 0., eq = 0., pos = 0., total;

extras/Hadrons/Global.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Global.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -39,31 +38,19 @@ HadronsLogger Hadrons::HadronsLogMessage(1,"Message");
 HadronsLogger Hadrons::HadronsLogIterative(1,"Iterative");
 HadronsLogger Hadrons::HadronsLogDebug(1,"Debug");
 
-// pretty size formatting //////////////////////////////////////////////////////
-std::string Hadrons::sizeString(long unsigned int bytes)
-
+void Hadrons::initLogger(void)
 {
-    constexpr unsigned int bufSize = 256;
-    const char             *suffixes[7] = {"", "K", "M", "G", "T", "P", "E"};
-    char                   buf[256];
-    long unsigned int      s     = 0;
-    double                 count = bytes;
-    
-    while (count >= 1024 && s < 7)
-    {
-        s++;
-        count /= 1024;
-    }
-    if (count - floor(count) == 0.0)
-    {
-        snprintf(buf, bufSize, "%d %sB", (int)count, suffixes[s]);
-    }
-    else
-    {
-        snprintf(buf, bufSize, "%.1f %sB", count, suffixes[s]);
-    }
-    
-    return std::string(buf);
+    auto w = std::string("Hadrons").length();
+    GridLogError.setTopWidth(w);
+    GridLogWarning.setTopWidth(w);
+    GridLogMessage.setTopWidth(w);
+    GridLogIterative.setTopWidth(w);
+    GridLogDebug.setTopWidth(w);
+    HadronsLogError.Active(GridLogError.isActive());
+    HadronsLogWarning.Active(GridLogWarning.isActive());
+    HadronsLogMessage.Active(GridLogMessage.isActive());
+    HadronsLogIterative.Active(GridLogIterative.isActive());
+    HadronsLogDebug.Active(GridLogDebug.isActive());
 }
 
 // type utilities //////////////////////////////////////////////////////////////
@@ -80,3 +67,10 @@ std::string Hadrons::typeName(const std::type_info *info)
     
     return name;
 }
+
+// default writers/readers /////////////////////////////////////////////////////
+#ifdef HAVE_HDF5
+const std::string Hadrons::resultFileExt = "h5";
+#else
+const std::string Hadrons::resultFileExt = "xml";
+#endif

extras/Hadrons/Global.hpp

@@ -4,10 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Global.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -35,6 +35,10 @@ See the full license in the file "LICENSE" in the top level distribution directo
 #include <Grid/Grid.h>
 #include <cxxabi.h>
 
+#ifndef SITE_SIZE_TYPE
+#define SITE_SIZE_TYPE size_t
+#endif
+
 #define BEGIN_HADRONS_NAMESPACE \
 namespace Grid {\
 using namespace QCD;\
@@ -51,23 +55,46 @@ using Grid::operator<<;
  * error with GCC 5 (clang & GCC 6 compile fine without it).
  */
 
-// FIXME: find a way to do that in a more general fashion
 #ifndef FIMPL
 #define FIMPL WilsonImplR
 #endif
+#ifndef SIMPL
+#define SIMPL ScalarImplCR
+#endif
+#ifndef GIMPL
+#define GIMPL GimplTypesR
+#endif
 
 BEGIN_HADRONS_NAMESPACE
 
 // type aliases
-#define TYPE_ALIASES(FImpl, suffix)\
-typedef FermionOperator<FImpl>                       FMat##suffix;             \
-typedef typename FImpl::FermionField                 FermionField##suffix;     \
-typedef typename FImpl::PropagatorField              PropagatorField##suffix;  \
-typedef typename FImpl::SitePropagator               SitePropagator##suffix;   \
-typedef typename FImpl::DoubledGaugeField            DoubledGaugeField##suffix;\
-typedef std::function<void(FermionField##suffix &,                             \
+#define FERM_TYPE_ALIASES(FImpl, suffix)\
+typedef FermionOperator<FImpl>                        FMat##suffix;            \
+typedef typename FImpl::FermionField                  FermionField##suffix;    \
+typedef typename FImpl::PropagatorField               PropagatorField##suffix; \
+typedef typename FImpl::SitePropagator::scalar_object SitePropagator##suffix;  \
+typedef std::vector<SitePropagator##suffix>           SlicedPropagator##suffix;
+
+#define GAUGE_TYPE_ALIASES(FImpl, suffix)\
+typedef typename FImpl::DoubledGaugeField DoubledGaugeField##suffix;
+
+#define SCALAR_TYPE_ALIASES(SImpl, suffix)\
+typedef typename SImpl::Field ScalarField##suffix;\
+typedef typename SImpl::Field PropagatorField##suffix;
+
+#define SOLVER_TYPE_ALIASES(FImpl, suffix)\
+typedef std::function<void(FermionField##suffix &,\
                       const FermionField##suffix &)> SolverFn##suffix;
 
+#define SINK_TYPE_ALIASES(suffix)\
+typedef std::function<SlicedPropagator##suffix\
+                      (const PropagatorField##suffix &)> SinkFn##suffix;
+
+#define FGS_TYPE_ALIASES(FImpl, suffix)\
+FERM_TYPE_ALIASES(FImpl, suffix)\
+GAUGE_TYPE_ALIASES(FImpl, suffix)\
+SOLVER_TYPE_ALIASES(FImpl, suffix)
+
 // logger
 class HadronsLogger: public Logger
 {
@@ -77,11 +104,6 @@ public:
 };
 
 #define LOG(channel) std::cout << HadronsLog##channel
-#define HADRON_ERROR(msg)\
-LOG(Error) << msg << " (" << __FUNCTION__ << " at " << __FILE__ << ":"\
-           << __LINE__ << ")" << std::endl;\
-abort();
-
 #define DEBUG_VAR(var) LOG(Debug) << #var << "= " << (var) << std::endl;
 
 extern HadronsLogger HadronsLogError;
@@ -90,6 +112,8 @@ extern HadronsLogger HadronsLogMessage;
 extern HadronsLogger HadronsLogIterative;
 extern HadronsLogger HadronsLogDebug;
 
+void initLogger(void);
+
 // singleton pattern
 #define SINGLETON(name)\
 public:\
@@ -115,9 +139,6 @@ public:\
 private:\
     name(void) = default;
 
-// pretty size formating
-std::string sizeString(long unsigned int bytes);
-
 // type utilities
 template <typename T>
 const std::type_info * typeIdPt(const T &x)
@@ -146,14 +167,21 @@ std::string typeName(void)
 }
 
 // default writers/readers
+extern const std::string resultFileExt;
+
 #ifdef HAVE_HDF5
-typedef Hdf5Reader CorrReader;
-typedef Hdf5Writer CorrWriter;
+typedef Hdf5Reader ResultReader;
+typedef Hdf5Writer ResultWriter;
 #else
-typedef XmlReader CorrReader;
-typedef XmlWriter CorrWriter;
+typedef XmlReader ResultReader;
+typedef XmlWriter ResultWriter;
 #endif
 
+#define RESULT_FILE_NAME(name) \
+name + "." + std::to_string(vm().getTrajectory()) + "." + resultFileExt
+
 END_HADRONS_NAMESPACE
 
+#include <Grid/Hadrons/Exceptions.hpp>
+
 #endif // Hadrons_Global_hpp_

extras/Hadrons/Graph.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Graph.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -185,7 +184,7 @@ void Graph<T>::removeVertex(const T &value)
     }
     else
     {
-        HADRON_ERROR("vertex " << value << " does not exists");
+        HADRON_ERROR(Range, "vertex does not exists");
     }
 
     // remove all edges containing the vertex
@@ -214,7 +213,7 @@ void Graph<T>::removeEdge(const Edge &e)
     }
     else
     {
-        HADRON_ERROR("edge "  << e << " does not exists");
+        HADRON_ERROR(Range, "edge does not exists");
     }
 }
 
@@ -260,7 +259,7 @@ void Graph<T>::mark(const T &value, const bool doMark)
     }
     else
     {
-        HADRON_ERROR("vertex " << value << " does not exists");
+        HADRON_ERROR(Range, "vertex does not exists");
     }
 }
 
@@ -298,7 +297,7 @@ bool Graph<T>::isMarked(const T &value) const
     }
     else
     {
-        HADRON_ERROR("vertex " << value << " does not exists");
+        HADRON_ERROR(Range, "vertex does not exists");
         
         return false;
     }
@@ -430,7 +429,7 @@ std::vector<T> Graph<T>::getAdjacentVertices(const T &value) const
     {
         return ((e.first == value) or (e.second == value));
     };
-    auto eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    auto eIt = std::find_if(edgeSet_.begin(), edgeSet_.end(), pred);
     
     while (eIt != edgeSet_.end())
     {
@@ -442,7 +441,7 @@ std::vector<T> Graph<T>::getAdjacentVertices(const T &value) const
         {
             adjacentVertex.push_back((*eIt).first);
         }
-        eIt = find_if(++eIt, edgeSet_.end(), pred);
+        eIt = std::find_if(++eIt, edgeSet_.end(), pred);
     }
     
     return adjacentVertex;
@@ -458,12 +457,12 @@ std::vector<T> Graph<T>::getChildren(const T &value) const
     {
         return (e.first == value);
     };
-    auto eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    auto eIt = std::find_if(edgeSet_.begin(), edgeSet_.end(), pred);
     
     while (eIt != edgeSet_.end())
     {
         child.push_back((*eIt).second);
-        eIt = find_if(++eIt, edgeSet_.end(), pred);
+        eIt = std::find_if(++eIt, edgeSet_.end(), pred);
     }
     
     return child;
@@ -479,12 +478,12 @@ std::vector<T> Graph<T>::getParents(const T &value) const
     {
         return (e.second == value);
     };
-    auto eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    auto eIt = std::find_if(edgeSet_.begin(), edgeSet_.end(), pred);
     
     while (eIt != edgeSet_.end())
     {
         parent.push_back((*eIt).first);
-        eIt = find_if(++eIt, edgeSet_.end(), pred);
+        eIt = std::find_if(++eIt, edgeSet_.end(), pred);
     }
     
     return parent;
@@ -544,7 +543,7 @@ std::vector<T> Graph<T>::topoSort(void)
     {
         if (tmpMarked.at(v))
         {
-            HADRON_ERROR("cannot topologically sort a cyclic graph");
+            HADRON_ERROR(Range, "cannot topologically sort a cyclic graph");
         }
         if (!isMarked(v))
         {
@@ -603,7 +602,7 @@ std::vector<T> Graph<T>::topoSort(Gen &gen)
     {
         if (tmpMarked.at(v))
         {
-            HADRON_ERROR("cannot topologically sort a cyclic graph");
+            HADRON_ERROR(Range, "cannot topologically sort a cyclic graph");
         }
         if (!isMarked(v))
         {

extras/Hadrons/HadronsXmlRun.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/HadronsXmlRun.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -55,12 +54,6 @@ int main(int argc, char *argv[])
     
     // initialization
     Grid_init(&argc, &argv);
-    HadronsLogError.Active(GridLogError.isActive());
-    HadronsLogWarning.Active(GridLogWarning.isActive());
-    HadronsLogMessage.Active(GridLogMessage.isActive());
-    HadronsLogIterative.Active(GridLogIterative.isActive());
-    HadronsLogDebug.Active(GridLogDebug.isActive());
-    LOG(Message) << "Grid initialized" << std::endl;
     
     // execution
     Application application(parameterFileName);

extras/Hadrons/HadronsXmlSchedule.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/HadronsXmlSchedule.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -49,12 +48,6 @@ int main(int argc, char *argv[])
     
     // initialization
     Grid_init(&argc, &argv);
-    HadronsLogError.Active(GridLogError.isActive());
-    HadronsLogWarning.Active(GridLogWarning.isActive());
-    HadronsLogMessage.Active(GridLogMessage.isActive());
-    HadronsLogIterative.Active(GridLogIterative.isActive());
-    HadronsLogDebug.Active(GridLogDebug.isActive());
-    LOG(Message) << "Grid initialized" << std::endl;
     
     // execution
     Application application;

extras/Hadrons/Makefile.am

@@ -7,20 +7,24 @@ libHadrons_a_SOURCES = \
     $(modules_cc)      \
     Application.cc     \
     Environment.cc     \
+	Exceptions.cc      \
     Global.cc          \
-    Module.cc
+    Module.cc		   \
+	VirtualMachine.cc
 libHadrons_adir = $(pkgincludedir)/Hadrons
 nobase_libHadrons_a_HEADERS = \
 	$(modules_hpp)            \
 	Application.hpp           \
 	Environment.hpp           \
+	Exceptions.hpp            \
 	Factory.hpp               \
 	GeneticScheduler.hpp      \
 	Global.hpp                \
 	Graph.hpp                 \
 	Module.hpp                \
 	Modules.hpp               \
-	ModuleFactory.hpp
+	ModuleFactory.hpp         \
+	VirtualMachine.hpp
 
 HadronsXmlRun_SOURCES = HadronsXmlRun.cc
 HadronsXmlRun_LDADD   = libHadrons.a -lGrid

extras/Hadrons/Module.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Module.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -39,7 +38,6 @@ using namespace Hadrons;
 // constructor /////////////////////////////////////////////////////////////////
 ModuleBase::ModuleBase(const std::string name)
 : name_(name)
-, env_(Environment::getInstance())
 {}
 
 // access //////////////////////////////////////////////////////////////////////
@@ -48,15 +46,10 @@ std::string ModuleBase::getName(void) const
     return name_;
 }
 
-Environment & ModuleBase::env(void) const
-{
-    return env_;
-}
-
 // get factory registration name if available
 std::string ModuleBase::getRegisteredName(void)
 {
-    HADRON_ERROR("module '" + getName() + "' has a type not registered"
+    HADRON_ERROR(Definition, "module '" + getName() + "' has no registered type"
                  + " in the factory");
 }
 
@@ -64,8 +57,5 @@ std::string ModuleBase::getRegisteredName(void)
 void ModuleBase::operator()(void)
 {
     setup();
-    if (!env().isDryRun())
-    {
-        execute();
-    }
+    execute();
 }

extras/Hadrons/Module.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Module.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -31,7 +30,7 @@ See the full license in the file "LICENSE" in the top level distribution directo
 #define Hadrons_Module_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
-#include <Grid/Hadrons/Environment.hpp>
+#include <Grid/Hadrons/VirtualMachine.hpp>
 
 BEGIN_HADRONS_NAMESPACE
 
@@ -87,6 +86,56 @@ public:\
 static ns##mod##ModuleRegistrar ns##mod##ModuleRegistrarInstance;
 
 #define ARG(...) __VA_ARGS__
+#define MACRO_REDIRECT(arg1, arg2, arg3, macro, ...) macro
+
+#define envGet(type, name)\
+*env().template getObject<type>(name)
+
+#define envGetTmp(type, var)\
+type &var = *env().template getObject<type>(getName() + "_tmp_" + #var)
+
+#define envHasType(type, name)\
+env().template isObjectOfType<type>(name)
+
+#define envCreate(type, name, Ls, ...)\
+env().template createObject<type>(name, Environment::Storage::object, Ls, __VA_ARGS__)
+
+#define envCreateDerived(base, type, name, Ls, ...)\
+env().template createDerivedObject<base, type>(name, Environment::Storage::object, Ls, __VA_ARGS__)
+
+#define envCreateLat4(type, name)\
+envCreate(type, name, 1, env().getGrid())
+
+#define envCreateLat5(type, name, Ls)\
+envCreate(type, name, Ls, env().getGrid(Ls))
+
+#define envCreateLat(...)\
+MACRO_REDIRECT(__VA_ARGS__, envCreateLat5, envCreateLat4)(__VA_ARGS__)
+
+#define envCache(type, name, Ls, ...)\
+env().template createObject<type>(name, Environment::Storage::cache, Ls, __VA_ARGS__)
+
+#define envCacheLat4(type, name)\
+envCache(type, name, 1, env().getGrid())
+
+#define envCacheLat5(type, name, Ls)\
+envCache(type, name, Ls, env().getGrid(Ls))
+
+#define envCacheLat(...)\
+MACRO_REDIRECT(__VA_ARGS__, envCacheLat5, envCacheLat4)(__VA_ARGS__)
+
+#define envTmp(type, name, Ls, ...)\
+env().template createObject<type>(getName() + "_tmp_" + name,         \
+                                  Environment::Storage::temporary, Ls, __VA_ARGS__)
+
+#define envTmpLat4(type, name)\
+envTmp(type, name, 1, env().getGrid())
+
+#define envTmpLat5(type, name, Ls)\
+envTmp(type, name, Ls, env().getGrid(Ls))
+
+#define envTmpLat(...)\
+MACRO_REDIRECT(__VA_ARGS__, envTmpLat5, envTmpLat4)(__VA_ARGS__)
 
 /******************************************************************************
  *                            Module class                                    *
@@ -101,23 +150,30 @@ public:
     virtual ~ModuleBase(void) = default;
     // access
     std::string getName(void) const;
-    Environment &env(void) const;
     // get factory registration name if available
     virtual std::string getRegisteredName(void);
     // dependencies/products
     virtual std::vector<std::string> getInput(void) = 0;
+    virtual std::vector<std::string> getReference(void)
+    {
+        return std::vector<std::string>(0);
+    };
     virtual std::vector<std::string> getOutput(void) = 0;
     // parse parameters
     virtual void parseParameters(XmlReader &reader, const std::string name) = 0;
     virtual void saveParameters(XmlWriter &writer, const std::string name) = 0;
     // setup
     virtual void setup(void) {};
+    virtual void execute(void) = 0;
     // execution
     void operator()(void);
-    virtual void execute(void) = 0;
+protected:
+    // environment shortcut
+    DEFINE_ENV_ALIAS;
+    // virtual machine shortcut
+    DEFINE_VM_ALIAS;
 private:
     std::string name_;
-    Environment &env_;
 };
 
 // derived class, templating the parameter class

extras/Hadrons/ModuleFactory.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/ModuleFactory.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 

extras/Hadrons/Modules.hpp

@@ -4,10 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,23 +26,39 @@ with this program; if not, write to the Free Software Foundation, Inc.,
 See the full license in the file "LICENSE" in the top level distribution directory
 *************************************************************************************/
 /*  END LEGAL */
-#include <Grid/Hadrons/Modules/MAction/DWF.hpp>
-#include <Grid/Hadrons/Modules/MAction/Wilson.hpp>
 #include <Grid/Hadrons/Modules/MContraction/Baryon.hpp>
-#include <Grid/Hadrons/Modules/MContraction/DiscLoop.hpp>
-#include <Grid/Hadrons/Modules/MContraction/Gamma3pt.hpp>
 #include <Grid/Hadrons/Modules/MContraction/Meson.hpp>
 #include <Grid/Hadrons/Modules/MContraction/WeakHamiltonian.hpp>
-#include <Grid/Hadrons/Modules/MContraction/WeakHamiltonianEye.hpp>
 #include <Grid/Hadrons/Modules/MContraction/WeakHamiltonianNonEye.hpp>
+#include <Grid/Hadrons/Modules/MContraction/DiscLoop.hpp>
 #include <Grid/Hadrons/Modules/MContraction/WeakNeutral4ptDisc.hpp>
-#include <Grid/Hadrons/Modules/MGauge/Load.hpp>
-#include <Grid/Hadrons/Modules/MGauge/Random.hpp>
-#include <Grid/Hadrons/Modules/MGauge/Unit.hpp>
-#include <Grid/Hadrons/Modules/MLoop/NoiseLoop.hpp>
-#include <Grid/Hadrons/Modules/MSolver/RBPrecCG.hpp>
-#include <Grid/Hadrons/Modules/MSource/Point.hpp>
+#include <Grid/Hadrons/Modules/MContraction/Gamma3pt.hpp>
+#include <Grid/Hadrons/Modules/MContraction/WardIdentity.hpp>
+#include <Grid/Hadrons/Modules/MContraction/WeakHamiltonianEye.hpp>
+#include <Grid/Hadrons/Modules/MFermion/GaugeProp.hpp>
 #include <Grid/Hadrons/Modules/MSource/SeqGamma.hpp>
+#include <Grid/Hadrons/Modules/MSource/Point.hpp>
 #include <Grid/Hadrons/Modules/MSource/Wall.hpp>
 #include <Grid/Hadrons/Modules/MSource/Z2.hpp>
-#include <Grid/Hadrons/Modules/Quark.hpp>
+#include <Grid/Hadrons/Modules/MSource/SeqConserved.hpp>
+#include <Grid/Hadrons/Modules/MSink/Smear.hpp>
+#include <Grid/Hadrons/Modules/MSink/Point.hpp>
+#include <Grid/Hadrons/Modules/MSolver/RBPrecCG.hpp>
+#include <Grid/Hadrons/Modules/MGauge/Unit.hpp>
+#include <Grid/Hadrons/Modules/MGauge/Random.hpp>
+#include <Grid/Hadrons/Modules/MGauge/StochEm.hpp>
+#include <Grid/Hadrons/Modules/MGauge/FundtoHirep.hpp>
+#include <Grid/Hadrons/Modules/MUtilities/TestSeqGamma.hpp>
+#include <Grid/Hadrons/Modules/MUtilities/TestSeqConserved.hpp>
+#include <Grid/Hadrons/Modules/MLoop/NoiseLoop.hpp>
+#include <Grid/Hadrons/Modules/MScalar/FreeProp.hpp>
+#include <Grid/Hadrons/Modules/MScalar/Scalar.hpp>
+#include <Grid/Hadrons/Modules/MScalar/ChargedProp.hpp>
+#include <Grid/Hadrons/Modules/MAction/DWF.hpp>
+#include <Grid/Hadrons/Modules/MAction/Wilson.hpp>
+#include <Grid/Hadrons/Modules/MAction/WilsonClover.hpp>
+#include <Grid/Hadrons/Modules/MScalarSUN/TrMag.hpp>
+#include <Grid/Hadrons/Modules/MScalarSUN/TwoPoint.hpp>
+#include <Grid/Hadrons/Modules/MScalarSUN/TrPhi.hpp>
+#include <Grid/Hadrons/Modules/MIO/LoadNersc.hpp>
+#include <Grid/Hadrons/Modules/MIO/LoadBinary.hpp>

extras/Hadrons/Modules/MAction/DWF.hpp

@@ -4,10 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MAction/DWF.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -27,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_DWF_hpp_
-#define Hadrons_DWF_hpp_
+#ifndef Hadrons_MAction_DWF_hpp_
+#define Hadrons_MAction_DWF_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -48,14 +48,15 @@ public:
                                     std::string, gauge,
                                     unsigned int, Ls,
                                     double      , mass,
-                                    double      , M5);
+                                    double      , M5,
+                                    std::string , boundary);
 };
 
 template <typename FImpl>
 class TDWF: public Module<DWFPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FGS_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TDWF(const std::string name);
@@ -64,6 +65,7 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -102,33 +104,32 @@ std::vector<std::string> TDWF<FImpl>::getOutput(void)
 template <typename FImpl>
 void TDWF<FImpl>::setup(void)
 {
-    unsigned int size;
-    
-    size = 2*env().template lattice4dSize<typename FImpl::DoubledGaugeField>();
-    env().registerObject(getName(), size, par().Ls);
+    LOG(Message) << "Setting up domain wall fermion matrix with m= "
+                 << par().mass << ", M5= " << par().M5 << " and Ls= "
+                 << par().Ls << " using gauge field '" << par().gauge << "'"
+                 << std::endl;
+    LOG(Message) << "Fermion boundary conditions: " << par().boundary
+                 << std::endl;
+                 
+    env().createGrid(par().Ls);
+    auto &U    = envGet(LatticeGaugeField, par().gauge);
+    auto &g4   = *env().getGrid();
+    auto &grb4 = *env().getRbGrid();
+    auto &g5   = *env().getGrid(par().Ls);
+    auto &grb5 = *env().getRbGrid(par().Ls);
+    std::vector<Complex> boundary = strToVec<Complex>(par().boundary);
+    typename DomainWallFermion<FImpl>::ImplParams implParams(boundary);
+    envCreateDerived(FMat, DomainWallFermion<FImpl>, getName(), par().Ls, U, g5,
+                     grb5, g4, grb4, par().mass, par().M5, implParams);
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 template <typename FImpl>
 void TDWF<FImpl>::execute(void)
-{
-    LOG(Message) << "Setting up domain wall fermion matrix with m= "
-                 << par().mass << ", M5= " << par().M5 << " and Ls= "
-                 << par().Ls << " using gauge field '" << par().gauge << "'"
-                 << std::endl;
-    env().createGrid(par().Ls);
-    auto &U      = *env().template getObject<LatticeGaugeField>(par().gauge);
-    auto &g4     = *env().getGrid();
-    auto &grb4   = *env().getRbGrid();
-    auto &g5     = *env().getGrid(par().Ls);
-    auto &grb5   = *env().getRbGrid(par().Ls);
-    FMat *fMatPt = new DomainWallFermion<FImpl>(U, g5, grb5, g4, grb4,
-                                                par().mass, par().M5);
-    env().setObject(getName(), fMatPt);
-}
+{}
 
 END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_DWF_hpp_
+#endif // Hadrons_MAction_DWF_hpp_

extras/Hadrons/Modules/MAction/Wilson.hpp

@@ -4,10 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MAction/Wilson.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -27,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Wilson_hpp_
-#define Hadrons_Wilson_hpp_
+#ifndef Hadrons_MAction_Wilson_hpp_
+#define Hadrons_MAction_Wilson_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -46,14 +46,15 @@ class WilsonPar: Serializable
 public:
     GRID_SERIALIZABLE_CLASS_MEMBERS(WilsonPar,
                                     std::string, gauge,
-                                    double     , mass);
+                                    double     , mass,
+                                    std::string, boundary);
 };
 
 template <typename FImpl>
 class TWilson: public Module<WilsonPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FGS_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TWilson(const std::string name);
@@ -62,6 +63,7 @@ public:
     // dependencies/products
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -100,24 +102,24 @@ std::vector<std::string> TWilson<FImpl>::getOutput(void)
 template <typename FImpl>
 void TWilson<FImpl>::setup(void)
 {
-    unsigned int size;
-    
-    size = 2*env().template lattice4dSize<typename FImpl::DoubledGaugeField>();
-    env().registerObject(getName(), size);
+    LOG(Message) << "Setting up TWilson fermion matrix with m= " << par().mass
+                 << " using gauge field '" << par().gauge << "'" << std::endl;
+    LOG(Message) << "Fermion boundary conditions: " << par().boundary
+                 << std::endl;
+                 
+    auto &U      = envGet(LatticeGaugeField, par().gauge);
+    auto &grid   = *env().getGrid();
+    auto &gridRb = *env().getRbGrid();
+    std::vector<Complex> boundary = strToVec<Complex>(par().boundary);
+    typename WilsonFermion<FImpl>::ImplParams implParams(boundary);
+    envCreateDerived(FMat, WilsonFermion<FImpl>, getName(), 1, U, grid, gridRb,
+                     par().mass, implParams);
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 template <typename FImpl>
 void TWilson<FImpl>::execute()
-{
-    LOG(Message) << "Setting up TWilson fermion matrix with m= " << par().mass
-                 << " using gauge field '" << par().gauge << "'" << std::endl;
-    auto &U      = *env().template getObject<LatticeGaugeField>(par().gauge);
-    auto &grid   = *env().getGrid();
-    auto &gridRb = *env().getRbGrid();
-    FMat *fMatPt = new WilsonFermion<FImpl>(U, grid, gridRb, par().mass);
-    env().setObject(getName(), fMatPt);
-}
+{}
 
 END_MODULE_NAMESPACE
 

extras/Hadrons/Modules/MAction/WilsonClover.hpp

@@ -0,0 +1,153 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MAction/Wilson.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MAction_WilsonClover_hpp_
+#define Hadrons_MAction_WilsonClover_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                            TWilson quark action                            *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MAction)
+
+class WilsonCloverPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(WilsonCloverPar,
+                                    std::string, gauge,
+                                    double     , mass,
+				                    double     , csw_r,
+				                    double     , csw_t,
+				                    WilsonAnisotropyCoefficients ,clover_anisotropy,
+                                    std::string, boundary
+				    );
+};
+
+template <typename FImpl>
+class TWilsonClover: public Module<WilsonCloverPar>
+{
+public:
+    FGS_TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TWilsonClover(const std::string name);
+    // destructor
+    virtual ~TWilsonClover(void) = default;
+    // dependencies/products
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(WilsonClover, TWilsonClover<FIMPL>, MAction);
+
+/******************************************************************************
+ *                     TWilsonClover template implementation                        *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TWilsonClover<FImpl>::TWilsonClover(const std::string name)
+: Module<WilsonCloverPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TWilsonClover<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().gauge};
+
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TWilsonClover<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TWilsonClover<FImpl>::setup(void)
+{
+    //unsigned int size;
+
+    // size = 2*env().template lattice4dSize<typename FImpl::DoubledGaugeField>();
+    // env().registerObject(getName(), size);
+
+
+    LOG(Message) << "Setting up TWilsonClover fermion matrix with m= " << par().mass
+                 << " using gauge field '" << par().gauge << "'" << std::endl;
+    LOG(Message) << "Fermion boundary conditions: " << par().boundary 
+                 << std::endl;
+    LOG(Message) << "Clover term csw_r: " << par().csw_r
+                 << " csw_t: " << par().csw_t
+                 << std::endl;
+    auto &U      = envGet(LatticeGaugeField, par().gauge);
+    auto &grid   = *env().getGrid();
+    auto &gridRb = *env().getRbGrid();
+    std::vector<Complex> boundary = strToVec<Complex>(par().boundary);
+    typename WilsonCloverFermion<FImpl>::ImplParams implParams(boundary);
+    envCreateDerived(FMat, WilsonCloverFermion<FImpl>, getName(), 1, U, grid, gridRb, par().mass,
+						  par().csw_r,
+						  par().csw_t,
+					      par().clover_anisotropy,
+						  implParams); 
+
+
+    //FMat *fMatPt = new WilsonCloverFermion<FImpl>(U, grid, gridRb, par().mass,
+	//					  par().csw_r,
+	//					  par().csw_t,
+	//				      par().clover_anisotropy,
+	//					  implParams);
+    //env().setObject(getName(), fMatPt);
+
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TWilsonClover<FImpl>::execute()
+{
+
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_WilsonClover_hpp_

extras/Hadrons/Modules/MContraction/Baryon.hpp

@@ -4,10 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/Baryon.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -27,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Baryon_hpp_
-#define Hadrons_Baryon_hpp_
+#ifndef Hadrons_MContraction_Baryon_hpp_
+#define Hadrons_MContraction_Baryon_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -55,9 +55,9 @@ template <typename FImpl1, typename FImpl2, typename FImpl3>
 class TBaryon: public Module<BaryonPar>
 {
 public:
-    TYPE_ALIASES(FImpl1, 1);
-    TYPE_ALIASES(FImpl2, 2);
-    TYPE_ALIASES(FImpl3, 3);
+    FERM_TYPE_ALIASES(FImpl1, 1);
+    FERM_TYPE_ALIASES(FImpl2, 2);
+    FERM_TYPE_ALIASES(FImpl3, 3);
     class Result: Serializable
     {
     public:
@@ -72,6 +72,9 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
     // execution
     virtual void execute(void);
 };
@@ -99,11 +102,18 @@ std::vector<std::string> TBaryon<FImpl1, FImpl2, FImpl3>::getInput(void)
 template <typename FImpl1, typename FImpl2, typename FImpl3>
 std::vector<std::string> TBaryon<FImpl1, FImpl2, FImpl3>::getOutput(void)
 {
-    std::vector<std::string> out = {getName()};
+    std::vector<std::string> out = {};
     
     return out;
 }
 
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+void TBaryon<FImpl1, FImpl2, FImpl3>::setup(void)
+{
+    envTmpLat(LatticeComplex, "c");
+}
+
 // execution ///////////////////////////////////////////////////////////////////
 template <typename FImpl1, typename FImpl2, typename FImpl3>
 void TBaryon<FImpl1, FImpl2, FImpl3>::execute(void)
@@ -112,20 +122,20 @@ void TBaryon<FImpl1, FImpl2, FImpl3>::execute(void)
                  << " quarks '" << par().q1 << "', '" << par().q2 << "', and '"
                  << par().q3 << "'" << std::endl;
     
-    CorrWriter             writer(par().output);
-    PropagatorField1      &q1 = *env().template getObject<PropagatorField1>(par().q1);
-    PropagatorField2      &q2 = *env().template getObject<PropagatorField2>(par().q2);
-    PropagatorField3      &q3 = *env().template getObject<PropagatorField3>(par().q2);
-    LatticeComplex        c(env().getGrid());
-    Result                result;
+    ResultWriter writer(RESULT_FILE_NAME(par().output));
+    auto       &q1 = envGet(PropagatorField1, par().q1);
+    auto       &q2 = envGet(PropagatorField2, par().q2);
+    auto       &q3 = envGet(PropagatorField3, par().q2);
+    envGetTmp(LatticeComplex, c);
+    Result     result;
     
     // FIXME: do contractions
     
-    write(writer, "meson", result);
+    // write(writer, "meson", result);
 }
 
 END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Baryon_hpp_
+#endif // Hadrons_MContraction_Baryon_hpp_

extras/Hadrons/Modules/MContraction/DiscLoop.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/DiscLoop.hpp
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_DiscLoop_hpp_
-#define Hadrons_DiscLoop_hpp_
+#ifndef Hadrons_MContraction_DiscLoop_hpp_
+#define Hadrons_MContraction_DiscLoop_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -52,7 +53,7 @@ public:
 template <typename FImpl>
 class TDiscLoop: public Module<DiscLoopPar>
 {
-    TYPE_ALIASES(FImpl,);
+    FERM_TYPE_ALIASES(FImpl,);
     class Result: Serializable
     {
     public:
@@ -68,6 +69,7 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -97,7 +99,7 @@ std::vector<std::string> TDiscLoop<FImpl>::getInput(void)
 template <typename FImpl>
 std::vector<std::string> TDiscLoop<FImpl>::getOutput(void)
 {
-    std::vector<std::string> out = {getName()};
+    std::vector<std::string> out = {};
     
     return out;
 }
@@ -106,7 +108,7 @@ std::vector<std::string> TDiscLoop<FImpl>::getOutput(void)
 template <typename FImpl>
 void TDiscLoop<FImpl>::setup(void)
 {
-    
+    envTmpLat(LatticeComplex, "c");
 }
 
 // execution ///////////////////////////////////////////////////////////////////
@@ -117,13 +119,13 @@ void TDiscLoop<FImpl>::execute(void)
                  << "' using '" << par().q_loop << "' with " << par().gamma 
                  << " insertion." << std::endl;
 
-    CorrWriter            writer(par().output);
-    PropagatorField       &q_loop = *env().template getObject<PropagatorField>(par().q_loop);
-    LatticeComplex        c(env().getGrid());
+    ResultWriter          writer(RESULT_FILE_NAME(par().output));
+    auto                  &q_loop = envGet(PropagatorField, par().q_loop);
     Gamma                 gamma(par().gamma);
     std::vector<TComplex> buf;
     Result                result;
 
+    envGetTmp(LatticeComplex, c);
     c = trace(gamma*q_loop);
     sliceSum(c, buf, Tp);
 
@@ -141,4 +143,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_DiscLoop_hpp_
+#endif // Hadrons_MContraction_DiscLoop_hpp_

extras/Hadrons/Modules/MContraction/Gamma3pt.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/Gamma3pt.hpp
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Gamma3pt_hpp_
-#define Hadrons_Gamma3pt_hpp_
+#ifndef Hadrons_MContraction_Gamma3pt_hpp_
+#define Hadrons_MContraction_Gamma3pt_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -51,6 +52,14 @@ BEGIN_HADRONS_NAMESPACE
  *                   q1
  *
  *      trace(g5*q1*adj(q2)*g5*gamma*q3)
+ * 
+ *  options:
+ *   - q1: sink smeared propagator, source at i
+ *   - q2: propagator, source at i
+ *   - q3: propagator, source at f
+ *   - gamma: gamma matrix to insert
+ *   - tSnk: sink position for propagator q1.
+ *
  */
 
 /******************************************************************************
@@ -66,15 +75,16 @@ public:
                                     std::string,    q2,
                                     std::string,    q3,
                                     Gamma::Algebra, gamma,
+                                    unsigned int,   tSnk,
                                     std::string,    output);
 };
 
 template <typename FImpl1, typename FImpl2, typename FImpl3>
 class TGamma3pt: public Module<Gamma3ptPar>
 {
-    TYPE_ALIASES(FImpl1, 1);
-    TYPE_ALIASES(FImpl2, 2);
-    TYPE_ALIASES(FImpl3, 3);
+    FERM_TYPE_ALIASES(FImpl1, 1);
+    FERM_TYPE_ALIASES(FImpl2, 2);
+    FERM_TYPE_ALIASES(FImpl3, 3);
     class Result: Serializable
     {
     public:
@@ -90,6 +100,7 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -119,7 +130,7 @@ std::vector<std::string> TGamma3pt<FImpl1, FImpl2, FImpl3>::getInput(void)
 template <typename FImpl1, typename FImpl2, typename FImpl3>
 std::vector<std::string> TGamma3pt<FImpl1, FImpl2, FImpl3>::getOutput(void)
 {
-    std::vector<std::string> out = {getName()};
+    std::vector<std::string> out = {};
     
     return out;
 }
@@ -128,7 +139,7 @@ std::vector<std::string> TGamma3pt<FImpl1, FImpl2, FImpl3>::getOutput(void)
 template <typename FImpl1, typename FImpl2, typename FImpl3>
 void TGamma3pt<FImpl1, FImpl2, FImpl3>::setup(void)
 {
-    
+    envTmpLat(LatticeComplex, "c");
 }
 
 // execution ///////////////////////////////////////////////////////////////////
@@ -140,17 +151,22 @@ void TGamma3pt<FImpl1, FImpl2, FImpl3>::execute(void)
                  << par().q3 << "', with " << par().gamma << " insertion." 
                  << std::endl;
 
-    CorrWriter            writer(par().output);
-    PropagatorField1      &q1 = *env().template getObject<PropagatorField1>(par().q1);
-    PropagatorField2      &q2 = *env().template getObject<PropagatorField2>(par().q2);
-    PropagatorField3      &q3 = *env().template getObject<PropagatorField3>(par().q3);
-    LatticeComplex        c(env().getGrid());
+    // Initialise variables. q2 and q3 are normal propagators, q1 may be 
+    // sink smeared.
+    ResultWriter          writer(RESULT_FILE_NAME(par().output));
+    auto                  &q1 = envGet(SlicedPropagator1, par().q1);
+    auto                  &q2 = envGet(PropagatorField2, par().q2);
+    auto                  &q3 = envGet(PropagatorField2, par().q3);
     Gamma                 g5(Gamma::Algebra::Gamma5);
     Gamma                 gamma(par().gamma);
     std::vector<TComplex> buf;
     Result                result;
-
-    c = trace(g5*q1*adj(q2)*(g5*gamma)*q3);
+    
+    // Extract relevant timeslice of sinked propagator q1, then contract &
+    // sum over all spacial positions of gamma insertion.
+    SitePropagator1 q1Snk = q1[par().tSnk];
+    envGetTmp(LatticeComplex, c);
+    c = trace(g5*q1Snk*adj(q2)*(g5*gamma)*q3);
     sliceSum(c, buf, Tp);
 
     result.gamma = par().gamma;
@@ -167,4 +183,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Gamma3pt_hpp_
+#endif // Hadrons_MContraction_Gamma3pt_hpp_

extras/Hadrons/Modules/MContraction/Meson.hpp

@@ -4,12 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/Meson.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
-        Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -29,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Meson_hpp_
-#define Hadrons_Meson_hpp_
+#ifndef Hadrons_MContraction_Meson_hpp_
+#define Hadrons_MContraction_Meson_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -51,8 +49,7 @@ BEGIN_HADRONS_NAMESPACE
            in a sequence (e.g. "<Gamma5 Gamma5><Gamma5 GammaT>").
 
            Special values: "all" - perform all possible contractions.
- - mom: momentum insertion, space-separated float sequence (e.g ".1 .2 1. 0."),
-        given as multiples of (2*pi) / L.
+ - sink: module to compute the sink to use in contraction (string).
 */
 
 /******************************************************************************
@@ -69,7 +66,7 @@ public:
                                     std::string, q1,
                                     std::string, q2,
                                     std::string, gammas,
-                                    std::string, mom,
+                                    std::string, sink,
                                     std::string, output);
 };
 
@@ -77,8 +74,10 @@ template <typename FImpl1, typename FImpl2>
 class TMeson: public Module<MesonPar>
 {
 public:
-    TYPE_ALIASES(FImpl1, 1);
-    TYPE_ALIASES(FImpl2, 2);
+    FERM_TYPE_ALIASES(FImpl1, 1);
+    FERM_TYPE_ALIASES(FImpl2, 2);
+    FERM_TYPE_ALIASES(ScalarImplCR, Scalar);
+    SINK_TYPE_ALIASES(Scalar);
     class Result: Serializable
     {
     public:
@@ -96,6 +95,9 @@ public:
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
     virtual void parseGammaString(std::vector<GammaPair> &gammaList);
+protected:
+    // execution
+    virtual void setup(void);
     // execution
     virtual void execute(void);
 };
@@ -115,7 +117,7 @@ TMeson<FImpl1, FImpl2>::TMeson(const std::string name)
 template <typename FImpl1, typename FImpl2>
 std::vector<std::string> TMeson<FImpl1, FImpl2>::getInput(void)
 {
-    std::vector<std::string> input = {par().q1, par().q2};
+    std::vector<std::string> input = {par().q1, par().q2, par().sink};
     
     return input;
 }
@@ -123,7 +125,7 @@ std::vector<std::string> TMeson<FImpl1, FImpl2>::getInput(void)
 template <typename FImpl1, typename FImpl2>
 std::vector<std::string> TMeson<FImpl1, FImpl2>::getOutput(void)
 {
-    std::vector<std::string> output = {getName()};
+    std::vector<std::string> output = {};
     
     return output;
 }
@@ -131,12 +133,11 @@ std::vector<std::string> TMeson<FImpl1, FImpl2>::getOutput(void)
 template <typename FImpl1, typename FImpl2>
 void TMeson<FImpl1, FImpl2>::parseGammaString(std::vector<GammaPair> &gammaList)
 {
+    gammaList.clear();
     // Determine gamma matrices to insert at source/sink.
     if (par().gammas.compare("all") == 0)
     {
         // Do all contractions.
-        unsigned int n_gam = Ns * Ns;
-        gammaList.resize(n_gam*n_gam);
         for (unsigned int i = 1; i < Gamma::nGamma; i += 2)
         {
             for (unsigned int j = 1; j < Gamma::nGamma; j += 2)
@@ -150,55 +151,92 @@ void TMeson<FImpl1, FImpl2>::parseGammaString(std::vector<GammaPair> &gammaList)
     {
         // Parse individual contractions from input string.
         gammaList = strToVec<GammaPair>(par().gammas);
-    }
+    } 
 }
 
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2>
+void TMeson<FImpl1, FImpl2>::setup(void)
+{
+    envTmpLat(LatticeComplex, "c");
+}
 
 // execution ///////////////////////////////////////////////////////////////////
+#define mesonConnected(q1, q2, gSnk, gSrc) \
+(g5*(gSnk))*(q1)*(adj(gSrc)*g5)*adj(q2)
+
 template <typename FImpl1, typename FImpl2>
 void TMeson<FImpl1, FImpl2>::execute(void)
 {
     LOG(Message) << "Computing meson contractions '" << getName() << "' using"
                  << " quarks '" << par().q1 << "' and '" << par().q2 << "'"
                  << std::endl;
-    
-    CorrWriter              writer(par().output);
-    PropagatorField1       &q1 = *env().template getObject<PropagatorField1>(par().q1);
-    PropagatorField2       &q2 = *env().template getObject<PropagatorField2>(par().q2);
-    LatticeComplex         c(env().getGrid());
-    Gamma                  g5(Gamma::Algebra::Gamma5);
-    std::vector<GammaPair> gammaList;
+
+    ResultWriter           writer(RESULT_FILE_NAME(par().output));
     std::vector<TComplex>  buf;
     std::vector<Result>    result;
-    std::vector<Real>      p;
-
-    p  = strToVec<Real>(par().mom);
-    LatticeComplex         ph(env().getGrid()), coor(env().getGrid());
-    Complex                i(0.0,1.0);
-    ph = zero;
-    for(unsigned int mu = 0; mu < env().getNd(); mu++)
-    {
-        LatticeCoordinate(coor, mu);
-        ph = ph + p[mu]*coor*((1./(env().getGrid()->_fdimensions[mu])));
-    }
-    ph = exp((Real)(2*M_PI)*i*ph);
+    Gamma                  g5(Gamma::Algebra::Gamma5);
+    std::vector<GammaPair> gammaList;
+    int                    nt = env().getDim(Tp);
     
     parseGammaString(gammaList);
-
     result.resize(gammaList.size());
     for (unsigned int i = 0; i < result.size(); ++i)
     {
-        Gamma gSnk(gammaList[i].first);
-        Gamma gSrc(gammaList[i].second);
-        c = trace((g5*gSnk)*q1*(adj(gSrc)*g5)*adj(q2))*ph;
-        sliceSum(c, buf, Tp);
-
         result[i].gamma_snk = gammaList[i].first;
         result[i].gamma_src = gammaList[i].second;
-        result[i].corr.resize(buf.size());
-        for (unsigned int t = 0; t < buf.size(); ++t)
+        result[i].corr.resize(nt);
+    }
+    if (envHasType(SlicedPropagator1, par().q1) and
+        envHasType(SlicedPropagator2, par().q2))
+    {
+        auto &q1 = envGet(SlicedPropagator1, par().q1);
+        auto &q2 = envGet(SlicedPropagator2, par().q2);
+        
+        LOG(Message) << "(propagator already sinked)" << std::endl;
+        for (unsigned int i = 0; i < result.size(); ++i)
         {
-            result[i].corr[t] = TensorRemove(buf[t]);
+            Gamma gSnk(gammaList[i].first);
+            Gamma gSrc(gammaList[i].second);
+            
+            for (unsigned int t = 0; t < buf.size(); ++t)
+            {
+                result[i].corr[t] = TensorRemove(trace(mesonConnected(q1[t], q2[t], gSnk, gSrc)));
+            }
+        }
+    }
+    else
+    {
+        auto &q1 = envGet(PropagatorField1, par().q1);
+        auto &q2 = envGet(PropagatorField2, par().q2);
+        
+        envGetTmp(LatticeComplex, c);
+        LOG(Message) << "(using sink '" << par().sink << "')" << std::endl;
+        for (unsigned int i = 0; i < result.size(); ++i)
+        {
+            Gamma       gSnk(gammaList[i].first);
+            Gamma       gSrc(gammaList[i].second);
+            std::string ns;
+                
+            ns = vm().getModuleNamespace(env().getObjectModule(par().sink));
+            if (ns == "MSource")
+            {
+                PropagatorField1 &sink = envGet(PropagatorField1, par().sink);
+                
+                c = trace(mesonConnected(q1, q2, gSnk, gSrc)*sink);
+                sliceSum(c, buf, Tp);
+            }
+            else if (ns == "MSink")
+            {
+                SinkFnScalar &sink = envGet(SinkFnScalar, par().sink);
+                
+                c   = trace(mesonConnected(q1, q2, gSnk, gSrc));
+                buf = sink(c);
+            }
+            for (unsigned int t = 0; t < buf.size(); ++t)
+            {
+                result[i].corr[t] = TensorRemove(buf[t]);
+            }
         }
     }
     write(writer, "meson", result);
@@ -208,4 +246,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Meson_hpp_
+#endif // Hadrons_MContraction_Meson_hpp_

extras/Hadrons/Modules/MContraction/WardIdentity.hpp

@@ -0,0 +1,224 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MContraction/WardIdentity.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MContraction_WardIdentity_hpp_
+#define Hadrons_MContraction_WardIdentity_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/*
+  Ward Identity contractions
+ -----------------------------
+ 
+ * options:
+ - q:          propagator, 5D if available (string)
+ - action:     action module used for propagator solution (string)
+ - mass:       mass of quark (double)
+ - test_axial: whether or not to test PCAC relation.
+*/
+
+/******************************************************************************
+ *                              WardIdentity                                  *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MContraction)
+
+class WardIdentityPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(WardIdentityPar,
+                                    std::string, q,
+                                    std::string, action,
+                                    double,      mass,
+                                    bool,        test_axial);
+};
+
+template <typename FImpl>
+class TWardIdentity: public Module<WardIdentityPar>
+{
+public:
+    FERM_TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TWardIdentity(const std::string name);
+    // destructor
+    virtual ~TWardIdentity(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+private:
+    unsigned int Ls_;
+};
+
+MODULE_REGISTER_NS(WardIdentity, TWardIdentity<FIMPL>, MContraction);
+
+/******************************************************************************
+ *                     TWardIdentity implementation                           *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TWardIdentity<FImpl>::TWardIdentity(const std::string name)
+: Module<WardIdentityPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TWardIdentity<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().q, par().action};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TWardIdentity<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TWardIdentity<FImpl>::setup(void)
+{
+    Ls_ = env().getObjectLs(par().q);
+    if (Ls_ != env().getObjectLs(par().action))
+    {
+        HADRON_ERROR(Size, "Ls mismatch between quark action and propagator");
+    }
+    envTmpLat(PropagatorField, "tmp");
+    envTmpLat(PropagatorField, "vector_WI");
+    if (par().test_axial)
+    {
+        envTmpLat(PropagatorField, "psi");
+        envTmpLat(LatticeComplex,  "PP");
+        envTmpLat(LatticeComplex,  "axial_defect");
+        envTmpLat(LatticeComplex,  "PJ5q");
+    }
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TWardIdentity<FImpl>::execute(void)
+{
+    LOG(Message) << "Performing Ward Identity checks for quark '" << par().q
+                 << "'." << std::endl;
+
+    auto  &q   = envGet(PropagatorField, par().q);
+    auto  &act = envGet(FMat, par().action);
+    Gamma g5(Gamma::Algebra::Gamma5);
+
+    // Compute D_mu V_mu, D here is backward derivative.
+    envGetTmp(PropagatorField, tmp);
+    envGetTmp(PropagatorField, vector_WI);
+    vector_WI    = zero;
+    for (unsigned int mu = 0; mu < Nd; ++mu)
+    {
+        act.ContractConservedCurrent(q, q, tmp, Current::Vector, mu);
+        tmp -= Cshift(tmp, mu, -1);
+        vector_WI += tmp;
+    }
+
+    // Test ward identity D_mu V_mu = 0;
+    LOG(Message) << "Vector Ward Identity check Delta_mu V_mu = " 
+                 << norm2(vector_WI) << std::endl;
+
+    if (par().test_axial)
+    {
+        envGetTmp(PropagatorField, psi);
+        envGetTmp(LatticeComplex, PP);
+        envGetTmp(LatticeComplex, axial_defect);
+        envGetTmp(LatticeComplex, PJ5q);
+        std::vector<TComplex> axial_buf;
+
+        // Compute <P|D_mu A_mu>, D is backwards derivative.
+        axial_defect = zero;
+        for (unsigned int mu = 0; mu < Nd; ++mu)
+        {
+            act.ContractConservedCurrent(q, q, tmp, Current::Axial, mu);
+            tmp -= Cshift(tmp, mu, -1);
+            axial_defect += trace(g5*tmp);
+        }
+
+        // Get <P|J5q> for 5D (zero for 4D) and <P|P>.
+        PJ5q = zero;
+        if (Ls_ > 1)
+        {
+            // <P|P>
+            ExtractSlice(tmp, q, 0, 0);
+            psi  = 0.5 * (tmp - g5*tmp);
+            ExtractSlice(tmp, q, Ls_ - 1, 0);
+            psi += 0.5 * (tmp + g5*tmp);
+            PP = trace(adj(psi)*psi);
+
+            // <P|5Jq>
+            ExtractSlice(tmp, q, Ls_/2 - 1, 0);
+            psi  = 0.5 * (tmp + g5*tmp);
+            ExtractSlice(tmp, q, Ls_/2, 0);
+            psi += 0.5 * (tmp - g5*tmp);
+            PJ5q = trace(adj(psi)*psi);
+        }
+        else
+        {
+            PP = trace(adj(q)*q);
+        }
+
+        // Test ward identity <P|D_mu A_mu> = 2m<P|P> + 2<P|J5q>
+        LOG(Message) << "|D_mu A_mu|^2 = " << norm2(axial_defect) << std::endl;
+        LOG(Message) << "|PP|^2        = " << norm2(PP) << std::endl;
+        LOG(Message) << "|PJ5q|^2      = " << norm2(PJ5q) << std::endl;
+        LOG(Message) << "Axial Ward Identity defect Delta_mu A_mu = "
+                     << norm2(axial_defect) << std::endl;
+    
+        // Axial defect by timeslice.
+        axial_defect -= 2.*(par().mass*PP + PJ5q);
+        LOG(Message) << "Check Axial defect by timeslice" << std::endl;
+        sliceSum(axial_defect, axial_buf, Tp);
+        for (int t = 0; t < axial_buf.size(); ++t)
+        {
+            LOG(Message) << "t = " << t << ": " 
+                         << TensorRemove(axial_buf[t]) << std::endl;
+        }
+    }
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_WardIdentity_hpp_

extras/Hadrons/Modules/MContraction/WeakHamiltonian.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/WeakHamiltonian.hpp
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_WeakHamiltonian_hpp_
-#define Hadrons_WeakHamiltonian_hpp_
+#ifndef Hadrons_MContraction_WeakHamiltonian_hpp_
+#define Hadrons_MContraction_WeakHamiltonian_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -76,6 +77,7 @@ public:
                                     std::string, q2,
                                     std::string, q3,
                                     std::string, q4,
+                                    unsigned int, tSnk,
                                     std::string, output);
 };
 
@@ -83,7 +85,7 @@ public:
 class T##modname: public Module<WeakHamiltonianPar>\
 {\
 public:\
-    TYPE_ALIASES(FIMPL,)\
+    FERM_TYPE_ALIASES(FIMPL,)\
     class Result: Serializable\
     {\
     public:\
@@ -99,11 +101,13 @@ public:\
     /* dependency relation */ \
     virtual std::vector<std::string> getInput(void);\
     virtual std::vector<std::string> getOutput(void);\
+public:\
+    std::vector<std::string> VA_label = {"V", "A"};\
+protected:\
     /* setup */ \
     virtual void setup(void);\
     /* execution */ \
     virtual void execute(void);\
-    std::vector<std::string> VA_label = {"V", "A"};\
 };\
 MODULE_REGISTER_NS(modname, T##modname, MContraction);
 
@@ -111,4 +115,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_WeakHamiltonian_hpp_
+#endif // Hadrons_MContraction_WeakHamiltonian_hpp_

extras/Hadrons/Modules/MContraction/WeakHamiltonianEye.cc

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/WeakHamiltonianEye.cc
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -54,6 +55,8 @@ using namespace MContraction;
  * 
  * S: trace(q3*g5*q1*adj(q2)*g5*gL[mu][p_1]*q4*gL[mu][p_2])
  * E: trace(q3*g5*q1*adj(q2)*g5*gL[mu][p_1])*trace(q4*gL[mu][p_2])
+ * 
+ * Note q1 must be sink smeared.
  */
 
 /******************************************************************************
@@ -74,7 +77,7 @@ std::vector<std::string> TWeakHamiltonianEye::getInput(void)
 
 std::vector<std::string> TWeakHamiltonianEye::getOutput(void)
 {
-    std::vector<std::string> out = {getName()};
+    std::vector<std::string> out = {};
     
     return out;
 }
@@ -82,7 +85,15 @@ std::vector<std::string> TWeakHamiltonianEye::getOutput(void)
 // setup ///////////////////////////////////////////////////////////////////////
 void TWeakHamiltonianEye::setup(void)
 {
+    unsigned int ndim = env().getNd();
 
+    envTmpLat(LatticeComplex,  "expbuf");
+    envTmpLat(PropagatorField, "tmp1");
+    envTmpLat(LatticeComplex,  "tmp2");
+    envTmp(std::vector<PropagatorField>, "S_body", 1, ndim, PropagatorField(env().getGrid()));
+    envTmp(std::vector<PropagatorField>, "S_loop", 1, ndim, PropagatorField(env().getGrid()));
+    envTmp(std::vector<LatticeComplex>,  "E_body", 1, ndim, LatticeComplex(env().getGrid()));
+    envTmp(std::vector<LatticeComplex>,  "E_loop", 1, ndim, LatticeComplex(env().getGrid()));
 }
 
 // execution ///////////////////////////////////////////////////////////////////
@@ -93,28 +104,31 @@ void TWeakHamiltonianEye::execute(void)
                  << par().q2 << ", '" << par().q3 << "' and '" << par().q4 
                  << "'." << std::endl;
 
-    CorrWriter             writer(par().output);
-    PropagatorField &q1 = *env().template getObject<PropagatorField>(par().q1);
-    PropagatorField &q2 = *env().template getObject<PropagatorField>(par().q2);
-    PropagatorField &q3 = *env().template getObject<PropagatorField>(par().q3);
-    PropagatorField &q4 = *env().template getObject<PropagatorField>(par().q4);
-    Gamma g5            = Gamma(Gamma::Algebra::Gamma5);
-    LatticeComplex        expbuf(env().getGrid());
-    std::vector<TComplex> corrbuf;
-    std::vector<Result>   result(n_eye_diag);
-    unsigned int ndim   = env().getNd();
+    ResultWriter           writer(RESULT_FILE_NAME(par().output));
+    auto                   &q1 = envGet(SlicedPropagator, par().q1);
+    auto                   &q2 = envGet(PropagatorField, par().q2);
+    auto                   &q3 = envGet(PropagatorField, par().q3);
+    auto                   &q4 = envGet(PropagatorField, par().q4);
+    Gamma                  g5  = Gamma(Gamma::Algebra::Gamma5);
+    std::vector<TComplex>  corrbuf;
+    std::vector<Result>    result(n_eye_diag);
+    unsigned int ndim    = env().getNd();
 
-    PropagatorField              tmp1(env().getGrid());
-    LatticeComplex               tmp2(env().getGrid());
-    std::vector<PropagatorField> S_body(ndim, tmp1);
-    std::vector<PropagatorField> S_loop(ndim, tmp1);
-    std::vector<LatticeComplex>  E_body(ndim, tmp2);
-    std::vector<LatticeComplex>  E_loop(ndim, tmp2);
+    envGetTmp(LatticeComplex,               expbuf); 
+    envGetTmp(PropagatorField,              tmp1);
+    envGetTmp(LatticeComplex,               tmp2);
+    envGetTmp(std::vector<PropagatorField>, S_body);
+    envGetTmp(std::vector<PropagatorField>, S_loop);
+    envGetTmp(std::vector<LatticeComplex>,  E_body);
+    envGetTmp(std::vector<LatticeComplex>,  E_loop);
+
+    // Get sink timeslice of q1.
+    SitePropagator q1Snk = q1[par().tSnk];
 
     // Setup for S-type contractions.
     for (int mu = 0; mu < ndim; ++mu)
     {
-        S_body[mu] = MAKE_SE_BODY(q1, q2, q3, GammaL(Gamma::gmu[mu]));
+        S_body[mu] = MAKE_SE_BODY(q1Snk, q2, q3, GammaL(Gamma::gmu[mu]));
         S_loop[mu] = MAKE_SE_LOOP(q4, GammaL(Gamma::gmu[mu]));
     }
 

extras/Hadrons/Modules/MContraction/WeakHamiltonianEye.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/WeakHamiltonianEye.hpp
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_WeakHamiltonianEye_hpp_
-#define Hadrons_WeakHamiltonianEye_hpp_
+#ifndef Hadrons_MContraction_WeakHamiltonianEye_hpp_
+#define Hadrons_MContraction_WeakHamiltonianEye_hpp_
 
 #include <Grid/Hadrons/Modules/MContraction/WeakHamiltonian.hpp>
 
@@ -55,4 +56,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_WeakHamiltonianEye_hpp_
+#endif // Hadrons_MContraction_WeakHamiltonianEye_hpp_

extras/Hadrons/Modules/MContraction/WeakHamiltonianNonEye.cc

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/WeakHamiltonianNonEye.cc
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -76,7 +77,7 @@ std::vector<std::string> TWeakHamiltonianNonEye::getInput(void)
 
 std::vector<std::string> TWeakHamiltonianNonEye::getOutput(void)
 {
-    std::vector<std::string> out = {getName()};
+    std::vector<std::string> out = {};
     
     return out;
 }
@@ -84,7 +85,15 @@ std::vector<std::string> TWeakHamiltonianNonEye::getOutput(void)
 // setup ///////////////////////////////////////////////////////////////////////
 void TWeakHamiltonianNonEye::setup(void)
 {
+    unsigned int ndim = env().getNd();
 
+    envTmpLat(LatticeComplex,  "expbuf");
+    envTmpLat(PropagatorField, "tmp1");
+    envTmpLat(LatticeComplex,  "tmp2");
+    envTmp(std::vector<PropagatorField>, "C_i_side_loop", 1, ndim, PropagatorField(env().getGrid()));
+    envTmp(std::vector<PropagatorField>, "C_f_side_loop", 1, ndim, PropagatorField(env().getGrid()));
+    envTmp(std::vector<LatticeComplex>,  "W_i_side_loop", 1, ndim, LatticeComplex(env().getGrid()));
+    envTmp(std::vector<LatticeComplex>,  "W_f_side_loop", 1, ndim, LatticeComplex(env().getGrid()));
 }
 
 // execution ///////////////////////////////////////////////////////////////////
@@ -95,23 +104,23 @@ void TWeakHamiltonianNonEye::execute(void)
                  << par().q2 << ", '" << par().q3 << "' and '" << par().q4 
                  << "'." << std::endl;
     
-    CorrWriter             writer(par().output);
-    PropagatorField &q1 = *env().template getObject<PropagatorField>(par().q1);
-    PropagatorField &q2 = *env().template getObject<PropagatorField>(par().q2);
-    PropagatorField &q3 = *env().template getObject<PropagatorField>(par().q3);
-    PropagatorField &q4 = *env().template getObject<PropagatorField>(par().q4);
-    Gamma g5            = Gamma(Gamma::Algebra::Gamma5);
-    LatticeComplex        expbuf(env().getGrid());
+    ResultWriter          writer(RESULT_FILE_NAME(par().output));
+    auto                  &q1 = envGet(PropagatorField, par().q1);
+    auto                  &q2 = envGet(PropagatorField, par().q2);
+    auto                  &q3 = envGet(PropagatorField, par().q3);
+    auto                  &q4 = envGet(PropagatorField, par().q4);
+    Gamma                 g5  = Gamma(Gamma::Algebra::Gamma5);
     std::vector<TComplex> corrbuf;
     std::vector<Result>   result(n_noneye_diag); 
-    unsigned int ndim   = env().getNd();
+    unsigned int          ndim = env().getNd();
 
-    PropagatorField              tmp1(env().getGrid());
-    LatticeComplex               tmp2(env().getGrid());
-    std::vector<PropagatorField> C_i_side_loop(ndim, tmp1);
-    std::vector<PropagatorField> C_f_side_loop(ndim, tmp1);
-    std::vector<LatticeComplex>  W_i_side_loop(ndim, tmp2);
-    std::vector<LatticeComplex>  W_f_side_loop(ndim, tmp2);
+    envGetTmp(LatticeComplex,               expbuf); 
+    envGetTmp(PropagatorField,              tmp1);
+    envGetTmp(LatticeComplex,               tmp2);
+    envGetTmp(std::vector<PropagatorField>, C_i_side_loop);
+    envGetTmp(std::vector<PropagatorField>, C_f_side_loop);
+    envGetTmp(std::vector<LatticeComplex>,  W_i_side_loop);
+    envGetTmp(std::vector<LatticeComplex>,  W_f_side_loop);
 
     // Setup for C-type contractions.
     for (int mu = 0; mu < ndim; ++mu)

extras/Hadrons/Modules/MContraction/WeakHamiltonianNonEye.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/WeakHamiltonianNonEye.hpp
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_WeakHamiltonianNonEye_hpp_
-#define Hadrons_WeakHamiltonianNonEye_hpp_
+#ifndef Hadrons_MContraction_WeakHamiltonianNonEye_hpp_
+#define Hadrons_MContraction_WeakHamiltonianNonEye_hpp_
 
 #include <Grid/Hadrons/Modules/MContraction/WeakHamiltonian.hpp>
 
@@ -54,4 +55,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_WeakHamiltonianNonEye_hpp_
+#endif // Hadrons_MContraction_WeakHamiltonianNonEye_hpp_

extras/Hadrons/Modules/MContraction/WeakNeutral4ptDisc.cc

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/WeakNeutral4ptDisc.cc
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -78,7 +79,7 @@ std::vector<std::string> TWeakNeutral4ptDisc::getInput(void)
 
 std::vector<std::string> TWeakNeutral4ptDisc::getOutput(void)
 {
-    std::vector<std::string> out = {getName()};
+    std::vector<std::string> out = {};
     
     return out;
 }
@@ -86,7 +87,13 @@ std::vector<std::string> TWeakNeutral4ptDisc::getOutput(void)
 // setup ///////////////////////////////////////////////////////////////////////
 void TWeakNeutral4ptDisc::setup(void)
 {
+    unsigned int ndim = env().getNd();
 
+    envTmpLat(LatticeComplex,  "expbuf");
+    envTmpLat(PropagatorField, "tmp");
+    envTmpLat(LatticeComplex,  "curr");
+    envTmp(std::vector<PropagatorField>, "meson", 1, ndim, PropagatorField(env().getGrid()));
+    envTmp(std::vector<PropagatorField>, "loop", 1, ndim,  PropagatorField(env().getGrid()));
 }
 
 // execution ///////////////////////////////////////////////////////////////////
@@ -97,21 +104,21 @@ void TWeakNeutral4ptDisc::execute(void)
                  << par().q2 << ", '" << par().q3 << "' and '" << par().q4 
                  << "'." << std::endl;
 
-    CorrWriter             writer(par().output);
-    PropagatorField &q1 = *env().template getObject<PropagatorField>(par().q1);
-    PropagatorField &q2 = *env().template getObject<PropagatorField>(par().q2);
-    PropagatorField &q3 = *env().template getObject<PropagatorField>(par().q3);
-    PropagatorField &q4 = *env().template getObject<PropagatorField>(par().q4);
-    Gamma g5            = Gamma(Gamma::Algebra::Gamma5);
-    LatticeComplex        expbuf(env().getGrid());
+    ResultWriter          writer(RESULT_FILE_NAME(par().output));
+    auto                  &q1 = envGet(PropagatorField, par().q1);
+    auto                  &q2 = envGet(PropagatorField, par().q2);
+    auto                  &q3 = envGet(PropagatorField, par().q3);
+    auto                  &q4 = envGet(PropagatorField, par().q4);
+    Gamma                 g5  = Gamma(Gamma::Algebra::Gamma5);
     std::vector<TComplex> corrbuf;
     std::vector<Result>   result(n_neut_disc_diag);
-    unsigned int ndim   = env().getNd();
+    unsigned int          ndim = env().getNd();
 
-    PropagatorField              tmp(env().getGrid());
-    std::vector<PropagatorField> meson(ndim, tmp);
-    std::vector<PropagatorField> loop(ndim, tmp);
-    LatticeComplex               curr(env().getGrid());
+    envGetTmp(LatticeComplex,               expbuf); 
+    envGetTmp(PropagatorField,              tmp);
+    envGetTmp(LatticeComplex,               curr);
+    envGetTmp(std::vector<PropagatorField>, meson);
+    envGetTmp(std::vector<PropagatorField>, loop);
 
     // Setup for type 1 contractions.
     for (int mu = 0; mu < ndim; ++mu)

extras/Hadrons/Modules/MContraction/WeakNeutral4ptDisc.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MContraction/WeakNeutral4ptDisc.hpp
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson    <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_WeakNeutral4ptDisc_hpp_
-#define Hadrons_WeakNeutral4ptDisc_hpp_
+#ifndef Hadrons_MContraction_WeakNeutral4ptDisc_hpp_
+#define Hadrons_MContraction_WeakNeutral4ptDisc_hpp_
 
 #include <Grid/Hadrons/Modules/MContraction/WeakHamiltonian.hpp>
 
@@ -56,4 +57,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_WeakNeutral4ptDisc_hpp_
+#endif // Hadrons_MContraction_WeakNeutral4ptDisc_hpp_

extras/Hadrons/Modules/MFermion/GaugeProp.hpp

@@ -2,12 +2,12 @@
 
 Grid physics library, www.github.com/paboyle/Grid 
 
-Source file: extras/Hadrons/Modules/Quark.hpp
+Source file: extras/Hadrons/Modules/MFermion/GaugeProp.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -27,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Quark_hpp_
-#define Hadrons_Quark_hpp_
+#ifndef Hadrons_MFermion_GaugeProp_hpp_
+#define Hadrons_MFermion_GaugeProp_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -37,29 +37,53 @@ See the full license in the file "LICENSE" in the top level distribution directo
 BEGIN_HADRONS_NAMESPACE
 
 /******************************************************************************
- *                               TQuark                                       *
+ * 5D -> 4D and 4D -> 5D conversions.                                         *
  ******************************************************************************/
-class QuarkPar: Serializable
+template<class vobj> // Note that 5D object is modified.
+inline void make_4D(Lattice<vobj> &in_5d, Lattice<vobj> &out_4d, int Ls)
+{
+    axpby_ssp_pminus(in_5d, 0., in_5d, 1., in_5d, 0, 0);
+    axpby_ssp_pplus(in_5d, 1., in_5d, 1., in_5d, 0, Ls-1);
+    ExtractSlice(out_4d, in_5d, 0, 0);
+}
+
+template<class vobj>
+inline void make_5D(Lattice<vobj> &in_4d, Lattice<vobj> &out_5d, int Ls)
+{
+    out_5d = zero;
+    InsertSlice(in_4d, out_5d, 0, 0);
+    InsertSlice(in_4d, out_5d, Ls-1, 0);
+    axpby_ssp_pplus(out_5d, 0., out_5d, 1., out_5d, 0, 0);
+    axpby_ssp_pminus(out_5d, 0., out_5d, 1., out_5d, Ls-1, Ls-1);
+}
+
+/******************************************************************************
+ *                                GaugeProp                                   *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MFermion)
+
+class GaugePropPar: Serializable
 {
 public:
-    GRID_SERIALIZABLE_CLASS_MEMBERS(QuarkPar,
+    GRID_SERIALIZABLE_CLASS_MEMBERS(GaugePropPar,
                                     std::string, source,
                                     std::string, solver);
 };
 
 template <typename FImpl>
-class TQuark: public Module<QuarkPar>
+class TGaugeProp: public Module<GaugePropPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FGS_TYPE_ALIASES(FImpl,);
 public:
     // constructor
-    TQuark(const std::string name);
+    TGaugeProp(const std::string name);
     // destructor
-    virtual ~TQuark(void) = default;
-    // dependencies/products
+    virtual ~TGaugeProp(void) = default;
+    // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -69,20 +93,19 @@ private:
     SolverFn     *solver_{nullptr};
 };
 
-MODULE_REGISTER(Quark, TQuark<FIMPL>);
-
+MODULE_REGISTER_NS(GaugeProp, TGaugeProp<FIMPL>, MFermion);
 /******************************************************************************
- *                          TQuark implementation                             *
+ *                      TGaugeProp implementation                             *
  ******************************************************************************/
 // constructor /////////////////////////////////////////////////////////////////
 template <typename FImpl>
-TQuark<FImpl>::TQuark(const std::string name)
-: Module(name)
+TGaugeProp<FImpl>::TGaugeProp(const std::string name)
+: Module<GaugePropPar>(name)
 {}
 
 // dependencies/products ///////////////////////////////////////////////////////
 template <typename FImpl>
-std::vector<std::string> TQuark<FImpl>::getInput(void)
+std::vector<std::string> TGaugeProp<FImpl>::getInput(void)
 {
     std::vector<std::string> in = {par().source, par().solver};
     
@@ -90,7 +113,7 @@ std::vector<std::string> TQuark<FImpl>::getInput(void)
 }
 
 template <typename FImpl>
-std::vector<std::string> TQuark<FImpl>::getOutput(void)
+std::vector<std::string> TGaugeProp<FImpl>::getOutput(void)
 {
     std::vector<std::string> out = {getName(), getName() + "_5d"};
     
@@ -99,56 +122,52 @@ std::vector<std::string> TQuark<FImpl>::getOutput(void)
 
 // setup ///////////////////////////////////////////////////////////////////////
 template <typename FImpl>
-void TQuark<FImpl>::setup(void)
+void TGaugeProp<FImpl>::setup(void)
 {
     Ls_ = env().getObjectLs(par().solver);
-    env().template registerLattice<PropagatorField>(getName());
+    envCreateLat(PropagatorField, getName());
+    envTmpLat(FermionField, "source", Ls_);
+    envTmpLat(FermionField, "sol", Ls_);
+    envTmpLat(FermionField, "tmp");
     if (Ls_ > 1)
     {
-        env().template registerLattice<PropagatorField>(getName() + "_5d", Ls_);
+        envCreateLat(PropagatorField, getName() + "_5d", Ls_);
     }
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 template <typename FImpl>
-void TQuark<FImpl>::execute(void)
+void TGaugeProp<FImpl>::execute(void)
 {
     LOG(Message) << "Computing quark propagator '" << getName() << "'"
                  << std::endl;
     
-    FermionField    source(env().getGrid(Ls_)), sol(env().getGrid(Ls_)),
-                    tmp(env().getGrid());
-    std::string     propName = (Ls_ == 1) ? getName() : (getName() + "_5d");
-    PropagatorField &prop    = *env().template createLattice<PropagatorField>(propName);
-    PropagatorField &fullSrc = *env().template getObject<PropagatorField>(par().source);
-    SolverFn        &solver  = *env().template getObject<SolverFn>(par().solver);
-    if (Ls_ > 1)
-    {
-        env().template createLattice<PropagatorField>(getName());
-    }
+    std::string propName = (Ls_ == 1) ? getName() : (getName() + "_5d");
+    auto        &prop    = envGet(PropagatorField, propName);
+    auto        &fullSrc = envGet(PropagatorField, par().source);
+    auto        &solver  = envGet(SolverFn, par().solver);
     
+    envGetTmp(FermionField, source);
+    envGetTmp(FermionField, sol);
+    envGetTmp(FermionField, tmp);
     LOG(Message) << "Inverting using solver '" << par().solver
                  << "' on source '" << par().source << "'" << std::endl;
     for (unsigned int s = 0; s < Ns; ++s)
-    for (unsigned int c = 0; c < Nc; ++c)
+      for (unsigned int c = 0; c < FImpl::Dimension; ++c)
     {
         LOG(Message) << "Inversion for spin= " << s << ", color= " << c
-        << std::endl;
+                     << std::endl;
         // source conversion for 4D sources
         if (!env().isObject5d(par().source))
         {
             if (Ls_ == 1)
             {
-                PropToFerm(source, fullSrc, s, c);
+               PropToFerm<FImpl>(source, fullSrc, s, c);
             }
             else
             {
-                source = zero;
-                PropToFerm(tmp, fullSrc, s, c);
-                InsertSlice(tmp, source, 0, 0);
-                InsertSlice(tmp, source, Ls_-1, 0);
-                axpby_ssp_pplus(source, 0., source, 1., source, 0, 0);
-                axpby_ssp_pminus(source, 0., source, 1., source, Ls_-1, Ls_-1);
+                PropToFerm<FImpl>(tmp, fullSrc, s, c);
+                make_5D(tmp, source, Ls_);
             }
         }
         // source conversion for 5D sources
@@ -156,30 +175,28 @@ void TQuark<FImpl>::execute(void)
         {
             if (Ls_ != env().getObjectLs(par().source))
             {
-                HADRON_ERROR("Ls mismatch between quark action and source");
+                HADRON_ERROR(Size, "Ls mismatch between quark action and source");
             }
             else
             {
-                PropToFerm(source, fullSrc, s, c);
+                PropToFerm<FImpl>(source, fullSrc, s, c);
             }
         }
         sol = zero;
         solver(sol, source);
-        FermToProp(prop, sol, s, c);
+        FermToProp<FImpl>(prop, sol, s, c);
         // create 4D propagators from 5D one if necessary
         if (Ls_ > 1)
         {
-            PropagatorField &p4d =
-                *env().template getObject<PropagatorField>(getName());
-            
-            axpby_ssp_pminus(sol, 0., sol, 1., sol, 0, 0);
-            axpby_ssp_pplus(sol, 1., sol, 1., sol, 0, Ls_-1);
-            ExtractSlice(tmp, sol, 0, 0);
-            FermToProp(p4d, tmp, s, c);
+            PropagatorField &p4d = envGet(PropagatorField, getName());
+            make_4D(sol, tmp, Ls_);
+            FermToProp<FImpl>(p4d, tmp, s, c);
         }
     }
 }
 
+END_MODULE_NAMESPACE
+
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Quark_hpp_
+#endif // Hadrons_MFermion_GaugeProp_hpp_

extras/Hadrons/Modules/MGauge/FundtoHirep.cc

@@ -0,0 +1,75 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/FundtoHirep.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Modules/MGauge/FundtoHirep.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MGauge;
+
+// constructor /////////////////////////////////////////////////////////////////
+template <class Rep>
+TFundtoHirep<Rep>::TFundtoHirep(const std::string name)
+: Module<FundtoHirepPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <class Rep>
+std::vector<std::string> TFundtoHirep<Rep>::getInput(void)
+{
+    std::vector<std::string> in;
+    return in;
+}
+
+template <class Rep>
+std::vector<std::string> TFundtoHirep<Rep>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename Rep>
+void TFundtoHirep<Rep>::setup(void)
+{
+    env().template registerLattice<typename Rep::LatticeField>(getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <class Rep>
+void TFundtoHirep<Rep>::execute(void)
+{
+    auto &U      = *env().template getObject<LatticeGaugeField>(par().gaugeconf);
+    LOG(Message) << "Transforming Representation" << std::endl;
+
+    Rep TargetRepresentation(U._grid);
+    TargetRepresentation.update_representation(U);
+
+   typename Rep::LatticeField &URep = *env().template createLattice<typename Rep::LatticeField>(getName());
+    URep = TargetRepresentation.U;
+}

extras/Hadrons/Modules/MGauge/FundtoHirep.hpp

@@ -0,0 +1,77 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/FundtoHirep.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: David Preti <david.preti@to.infn.it>
+	Guido Cossu <guido.cossu@ed.ac.uk>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MGauge_FundtoHirep_hpp_
+#define Hadrons_MGauge_FundtoHirep_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         Load a NERSC configuration                         *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MGauge)
+
+class FundtoHirepPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(FundtoHirepPar,
+                                    std::string, gaugeconf);
+};
+
+template <class Rep>
+class TFundtoHirep: public Module<FundtoHirepPar>
+{
+public:
+    // constructor
+    TFundtoHirep(const std::string name);
+    // destructor
+    virtual ~TFundtoHirep(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    void setup(void);
+    // execution
+    void execute(void);
+};
+
+//MODULE_REGISTER_NS(FundtoAdjoint,   TFundtoHirep<AdjointRepresentation>, MGauge);
+//MODULE_REGISTER_NS(FundtoTwoIndexSym, TFundtoHirep<TwoIndexSymmetricRepresentation>, MGauge);
+//MODULE_REGISTER_NS(FundtoTwoIndexAsym, TFundtoHirep<TwoIndexAntiSymmetricRepresentation>, MGauge);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MGauge_FundtoHirep_hpp_

extras/Hadrons/Modules/MGauge/Random.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MGauge/Random.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -44,7 +43,9 @@ TRandom::TRandom(const std::string name)
 // dependencies/products ///////////////////////////////////////////////////////
 std::vector<std::string> TRandom::getInput(void)
 {
-    return std::vector<std::string>();
+    std::vector<std::string> in;
+    
+    return in;
 }
 
 std::vector<std::string> TRandom::getOutput(void)
@@ -57,13 +58,14 @@ std::vector<std::string> TRandom::getOutput(void)
 // setup ///////////////////////////////////////////////////////////////////////
 void TRandom::setup(void)
 {
-    env().registerLattice<LatticeGaugeField>(getName());
+    envCreateLat(LatticeGaugeField, getName());
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 void TRandom::execute(void)
 {
     LOG(Message) << "Generating random gauge configuration" << std::endl;
-    LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName());
+    
+    auto &U = envGet(LatticeGaugeField, getName());
     SU3::HotConfiguration(*env().get4dRng(), U);
 }

extras/Hadrons/Modules/MGauge/Random.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MGauge/Random.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -27,8 +26,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Random_hpp_
-#define Hadrons_Random_hpp_
+#ifndef Hadrons_MGauge_Random_hpp_
+#define Hadrons_MGauge_Random_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -51,6 +50,7 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -63,4 +63,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Random_hpp_
+#endif // Hadrons_MGauge_Random_hpp_

extras/Hadrons/Modules/MGauge/StochEm.cc

@@ -0,0 +1,84 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/StochEm.cc
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#include <Grid/Hadrons/Modules/MGauge/StochEm.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MGauge;
+
+/******************************************************************************
+*                  TStochEm implementation                             *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+TStochEm::TStochEm(const std::string name)
+: Module<StochEmPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> TStochEm::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+std::vector<std::string> TStochEm::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void TStochEm::setup(void)
+{
+    if (!env().hasCreatedObject("_" + getName() + "_weight"))
+    {
+        envCacheLat(EmComp, "_" + getName() + "_weight");
+    }
+    envCreateLat(EmField, getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void TStochEm::execute(void)
+{
+    LOG(Message) << "Generating stochatic EM potential..." << std::endl;
+
+    PhotonR photon(par().gauge, par().zmScheme);
+    auto    &a = envGet(EmField, getName());
+    auto    &w = envGet(EmComp, "_" + getName() + "_weight");
+    
+    if (!env().hasCreatedObject("_" + getName() + "_weight"))
+    {
+        LOG(Message) << "Caching stochatic EM potential weight (gauge: "
+                     << par().gauge << ", zero-mode scheme: "
+                     << par().zmScheme << ")..." << std::endl;
+        photon.StochasticWeight(w);
+    }
+    photon.StochasticField(a, *env().get4dRng(), w);
+}

extras/Hadrons/Modules/MGauge/StochEm.hpp

@@ -0,0 +1,76 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/StochEm.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_MGauge_StochEm_hpp_
+#define Hadrons_MGauge_StochEm_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         StochEm                                 *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MGauge)
+
+class StochEmPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(StochEmPar,
+                                    PhotonR::Gauge,    gauge,
+                                    PhotonR::ZmScheme, zmScheme);
+};
+
+class TStochEm: public Module<StochEmPar>
+{
+public:
+    typedef PhotonR::GaugeField     EmField;
+    typedef PhotonR::GaugeLinkField EmComp;
+public:
+    // constructor
+    TStochEm(const std::string name);
+    // destructor
+    virtual ~TStochEm(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(StochEm, TStochEm, MGauge);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MGauge_StochEm_hpp_

extras/Hadrons/Modules/MGauge/Unit.cc

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MGauge/Unit.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -57,13 +56,14 @@ std::vector<std::string> TUnit::getOutput(void)
 // setup ///////////////////////////////////////////////////////////////////////
 void TUnit::setup(void)
 {
-    env().registerLattice<LatticeGaugeField>(getName());
+    envCreateLat(LatticeGaugeField, getName());
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 void TUnit::execute(void)
 {
     LOG(Message) << "Creating unit gauge configuration" << std::endl;
-    LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName());
+    
+    auto &U = envGet(LatticeGaugeField, getName());
     SU3::ColdConfiguration(*env().get4dRng(), U);
 }

extras/Hadrons/Modules/MGauge/Unit.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MGauge/Unit.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -27,8 +26,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Unit_hpp_
-#define Hadrons_Unit_hpp_
+#ifndef Hadrons_MGauge_Unit_hpp_
+#define Hadrons_MGauge_Unit_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -51,6 +50,7 @@ public:
     // dependencies/products
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -63,4 +63,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Unit_hpp_
+#endif // Hadrons_MGauge_Unit_hpp_

extras/Hadrons/Modules/MIO/LoadBinary.hpp

@@ -0,0 +1,140 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MIO/LoadBinary.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_MIO_LoadBinary_hpp_
+#define Hadrons_MIO_LoadBinary_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                       Load a binary configurations                         *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MIO)
+
+class LoadBinaryPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(LoadBinaryPar,
+                                    std::string, file,
+                                    std::string, format);
+};
+
+template <typename Impl>
+class TLoadBinary: public Module<LoadBinaryPar>
+{
+public:
+    typedef typename Impl::Field                  Field;
+    typedef typename Impl::Simd                   Simd;
+    typedef typename Field::vector_object         vobj;
+    typedef typename vobj::scalar_object          sobj;
+    typedef typename sobj::DoublePrecision        sobj_double;
+    typedef BinarySimpleMunger<sobj_double, sobj> Munger;
+public:
+    // constructor
+    TLoadBinary(const std::string name);
+    // destructor
+    virtual ~TLoadBinary(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(LoadBinary, TLoadBinary<GIMPL>, MIO);
+MODULE_REGISTER_NS(LoadBinaryScalarSU2, TLoadBinary<ScalarNxNAdjImplR<2>>, MIO);
+MODULE_REGISTER_NS(LoadBinaryScalarSU3, TLoadBinary<ScalarNxNAdjImplR<3>>, MIO);
+MODULE_REGISTER_NS(LoadBinaryScalarSU4, TLoadBinary<ScalarNxNAdjImplR<4>>, MIO);
+MODULE_REGISTER_NS(LoadBinaryScalarSU5, TLoadBinary<ScalarNxNAdjImplR<5>>, MIO);
+MODULE_REGISTER_NS(LoadBinaryScalarSU6, TLoadBinary<ScalarNxNAdjImplR<6>>, MIO);
+
+/******************************************************************************
+ *                         TLoadBinary implementation                         *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename Impl>
+TLoadBinary<Impl>::TLoadBinary(const std::string name)
+: Module<LoadBinaryPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename Impl>
+std::vector<std::string> TLoadBinary<Impl>::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+template <typename Impl>
+std::vector<std::string> TLoadBinary<Impl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename Impl>
+void TLoadBinary<Impl>::setup(void)
+{
+    envCreateLat(Field, getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename Impl>
+void TLoadBinary<Impl>::execute(void)
+{
+    Munger      munge;
+    uint32_t    nersc_csum, scidac_csuma, scidac_csumb;
+    auto        &U = envGet(Field, getName());
+    std::string filename = par().file + "."
+                           + std::to_string(vm().getTrajectory());
+
+    LOG(Message) << "Loading " << par().format 
+                 << " binary configuration from file '" << filename
+                 << "'" << std::endl;
+    BinaryIO::readLatticeObject<vobj, sobj_double>(U, filename, munge, 0, 
+                                                   par().format, nersc_csum,
+                                                   scidac_csuma, scidac_csumb);
+    LOG(Message) << "Checksums:" << std::endl;
+    LOG(Message) << "  NERSC    " << nersc_csum << std::endl;
+    LOG(Message) << "  SciDAC A " << scidac_csuma << std::endl;
+    LOG(Message) << "  SciDAC B " << scidac_csumb << std::endl;
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MIO_LoadBinary_hpp_

extras/Hadrons/Modules/MIO/LoadNersc.cc

@@ -2,10 +2,9 @@
 
 Grid physics library, www.github.com/paboyle/Grid 
 
-Source file: extras/Hadrons/Modules/MGauge/Load.cc
+Source file: extras/Hadrons/Modules/MIO/LoadNersc.cc
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -26,30 +25,29 @@ with this program; if not, write to the Free Software Foundation, Inc.,
 See the full license in the file "LICENSE" in the top level distribution directory
 *************************************************************************************/
 /*  END LEGAL */
-
-#include <Grid/Hadrons/Modules/MGauge/Load.hpp>
+#include <Grid/Hadrons/Modules/MIO/LoadNersc.hpp>
 
 using namespace Grid;
 using namespace Hadrons;
-using namespace MGauge;
+using namespace MIO;
 
 /******************************************************************************
-*                           TLoad implementation                               *
+*                       TLoadNersc implementation                             *
 ******************************************************************************/
 // constructor /////////////////////////////////////////////////////////////////
-TLoad::TLoad(const std::string name)
-: Module<LoadPar>(name)
+TLoadNersc::TLoadNersc(const std::string name)
+: Module<LoadNerscPar>(name)
 {}
 
 // dependencies/products ///////////////////////////////////////////////////////
-std::vector<std::string> TLoad::getInput(void)
+std::vector<std::string> TLoadNersc::getInput(void)
 {
     std::vector<std::string> in;
     
     return in;
 }
 
-std::vector<std::string> TLoad::getOutput(void)
+std::vector<std::string> TLoadNersc::getOutput(void)
 {
     std::vector<std::string> out = {getName()};
     
@@ -57,22 +55,22 @@ std::vector<std::string> TLoad::getOutput(void)
 }
 
 // setup ///////////////////////////////////////////////////////////////////////
-void TLoad::setup(void)
+void TLoadNersc::setup(void)
 {
-    env().registerLattice<LatticeGaugeField>(getName());
+    envCreateLat(LatticeGaugeField, getName());
 }
 
 // execution ///////////////////////////////////////////////////////////////////
-void TLoad::execute(void)
+void TLoadNersc::execute(void)
 {
-    NerscField  header;
-    std::string fileName = par().file + "."
-                           + std::to_string(env().getTrajectory());
-    
+    FieldMetaData header;
+    std::string   fileName = par().file + "."
+                             + std::to_string(vm().getTrajectory());
     LOG(Message) << "Loading NERSC configuration from file '" << fileName
                  << "'" << std::endl;
-    LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName());
+
+    auto &U = envGet(LatticeGaugeField, getName());
     NerscIO::readConfiguration(U, header, fileName);
     LOG(Message) << "NERSC header:" << std::endl;
-    dump_nersc_header(header, LOG(Message));
+    dump_meta_data(header, LOG(Message));
 }

extras/Hadrons/Modules/MIO/LoadNersc.hpp

@@ -2,10 +2,9 @@
 
 Grid physics library, www.github.com/paboyle/Grid 
 
-Source file: extras/Hadrons/Modules/MGauge/Load.hpp
+Source file: extras/Hadrons/Modules/MIO/LoadNersc.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -26,9 +25,8 @@ with this program; if not, write to the Free Software Foundation, Inc.,
 See the full license in the file "LICENSE" in the top level distribution directory
 *************************************************************************************/
 /*  END LEGAL */
-
-#ifndef Hadrons_Load_hpp_
-#define Hadrons_Load_hpp_
+#ifndef Hadrons_MIO_LoadNersc_hpp_
+#define Hadrons_MIO_LoadNersc_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -37,24 +35,24 @@ See the full license in the file "LICENSE" in the top level distribution directo
 BEGIN_HADRONS_NAMESPACE
 
 /******************************************************************************
- *                         Load a NERSC configuration                         *
+ *                       Load a NERSC configuration                           *
  ******************************************************************************/
-BEGIN_MODULE_NAMESPACE(MGauge)
+BEGIN_MODULE_NAMESPACE(MIO)
 
-class LoadPar: Serializable
+class LoadNerscPar: Serializable
 {
 public:
-    GRID_SERIALIZABLE_CLASS_MEMBERS(LoadPar,
+    GRID_SERIALIZABLE_CLASS_MEMBERS(LoadNerscPar,
                                     std::string, file);
 };
 
-class TLoad: public Module<LoadPar>
+class TLoadNersc: public Module<LoadNerscPar>
 {
 public:
     // constructor
-    TLoad(const std::string name);
+    TLoadNersc(const std::string name);
     // destructor
-    virtual ~TLoad(void) = default;
+    virtual ~TLoadNersc(void) = default;
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
@@ -64,10 +62,10 @@ public:
     virtual void execute(void);
 };
 
-MODULE_REGISTER_NS(Load, TLoad, MGauge);
+MODULE_REGISTER_NS(LoadNersc, TLoadNersc, MIO);
 
 END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Load_hpp_
+#endif // Hadrons_MIO_LoadNersc_hpp_

extras/Hadrons/Modules/MLoop/NoiseLoop.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MLoop/NoiseLoop.hpp
 
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_NoiseLoop_hpp_
-#define Hadrons_NoiseLoop_hpp_
+#ifndef Hadrons_MLoop_NoiseLoop_hpp_
+#define Hadrons_MLoop_NoiseLoop_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -65,7 +66,7 @@ template <typename FImpl>
 class TNoiseLoop: public Module<NoiseLoopPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FERM_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TNoiseLoop(const std::string name);
@@ -74,6 +75,7 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -112,16 +114,16 @@ std::vector<std::string> TNoiseLoop<FImpl>::getOutput(void)
 template <typename FImpl>
 void TNoiseLoop<FImpl>::setup(void)
 {
-    env().template registerLattice<PropagatorField>(getName());
+    envCreateLat(PropagatorField, getName());
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 template <typename FImpl>
 void TNoiseLoop<FImpl>::execute(void)
 {
-    PropagatorField &loop = *env().template createLattice<PropagatorField>(getName());
-    PropagatorField &q    = *env().template getObject<PropagatorField>(par().q);
-    PropagatorField &eta  = *env().template getObject<PropagatorField>(par().eta);
+    auto &loop = envGet(PropagatorField, getName());
+    auto &q    = envGet(PropagatorField, par().q);
+    auto &eta  = envGet(PropagatorField, par().eta);
     loop = q*adj(eta);
 }
 
@@ -129,4 +131,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_NoiseLoop_hpp_
+#endif // Hadrons_MLoop_NoiseLoop_hpp_

extras/Hadrons/Modules/MScalar/ChargedProp.cc

@@ -0,0 +1,249 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalar/ChargedProp.cc
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: James Harrison <jch1g10@soton.ac.uk>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#include <Grid/Hadrons/Modules/MScalar/ChargedProp.hpp>
+#include <Grid/Hadrons/Modules/MScalar/Scalar.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MScalar;
+
+/******************************************************************************
+*                     TChargedProp implementation                             *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+TChargedProp::TChargedProp(const std::string name)
+: Module<ChargedPropPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> TChargedProp::getInput(void)
+{
+    std::vector<std::string> in = {par().source, par().emField};
+    
+    return in;
+}
+
+std::vector<std::string> TChargedProp::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void TChargedProp::setup(void)
+{
+    freeMomPropName_ = FREEMOMPROP(par().mass);
+    phaseName_.clear();
+    for (unsigned int mu = 0; mu < env().getNd(); ++mu)
+    {
+        phaseName_.push_back("_shiftphase_" + std::to_string(mu));
+    }
+    GFSrcName_ = getName() + "_DinvSrc";
+    fftName_   = getName() + "_fft";
+
+    freeMomPropDone_ = env().hasCreatedObject(freeMomPropName_);
+    GFSrcDone_       = env().hasCreatedObject(GFSrcName_);
+    phasesDone_      = env().hasCreatedObject(phaseName_[0]);
+    envCacheLat(ScalarField, freeMomPropName_);
+    for (unsigned int mu = 0; mu < env().getNd(); ++mu)
+    {
+        envCacheLat(ScalarField, phaseName_[mu]);
+    }
+    envCacheLat(ScalarField, GFSrcName_);
+    envCreateLat(ScalarField, getName());
+    envTmpLat(ScalarField, "buf");
+    envTmpLat(ScalarField, "result");
+    envTmpLat(ScalarField, "Amu");
+    envCache(FFT, fftName_, 1, env().getGrid());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void TChargedProp::execute(void)
+{
+    // CACHING ANALYTIC EXPRESSIONS
+    makeCaches();
+
+    // PROPAGATOR CALCULATION
+    LOG(Message) << "Computing charged scalar propagator"
+                 << " (mass= " << par().mass
+                 << ", charge= " << par().charge << ")..." << std::endl;
+    
+    auto   &prop  = envGet(ScalarField, getName());
+    auto   &GFSrc = envGet(ScalarField, GFSrcName_);
+    auto   &G     = envGet(ScalarField, freeMomPropName_);
+    auto   &fft   = envGet(FFT, fftName_);
+    double q      = par().charge;
+    envGetTmp(ScalarField, result); 
+    envGetTmp(ScalarField, buf); 
+
+    // G*F*Src
+    prop = GFSrc;
+
+    // - q*G*momD1*G*F*Src (momD1 = F*D1*Finv)
+    buf = GFSrc;
+    momD1(buf, fft);
+    buf = G*buf;
+    prop = prop - q*buf;
+
+    // + q^2*G*momD1*G*momD1*G*F*Src (here buf = G*momD1*G*F*Src)
+    momD1(buf, fft);
+    prop = prop + q*q*G*buf;
+
+    // - q^2*G*momD2*G*F*Src (momD2 = F*D2*Finv)
+    buf = GFSrc;
+    momD2(buf, fft);
+    prop = prop - q*q*G*buf;
+
+    // final FT
+    fft.FFT_all_dim(prop, prop, FFT::backward);
+    
+    // OUTPUT IF NECESSARY
+    if (!par().output.empty())
+    {
+        std::string           filename = par().output + "." +
+                                         std::to_string(vm().getTrajectory());
+        
+        LOG(Message) << "Saving zero-momentum projection to '"
+                     << filename << "'..." << std::endl;
+        
+        ResultWriter          writer(RESULT_FILE_NAME(par().output));
+        std::vector<TComplex> vecBuf;
+        std::vector<Complex>  result;
+        
+        sliceSum(prop, vecBuf, Tp);
+        result.resize(vecBuf.size());
+        for (unsigned int t = 0; t < vecBuf.size(); ++t)
+        {
+            result[t] = TensorRemove(vecBuf[t]);
+        }
+        write(writer, "charge", q);
+        write(writer, "prop", result);
+    }
+}
+
+void TChargedProp::makeCaches(void)
+{
+    auto &freeMomProp = envGet(ScalarField, freeMomPropName_);
+    auto &GFSrc       = envGet(ScalarField, GFSrcName_);
+    auto &fft         = envGet(FFT, fftName_);
+
+    if (!freeMomPropDone_)
+    {
+        LOG(Message) << "Caching momentum space free scalar propagator"
+                     << " (mass= " << par().mass << ")..." << std::endl;
+        SIMPL::MomentumSpacePropagator(freeMomProp, par().mass);
+    }
+    if (!GFSrcDone_)
+    {   
+        FFT  fft(env().getGrid());
+        auto &source = envGet(ScalarField, par().source);
+
+        LOG(Message) << "Caching G*F*src..." << std::endl;
+        fft.FFT_all_dim(GFSrc, source, FFT::forward);
+        GFSrc = freeMomProp*GFSrc;
+    }
+    if (!phasesDone_)
+    {
+        std::vector<int> &l = env().getGrid()->_fdimensions;
+        Complex          ci(0.0,1.0);
+        
+        LOG(Message) << "Caching shift phases..." << std::endl;
+        for (unsigned int mu = 0; mu < env().getNd(); ++mu)
+        {
+            Real twoPiL = M_PI*2./l[mu];
+            auto &phmu  = envGet(ScalarField, phaseName_[mu]);
+            
+            LatticeCoordinate(phmu, mu);
+            phmu = exp(ci*twoPiL*phmu);
+            phase_.push_back(&phmu);
+        }
+    }
+}
+
+void TChargedProp::momD1(ScalarField &s, FFT &fft)
+{
+    auto        &A = envGet(EmField, par().emField);
+    Complex     ci(0.0,1.0);
+
+    envGetTmp(ScalarField, buf);
+    envGetTmp(ScalarField, result);
+    envGetTmp(ScalarField, Amu);
+
+    result = zero;
+    for (unsigned int mu = 0; mu < env().getNd(); ++mu)
+    {
+        Amu = peekLorentz(A, mu);
+        buf = (*phase_[mu])*s;
+        fft.FFT_all_dim(buf, buf, FFT::backward);
+        buf = Amu*buf;
+        fft.FFT_all_dim(buf, buf, FFT::forward);
+        result = result - ci*buf;
+    }
+    fft.FFT_all_dim(s, s, FFT::backward);
+    for (unsigned int mu = 0; mu < env().getNd(); ++mu)
+    {
+        Amu = peekLorentz(A, mu);
+        buf = Amu*s;
+        fft.FFT_all_dim(buf, buf, FFT::forward);
+        result = result + ci*adj(*phase_[mu])*buf;
+    }
+
+    s = result;
+}
+
+void TChargedProp::momD2(ScalarField &s, FFT &fft)
+{
+    auto &A = envGet(EmField, par().emField);
+
+    envGetTmp(ScalarField, buf);
+    envGetTmp(ScalarField, result);
+    envGetTmp(ScalarField, Amu);
+
+    result = zero;
+    for (unsigned int mu = 0; mu < env().getNd(); ++mu)
+    {
+        Amu = peekLorentz(A, mu);
+        buf = (*phase_[mu])*s;
+        fft.FFT_all_dim(buf, buf, FFT::backward);
+        buf = Amu*Amu*buf;
+        fft.FFT_all_dim(buf, buf, FFT::forward);
+        result = result + .5*buf;
+    }
+    fft.FFT_all_dim(s, s, FFT::backward);
+    for (unsigned int mu = 0; mu < env().getNd(); ++mu)
+    {
+        Amu = peekLorentz(A, mu);        
+        buf = Amu*Amu*s;
+        fft.FFT_all_dim(buf, buf, FFT::forward);
+        result = result + .5*adj(*phase_[mu])*buf;
+    }
+
+    s = result;
+}

extras/Hadrons/Modules/MScalar/ChargedProp.hpp

@@ -0,0 +1,89 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalar/ChargedProp.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_MScalar_ChargedProp_hpp_
+#define Hadrons_MScalar_ChargedProp_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                       Charged scalar propagator                            *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MScalar)
+
+class ChargedPropPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(ChargedPropPar,
+                                    std::string, emField,
+                                    std::string, source,
+                                    double,      mass,
+                                    double,      charge,
+                                    std::string, output);
+};
+
+class TChargedProp: public Module<ChargedPropPar>
+{
+public:
+    SCALAR_TYPE_ALIASES(SIMPL,);
+    typedef PhotonR::GaugeField     EmField;
+    typedef PhotonR::GaugeLinkField EmComp;
+public:
+    // constructor
+    TChargedProp(const std::string name);
+    // destructor
+    virtual ~TChargedProp(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+private:
+    void makeCaches(void);
+    void momD1(ScalarField &s, FFT &fft);
+    void momD2(ScalarField &s, FFT &fft);
+private:
+    bool                       freeMomPropDone_, GFSrcDone_, phasesDone_;
+    std::string                freeMomPropName_, GFSrcName_, fftName_;
+    std::vector<std::string>   phaseName_;
+    std::vector<ScalarField *> phase_;
+};
+
+MODULE_REGISTER_NS(ChargedProp, TChargedProp, MScalar);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MScalar_ChargedProp_hpp_

extras/Hadrons/Modules/MScalar/FreeProp.cc

@@ -0,0 +1,99 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalar/FreeProp.cc
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#include <Grid/Hadrons/Modules/MScalar/FreeProp.hpp>
+#include <Grid/Hadrons/Modules/MScalar/Scalar.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MScalar;
+
+/******************************************************************************
+*                        TFreeProp implementation                             *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+TFreeProp::TFreeProp(const std::string name)
+: Module<FreePropPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> TFreeProp::getInput(void)
+{
+    std::vector<std::string> in = {par().source};
+    
+    return in;
+}
+
+std::vector<std::string> TFreeProp::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void TFreeProp::setup(void)
+{
+    freeMomPropName_ = FREEMOMPROP(par().mass);
+    
+    freePropDone_ = env().hasCreatedObject(freeMomPropName_);
+    envCacheLat(ScalarField, freeMomPropName_);
+    envCreateLat(ScalarField, getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void TFreeProp::execute(void)
+{
+    auto &freeMomProp = envGet(ScalarField, freeMomPropName_);
+    auto &prop        = envGet(ScalarField, getName());
+    auto &source      = envGet(ScalarField, par().source);
+
+    if (!freePropDone_)
+    {
+        LOG(Message) << "Caching momentum space free scalar propagator"
+                     << " (mass= " << par().mass << ")..." << std::endl;
+        SIMPL::MomentumSpacePropagator(freeMomProp, par().mass);
+    }
+    LOG(Message) << "Computing free scalar propagator..." << std::endl;
+    SIMPL::FreePropagator(source, prop, freeMomProp);
+    
+    if (!par().output.empty())
+    {
+        TextWriter            writer(par().output + "." +
+                                     std::to_string(vm().getTrajectory()));
+        std::vector<TComplex> buf;
+        std::vector<Complex>  result;
+        
+        sliceSum(prop, buf, Tp);
+        result.resize(buf.size());
+        for (unsigned int t = 0; t < buf.size(); ++t)
+        {
+            result[t] = TensorRemove(buf[t]);
+        }
+        write(writer, "prop", result);
+    }
+}

extras/Hadrons/Modules/MScalar/FreeProp.hpp

@@ -0,0 +1,79 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalar/FreeProp.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_MScalar_FreeProp_hpp_
+#define Hadrons_MScalar_FreeProp_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                               FreeProp                                     *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MScalar)
+
+class FreePropPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(FreePropPar,
+                                    std::string, source,
+                                    double,      mass,
+                                    std::string, output);
+};
+
+class TFreeProp: public Module<FreePropPar>
+{
+public:
+    SCALAR_TYPE_ALIASES(SIMPL,);
+public:
+    // constructor
+    TFreeProp(const std::string name);
+    // destructor
+    virtual ~TFreeProp(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+private:
+    std::string freeMomPropName_;
+    bool        freePropDone_;
+};
+
+MODULE_REGISTER_NS(FreeProp, TFreeProp, MScalar);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MScalar_FreeProp_hpp_

extras/Hadrons/Modules/MScalar/Scalar.hpp

@@ -0,0 +1,33 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalar/Scalar.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_Scalar_hpp_
+#define Hadrons_Scalar_hpp_
+
+#define FREEMOMPROP(m) "_scalar_mom_prop_" + std::to_string(m)
+
+#endif // Hadrons_Scalar_hpp_

extras/Hadrons/Modules/MScalarSUN/TrMag.hpp

@@ -0,0 +1,146 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalarSUN/TrMag.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_MScalarSUN_TrMag_hpp_
+#define Hadrons_MScalarSUN_TrMag_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                       Module to compute tr(mag^n)                          *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MScalarSUN)
+
+class TrMagPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(TrMagPar,
+                                    std::string,  field,
+                                    unsigned int, maxPow,
+                                    std::string,  output);
+};
+
+template <typename SImpl>
+class TTrMag: public Module<TrMagPar>
+{
+public:
+    typedef typename SImpl::Field        Field;
+    typedef typename SImpl::ComplexField ComplexField;
+    class Result: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(Result,
+                                        std::string, op,
+                                        Real,        value);
+    };
+public:
+    // constructor
+    TTrMag(const std::string name);
+    // destructor
+    virtual ~TTrMag(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(TrMagSU2, TTrMag<ScalarNxNAdjImplR<2>>, MScalarSUN);
+MODULE_REGISTER_NS(TrMagSU3, TTrMag<ScalarNxNAdjImplR<3>>, MScalarSUN);
+MODULE_REGISTER_NS(TrMagSU4, TTrMag<ScalarNxNAdjImplR<4>>, MScalarSUN);
+MODULE_REGISTER_NS(TrMagSU5, TTrMag<ScalarNxNAdjImplR<5>>, MScalarSUN);
+MODULE_REGISTER_NS(TrMagSU6, TTrMag<ScalarNxNAdjImplR<6>>, MScalarSUN);
+
+/******************************************************************************
+ *                         TTrMag implementation                              *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename SImpl>
+TTrMag<SImpl>::TTrMag(const std::string name)
+: Module<TrMagPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename SImpl>
+std::vector<std::string> TTrMag<SImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().field};
+    
+    return in;
+}
+
+template <typename SImpl>
+std::vector<std::string> TTrMag<SImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename SImpl>
+void TTrMag<SImpl>::setup(void)
+{}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename SImpl>
+void TTrMag<SImpl>::execute(void)
+{
+    LOG(Message) << "Computing tr(mag^n) for n even up to " << par().maxPow
+                 << "..." << std::endl;
+
+    std::vector<Result> result;
+    ResultWriter        writer(RESULT_FILE_NAME(par().output));
+    auto                &phi = envGet(Field, par().field);
+
+    auto m2 = sum(phi), mn = m2;
+
+    m2 = -m2*m2;
+    mn = 1.;
+    for (unsigned int n = 2; n <= par().maxPow; n += 2)
+    {
+        Result r;
+
+        mn = mn*m2;
+        r.op    = "tr(mag^" + std::to_string(n) + ")";
+        r.value = TensorRemove(trace(mn)).real();
+        result.push_back(r);
+    }
+    write(writer, "trmag", result);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MScalarSUN_TrMag_hpp_

extras/Hadrons/Modules/MScalarSUN/TrPhi.hpp

@@ -0,0 +1,182 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalarSUN/TrPhi.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_MScalarSUN_TrPhi_hpp_
+#define Hadrons_MScalarSUN_TrPhi_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         Module to compute tr(phi^n)                        *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MScalarSUN)
+
+class TrPhiPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(TrPhiPar,
+                                    std::string,  field,
+                                    unsigned int, maxPow,
+                                    std::string,  output);
+};
+
+template <typename SImpl>
+class TTrPhi: public Module<TrPhiPar>
+{
+public:
+    typedef typename SImpl::Field        Field;
+    typedef typename SImpl::ComplexField ComplexField;
+    class Result: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(Result,
+                                        std::string, op,
+                                        Real,        value);
+    };
+public:
+    // constructor
+    TTrPhi(const std::string name);
+    // destructor
+    virtual ~TTrPhi(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+private:
+    // output name generator
+    std::string outName(const unsigned int n);
+};
+
+MODULE_REGISTER_NS(TrPhiSU2, TTrPhi<ScalarNxNAdjImplR<2>>, MScalarSUN);
+MODULE_REGISTER_NS(TrPhiSU3, TTrPhi<ScalarNxNAdjImplR<3>>, MScalarSUN);
+MODULE_REGISTER_NS(TrPhiSU4, TTrPhi<ScalarNxNAdjImplR<4>>, MScalarSUN);
+MODULE_REGISTER_NS(TrPhiSU5, TTrPhi<ScalarNxNAdjImplR<5>>, MScalarSUN);
+MODULE_REGISTER_NS(TrPhiSU6, TTrPhi<ScalarNxNAdjImplR<6>>, MScalarSUN);
+
+/******************************************************************************
+ *                          TTrPhi implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename SImpl>
+TTrPhi<SImpl>::TTrPhi(const std::string name)
+: Module<TrPhiPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename SImpl>
+std::vector<std::string> TTrPhi<SImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().field};
+    
+    return in;
+}
+
+template <typename SImpl>
+std::vector<std::string> TTrPhi<SImpl>::getOutput(void)
+{
+    std::vector<std::string> out;
+
+    for (unsigned int n = 2; n <= par().maxPow; n += 2)
+    {
+        out.push_back(outName(n));
+    }
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename SImpl>
+void TTrPhi<SImpl>::setup(void)
+{
+    if (par().maxPow < 2)
+    {
+        HADRON_ERROR(Size, "'maxPow' should be at least equal to 2");
+    }
+    envTmpLat(Field, "phi2");
+    envTmpLat(Field, "buf");
+    for (unsigned int n = 2; n <= par().maxPow; n += 2)
+    {
+        envCreateLat(ComplexField, outName(n));
+    }
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename SImpl>
+void TTrPhi<SImpl>::execute(void)
+{
+    LOG(Message) << "Computing tr(phi^n) for n even up to " << par().maxPow
+                 << "..." << std::endl; 
+
+    std::vector<Result> result;
+    auto                &phi = envGet(Field, par().field);
+
+    envGetTmp(Field, phi2);
+    envGetTmp(Field, buf);
+    buf  = 1.;
+    phi2 = -phi*phi; 
+    for (unsigned int n = 2; n <= par().maxPow; n += 2)
+    {
+        auto &phin = envGet(ComplexField, outName(n));
+
+        buf  = buf*phi2;
+        phin = trace(buf);
+        if (!par().output.empty())
+        {
+            Result r;
+
+            r.op    = "tr(phi^" + std::to_string(n) + ")";
+            r.value = TensorRemove(sum(phin)).real();
+            result.push_back(r);
+        }
+    }
+    if (result.size() > 0)
+    {
+        ResultWriter writer(RESULT_FILE_NAME(par().output));
+
+        write(writer, "trphi", result);
+    }
+}
+
+// output name generator ///////////////////////////////////////////////////////
+template <typename SImpl>
+std::string TTrPhi<SImpl>::outName(const unsigned int n)
+{
+    return getName() + "_" + std::to_string(n);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MScalarSUN_TrPhi_hpp_

extras/Hadrons/Modules/MScalarSUN/TwoPoint.hpp

@@ -0,0 +1,184 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MScalarSUN/TwoPoint.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef Hadrons_MScalarSUN_TwoPoint_hpp_
+#define Hadrons_MScalarSUN_TwoPoint_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                 2-pt functions for a given set of operators                *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MScalarSUN)
+
+class TwoPointPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(TwoPointPar,
+                                    std::vector<std::string>, op,
+                                    std::string,              output);
+};
+
+template <typename SImpl>
+class TTwoPoint: public Module<TwoPointPar>
+{
+public:
+    typedef typename SImpl::Field        Field;
+    typedef typename SImpl::ComplexField ComplexField;
+    class Result: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(Result,
+                                        std::string, sink,
+                                        std::string, source,
+                                        std::vector<Complex>, data);
+    };
+public:
+    // constructor
+    TTwoPoint(const std::string name);
+    // destructor
+    virtual ~TTwoPoint(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+private:
+    // make 2-pt function
+    template <class SinkSite, class SourceSite>
+    std::vector<Complex> makeTwoPoint(const std::vector<SinkSite>   &sink,
+                                      const std::vector<SourceSite> &source);
+};
+
+MODULE_REGISTER_NS(TwoPointSU2, TTwoPoint<ScalarNxNAdjImplR<2>>, MScalarSUN);
+MODULE_REGISTER_NS(TwoPointSU3, TTwoPoint<ScalarNxNAdjImplR<3>>, MScalarSUN);
+MODULE_REGISTER_NS(TwoPointSU4, TTwoPoint<ScalarNxNAdjImplR<4>>, MScalarSUN);
+MODULE_REGISTER_NS(TwoPointSU5, TTwoPoint<ScalarNxNAdjImplR<5>>, MScalarSUN);
+MODULE_REGISTER_NS(TwoPointSU6, TTwoPoint<ScalarNxNAdjImplR<6>>, MScalarSUN);
+
+/******************************************************************************
+ *                 TTwoPoint implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename SImpl>
+TTwoPoint<SImpl>::TTwoPoint(const std::string name)
+: Module<TwoPointPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename SImpl>
+std::vector<std::string> TTwoPoint<SImpl>::getInput(void)
+{   
+    return par().op;
+}
+
+template <typename SImpl>
+std::vector<std::string> TTwoPoint<SImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {};
+
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename SImpl>
+void TTwoPoint<SImpl>::setup(void)
+{
+    const unsigned int nt = env().getDim().back();
+    envTmp(std::vector<std::vector<TComplex>>, "slicedOp", 1, par().op.size(), 
+           std::vector<TComplex>(nt));
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename SImpl>
+void TTwoPoint<SImpl>::execute(void)
+{
+    LOG(Message) << "Computing 2-point functions for operators:" << std::endl;
+    for (auto &o: par().op)
+    {
+        LOG(Message) << "  '" << o << "'" << std::endl;
+    }
+
+    ResultWriter        writer(RESULT_FILE_NAME(par().output));
+    const unsigned int  nd = env().getDim().size();
+    std::vector<Result> result;
+    
+    envGetTmp(std::vector<std::vector<TComplex>>, slicedOp);
+    for (unsigned int i = 0; i < par().op.size(); ++i)
+    {
+        auto &op = envGet(ComplexField, par().op[i]);
+
+        sliceSum(op, slicedOp[i], nd - 1);
+    }
+    for (unsigned int i = 0; i < par().op.size(); ++i)
+    for (unsigned int j = 0; j < par().op.size(); ++j)
+    {
+        Result r;
+
+        r.sink   = par().op[i];
+        r.source = par().op[j];
+        r.data   = makeTwoPoint(slicedOp[i], slicedOp[j]);
+        result.push_back(r);
+    }
+    write(writer, "twopt", result);
+}
+
+// make 2-pt function //////////////////////////////////////////////////////////
+template <class SImpl>
+template <class SinkSite, class SourceSite>
+std::vector<Complex> TTwoPoint<SImpl>::makeTwoPoint(
+                                  const std::vector<SinkSite>   &sink,
+                                  const std::vector<SourceSite> &source)
+{
+    assert(sink.size() == source.size());
+    
+    unsigned int         nt = sink.size();
+    std::vector<Complex> res(nt, 0.);
+    
+    for (unsigned int dt = 0; dt < nt; ++dt)
+    {
+        for (unsigned int t  = 0; t < nt; ++t)
+        {
+            res[dt] += TensorRemove(trace(sink[(t+dt)%nt]*source[t]));
+        }
+        res[dt] *= 1./static_cast<double>(nt);
+    }
+    
+    return res;
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MScalarSUN_TwoPoint_hpp_

extras/Hadrons/Modules/MSink/Point.hpp

@@ -0,0 +1,155 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MSink/Point.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MSink_Point_hpp_
+#define Hadrons_MSink_Point_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                                   Point                                    *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MSink)
+
+class PointPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(PointPar,
+                                    std::string, mom);
+};
+
+template <typename FImpl>
+class TPoint: public Module<PointPar>
+{
+public:
+    FERM_TYPE_ALIASES(FImpl,);
+    SINK_TYPE_ALIASES();
+public:
+    // constructor
+    TPoint(const std::string name);
+    // destructor
+    virtual ~TPoint(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+private:
+    bool        hasPhase_{false}; 
+    std::string momphName_;
+};
+
+MODULE_REGISTER_NS(Point,       TPoint<FIMPL>,        MSink);
+MODULE_REGISTER_NS(ScalarPoint, TPoint<ScalarImplCR>, MSink);
+
+/******************************************************************************
+ *                          TPoint implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TPoint<FImpl>::TPoint(const std::string name)
+: Module<PointPar>(name)
+, momphName_ (name + "_momph")
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TPoint<FImpl>::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TPoint<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TPoint<FImpl>::setup(void)
+{
+    envTmpLat(LatticeComplex, "coor");
+    envCacheLat(LatticeComplex, momphName_);
+    envCreate(SinkFn, getName(), 1, nullptr);
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TPoint<FImpl>::execute(void)
+{   
+    LOG(Message) << "Setting up point sink function for momentum ["
+                 << par().mom << "]" << std::endl;
+
+    auto &ph = envGet(LatticeComplex, momphName_);
+    
+    if (!hasPhase_)
+    {
+        Complex           i(0.0,1.0);
+        std::vector<Real> p;
+
+        envGetTmp(LatticeComplex, coor);
+        p  = strToVec<Real>(par().mom);
+        ph = zero;
+        for(unsigned int mu = 0; mu < env().getNd(); mu++)
+        {
+            LatticeCoordinate(coor, mu);
+            ph = ph + (p[mu]/env().getGrid()->_fdimensions[mu])*coor;
+        }
+        ph = exp((Real)(2*M_PI)*i*ph);
+        hasPhase_ = true;
+    }
+    auto sink = [&ph](const PropagatorField &field)
+    {
+        SlicedPropagator res;
+        PropagatorField  tmp = ph*field;
+        
+        sliceSum(tmp, res, Tp);
+        
+        return res;
+    };
+    envGet(SinkFn, getName()) = sink;
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MSink_Point_hpp_

extras/Hadrons/Modules/MSink/Smear.hpp

@@ -0,0 +1,127 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MSink/Smear.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MSink_Smear_hpp_
+#define Hadrons_MSink_Smear_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                                 Smear                                      *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MSink)
+
+class SmearPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(SmearPar,
+                                    std::string, q,
+                                    std::string, sink);
+};
+
+template <typename FImpl>
+class TSmear: public Module<SmearPar>
+{
+public:
+    FERM_TYPE_ALIASES(FImpl,);
+    SINK_TYPE_ALIASES();
+public:
+    // constructor
+    TSmear(const std::string name);
+    // destructor
+    virtual ~TSmear(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Smear, TSmear<FIMPL>, MSink);
+
+/******************************************************************************
+ *                          TSmear implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TSmear<FImpl>::TSmear(const std::string name)
+: Module<SmearPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TSmear<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().q, par().sink};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TSmear<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TSmear<FImpl>::setup(void)
+{
+    envCreate(SlicedPropagator, getName(), 1, env().getDim(Tp));
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TSmear<FImpl>::execute(void)
+{
+    LOG(Message) << "Sink smearing propagator '" << par().q
+                 << "' using sink function '" << par().sink << "'."
+                 << std::endl;
+
+    auto &sink = envGet(SinkFn, par().sink);
+    auto &q    = envGet(PropagatorField, par().q);
+    auto &out  = envGet(SlicedPropagator, getName());
+    
+    out = sink(q);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MSink_Smear_hpp_

extras/Hadrons/Modules/MSolver/RBPrecCG.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MSolver/RBPrecCG.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -27,8 +26,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_RBPrecCG_hpp_
-#define Hadrons_RBPrecCG_hpp_
+#ifndef Hadrons_MSolver_RBPrecCG_hpp_
+#define Hadrons_MSolver_RBPrecCG_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -53,7 +52,7 @@ template <typename FImpl>
 class TRBPrecCG: public Module<RBPrecCGPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FGS_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TRBPrecCG(const std::string name);
@@ -61,7 +60,9 @@ public:
     virtual ~TRBPrecCG(void) = default;
     // dependencies/products
     virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getReference(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
@@ -83,11 +84,19 @@ TRBPrecCG<FImpl>::TRBPrecCG(const std::string name)
 template <typename FImpl>
 std::vector<std::string> TRBPrecCG<FImpl>::getInput(void)
 {
-    std::vector<std::string> in = {par().action};
+    std::vector<std::string> in = {};
     
     return in;
 }
 
+template <typename FImpl>
+std::vector<std::string> TRBPrecCG<FImpl>::getReference(void)
+{
+    std::vector<std::string> ref = {par().action};
+    
+    return ref;
+}
+
 template <typename FImpl>
 std::vector<std::string> TRBPrecCG<FImpl>::getOutput(void)
 {
@@ -100,17 +109,12 @@ std::vector<std::string> TRBPrecCG<FImpl>::getOutput(void)
 template <typename FImpl>
 void TRBPrecCG<FImpl>::setup(void)
 {
-    auto Ls = env().getObjectLs(par().action);
-    
-    env().registerObject(getName(), 0, Ls);
-    env().addOwnership(getName(), par().action);
-}
+    LOG(Message) << "setting up Schur red-black preconditioned CG for"
+                 << " action '" << par().action << "' with residual "
+                 << par().residual << std::endl;
 
-// execution ///////////////////////////////////////////////////////////////////
-template <typename FImpl>
-void TRBPrecCG<FImpl>::execute(void)
-{
-    auto &mat   = *(env().template getObject<FMat>(par().action));
+    auto Ls     = env().getObjectLs(par().action);
+    auto &mat   = envGet(FMat, par().action);
     auto solver = [&mat, this](FermionField &sol, const FermionField &source)
     {
         ConjugateGradient<FermionField>           cg(par().residual, 10000);
@@ -118,15 +122,16 @@ void TRBPrecCG<FImpl>::execute(void)
         
         schurSolver(mat, source, sol);
     };
-    
-    LOG(Message) << "setting up Schur red-black preconditioned CG for"
-                 << " action '" << par().action << "' with residual "
-                 << par().residual << std::endl;
-    env().setObject(getName(), new SolverFn(solver));
+    envCreate(SolverFn, getName(), Ls, solver);
 }
 
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TRBPrecCG<FImpl>::execute(void)
+{}
+
 END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_RBPrecCG_hpp_
+#endif // Hadrons_MSolver_RBPrecCG_hpp_

extras/Hadrons/Modules/MSource/Point.hpp

@@ -4,10 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MSource/Point.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -27,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Point_hpp_
-#define Hadrons_Point_hpp_
+#ifndef Hadrons_MSource_Point_hpp_
+#define Hadrons_MSource_Point_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -63,7 +63,7 @@ template <typename FImpl>
 class TPoint: public Module<PointPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FERM_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TPoint(const std::string name);
@@ -72,13 +72,15 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
     virtual void execute(void);
 };
 
-MODULE_REGISTER_NS(Point, TPoint<FIMPL>, MSource);
+MODULE_REGISTER_NS(Point,       TPoint<FIMPL>,        MSource);
+MODULE_REGISTER_NS(ScalarPoint, TPoint<ScalarImplCR>, MSource);
 
 /******************************************************************************
  *                       TPoint template implementation                       *
@@ -110,19 +112,20 @@ std::vector<std::string> TPoint<FImpl>::getOutput(void)
 template <typename FImpl>
 void TPoint<FImpl>::setup(void)
 {
-    env().template registerLattice<PropagatorField>(getName());
+    envCreateLat(PropagatorField, getName());
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 template <typename FImpl>
 void TPoint<FImpl>::execute(void)
 {
-    std::vector<int> position = strToVec<int>(par().position);
-    typename SitePropagator::scalar_object id;
-    
     LOG(Message) << "Creating point source at position [" << par().position
-                 << "]" << std::endl;
-    PropagatorField &src = *env().template createLattice<PropagatorField>(getName());
+                << "]" << std::endl;
+
+    std::vector<int> position = strToVec<int>(par().position);
+    auto             &src     = envGet(PropagatorField, getName());
+    SitePropagator   id;
+    
     id  = 1.;
     src = zero;
     pokeSite(id, src, position);
@@ -132,4 +135,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Point_hpp_
+#endif // Hadrons_MSource_Point_hpp_

extras/Hadrons/Modules/MSource/SeqConserved.hpp

@@ -0,0 +1,160 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MSource/SeqConserved.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MSource_SeqConserved_hpp_
+#define Hadrons_MSource_SeqConserved_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/*
+ 
+ Sequential source
+ -----------------------------
+ * src_x = q_x * theta(x_3 - tA) * theta(tB - x_3) * J_mu * exp(i x.mom)
+ 
+ * options:
+ - q: input propagator (string)
+ - action: fermion action used for propagator q (string)
+ - tA: begin timeslice (integer)
+ - tB: end timesilce (integer)
+ - curr_type: type of conserved current to insert (Current)
+ - mu: Lorentz index of current to insert (integer)
+ - mom: momentum insertion, space-separated float sequence (e.g ".1 .2 1. 0.")
+ 
+ */
+
+/******************************************************************************
+ *                              SeqConserved                                  *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MSource)
+
+class SeqConservedPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(SeqConservedPar,
+                                    std::string,  q,
+                                    std::string,  action,
+                                    unsigned int, tA,
+                                    unsigned int, tB,
+                                    Current,      curr_type,
+                                    unsigned int, mu,
+                                    std::string,  mom);
+};
+
+template <typename FImpl>
+class TSeqConserved: public Module<SeqConservedPar>
+{
+public:
+    FERM_TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TSeqConserved(const std::string name);
+    // destructor
+    virtual ~TSeqConserved(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(SeqConserved, TSeqConserved<FIMPL>, MSource);
+
+/******************************************************************************
+ *                      TSeqConserved implementation                          *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TSeqConserved<FImpl>::TSeqConserved(const std::string name)
+: Module<SeqConservedPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TSeqConserved<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().q, par().action};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TSeqConserved<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TSeqConserved<FImpl>::setup(void)
+{
+    auto Ls_ = env().getObjectLs(par().action);
+    envCreateLat(PropagatorField, getName(), Ls_);
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TSeqConserved<FImpl>::execute(void)
+{
+    if (par().tA == par().tB)
+    {
+        LOG(Message) << "Generating sequential source with conserved "
+                     << par().curr_type << " current insertion (mu = " 
+                     << par().mu << ") at " << "t = " << par().tA << std::endl;
+    }
+    else
+    {
+        LOG(Message) << "Generating sequential source with conserved "
+                     << par().curr_type << " current insertion (mu = " 
+                     << par().mu << ") for " << par().tA << " <= t <= " 
+                     << par().tB << std::endl;
+    }
+    auto &src = envGet(PropagatorField, getName());
+    auto &q   = envGet(PropagatorField, par().q);
+    auto &mat = envGet(FMat, par().action);
+
+    std::vector<Real> mom = strToVec<Real>(par().mom);
+    mat.SeqConservedCurrent(q, src, par().curr_type, par().mu, 
+                            mom, par().tA, par().tB);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_SeqConserved_hpp_

extras/Hadrons/Modules/MSource/SeqGamma.hpp

@@ -4,11 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MSource/SeqGamma.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -28,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_SeqGamma_hpp_
-#define Hadrons_SeqGamma_hpp_
+#ifndef Hadrons_MSource_SeqGamma_hpp_
+#define Hadrons_MSource_SeqGamma_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -72,7 +71,7 @@ template <typename FImpl>
 class TSeqGamma: public Module<SeqGammaPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FGS_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TSeqGamma(const std::string name);
@@ -81,10 +80,14 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
     virtual void execute(void);
+private:
+    bool        hasPhase_{false};
+    std::string momphName_, tName_;
 };
 
 MODULE_REGISTER_NS(SeqGamma, TSeqGamma<FIMPL>, MSource);
@@ -96,6 +99,8 @@ MODULE_REGISTER_NS(SeqGamma, TSeqGamma<FIMPL>, MSource);
 template <typename FImpl>
 TSeqGamma<FImpl>::TSeqGamma(const std::string name)
 : Module<SeqGammaPar>(name)
+, momphName_ (name + "_momph")
+, tName_ (name + "_t")
 {}
 
 // dependencies/products ///////////////////////////////////////////////////////
@@ -119,7 +124,10 @@ std::vector<std::string> TSeqGamma<FImpl>::getOutput(void)
 template <typename FImpl>
 void TSeqGamma<FImpl>::setup(void)
 {
-    env().template registerLattice<PropagatorField>(getName());
+    envCreateLat(PropagatorField, getName());
+    envCacheLat(Lattice<iScalar<vInteger>>, tName_);
+    envCacheLat(LatticeComplex, momphName_);
+    envTmpLat(LatticeComplex, "coor");
 }
 
 // execution ///////////////////////////////////////////////////////////////////
@@ -137,23 +145,29 @@ void TSeqGamma<FImpl>::execute(void)
                      << " sequential source for "
                      << par().tA << " <= t <= " << par().tB << std::endl;
     }
-    PropagatorField &src = *env().template createLattice<PropagatorField>(getName());
-    PropagatorField &q   = *env().template getObject<PropagatorField>(par().q);
-    Lattice<iScalar<vInteger>> t(env().getGrid());
-    LatticeComplex             ph(env().getGrid()), coor(env().getGrid());
-    Gamma                      g(par().gamma);
-    std::vector<Real>          p;
-    Complex                    i(0.0,1.0);
+    auto  &src = envGet(PropagatorField, getName());
+    auto  &q   = envGet(PropagatorField, par().q);
+    auto  &ph  = envGet(LatticeComplex, momphName_);
+    auto  &t   = envGet(Lattice<iScalar<vInteger>>, tName_);
+    Gamma g(par().gamma);
     
-    p  = strToVec<Real>(par().mom);
-    ph = zero;
-    for(unsigned int mu = 0; mu < env().getNd(); mu++)
+    if (!hasPhase_)
     {
-        LatticeCoordinate(coor, mu);
-        ph = ph + p[mu]*coor*((1./(env().getGrid()->_fdimensions[mu])));
+        Complex           i(0.0,1.0);
+        std::vector<Real> p;
+
+        envGetTmp(LatticeComplex, coor);
+        p  = strToVec<Real>(par().mom);
+        ph = zero;
+        for(unsigned int mu = 0; mu < env().getNd(); mu++)
+        {
+            LatticeCoordinate(coor, mu);
+            ph = ph + (p[mu]/env().getGrid()->_fdimensions[mu])*coor;
+        }
+        ph = exp((Real)(2*M_PI)*i*ph);
+        LatticeCoordinate(t, Tp);
+        hasPhase_ = true;
     }
-    ph = exp((Real)(2*M_PI)*i*ph);
-    LatticeCoordinate(t, Tp);
     src = where((t >= par().tA) and (t <= par().tB), ph*(g*q), 0.*q);
 }
 
@@ -161,4 +175,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_SeqGamma_hpp_
+#endif // Hadrons_MSource_SeqGamma_hpp_

extras/Hadrons/Modules/MSource/Wall.hpp

@@ -4,9 +4,10 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MSource/Wall.hpp
 
-Copyright (C) 2017
+Copyright (C) 2015-2018
 
-Author: Andrew Lawson <andrew.lawson1991@gmail.com>
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -26,8 +27,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_WallSource_hpp_
-#define Hadrons_WallSource_hpp_
+#ifndef Hadrons_MSource_WallSource_hpp_
+#define Hadrons_MSource_WallSource_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -64,7 +65,7 @@ template <typename FImpl>
 class TWall: public Module<WallPar>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FERM_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TWall(const std::string name);
@@ -73,10 +74,14 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
     virtual void execute(void);
+private:
+    bool        hasPhase_{false};
+    std::string momphName_, tName_;
 };
 
 MODULE_REGISTER_NS(Wall, TWall<FIMPL>, MSource);
@@ -88,13 +93,15 @@ MODULE_REGISTER_NS(Wall, TWall<FIMPL>, MSource);
 template <typename FImpl>
 TWall<FImpl>::TWall(const std::string name)
 : Module<WallPar>(name)
+, momphName_ (name + "_momph")
+, tName_ (name + "_t")
 {}
 
 // dependencies/products ///////////////////////////////////////////////////////
 template <typename FImpl>
 std::vector<std::string> TWall<FImpl>::getInput(void)
 {
-    std::vector<std::string> in;
+    std::vector<std::string> in = {};
     
     return in;
 }
@@ -111,7 +118,7 @@ std::vector<std::string> TWall<FImpl>::getOutput(void)
 template <typename FImpl>
 void TWall<FImpl>::setup(void)
 {
-    env().template registerLattice<PropagatorField>(getName());
+    envCreateLat(PropagatorField, getName());
 }
 
 // execution ///////////////////////////////////////////////////////////////////
@@ -121,21 +128,28 @@ void TWall<FImpl>::execute(void)
     LOG(Message) << "Generating wall source at t = " << par().tW 
                  << " with momentum " << par().mom << std::endl;
     
-    PropagatorField &src = *env().template createLattice<PropagatorField>(getName());
-    Lattice<iScalar<vInteger>> t(env().getGrid());
-    LatticeComplex             ph(env().getGrid()), coor(env().getGrid());
-    std::vector<Real>          p;
-    Complex                    i(0.0,1.0);
+    auto  &src = envGet(PropagatorField, getName());
+    auto  &ph  = envGet(LatticeComplex, momphName_);
+    auto  &t   = envGet(Lattice<iScalar<vInteger>>, tName_);
     
-    p  = strToVec<Real>(par().mom);
-    ph = zero;
-    for(unsigned int mu = 0; mu < Nd; mu++)
+    if (!hasPhase_)
     {
-        LatticeCoordinate(coor, mu);
-        ph = ph + p[mu]*coor*((1./(env().getGrid()->_fdimensions[mu])));
+        Complex           i(0.0,1.0);
+        std::vector<Real> p;
+
+        envGetTmp(LatticeComplex, coor);
+        p  = strToVec<Real>(par().mom);
+        ph = zero;
+        for(unsigned int mu = 0; mu < env().getNd(); mu++)
+        {
+            LatticeCoordinate(coor, mu);
+            ph = ph + (p[mu]/env().getGrid()->_fdimensions[mu])*coor;
+        }
+        ph = exp((Real)(2*M_PI)*i*ph);
+        LatticeCoordinate(t, Tp);
+        hasPhase_ = true;
     }
-    ph = exp((Real)(2*M_PI)*i*ph);
-    LatticeCoordinate(t, Tp);
+
     src = 1.;
     src = where((t == par().tW), src*ph, 0.*src);
 }
@@ -144,4 +158,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_WallSource_hpp_
+#endif // Hadrons_MSource_WallSource_hpp_

extras/Hadrons/Modules/MSource/Z2.hpp

@@ -4,8 +4,7 @@ Grid physics library, www.github.com/paboyle/Grid
 
 Source file: extras/Hadrons/Modules/MSource/Z2.hpp
 
-Copyright (C) 2015
-Copyright (C) 2016
+Copyright (C) 2015-2018
 
 Author: Antonin Portelli <antonin.portelli@me.com>
 
@@ -27,8 +26,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
 *************************************************************************************/
 /*  END LEGAL */
 
-#ifndef Hadrons_Z2_hpp_
-#define Hadrons_Z2_hpp_
+#ifndef Hadrons_MSource_Z2_hpp_
+#define Hadrons_MSource_Z2_hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -67,7 +66,7 @@ template <typename FImpl>
 class TZ2: public Module<Z2Par>
 {
 public:
-    TYPE_ALIASES(FImpl,);
+    FERM_TYPE_ALIASES(FImpl,);
 public:
     // constructor
     TZ2(const std::string name);
@@ -76,13 +75,18 @@ public:
     // dependency relation
     virtual std::vector<std::string> getInput(void);
     virtual std::vector<std::string> getOutput(void);
+protected:
     // setup
     virtual void setup(void);
     // execution
     virtual void execute(void);
+private:
+    bool        hasT_{false};
+    std::string tName_;
 };
 
-MODULE_REGISTER_NS(Z2, TZ2<FIMPL>, MSource);
+MODULE_REGISTER_NS(Z2,       TZ2<FIMPL>,        MSource);
+MODULE_REGISTER_NS(ScalarZ2, TZ2<ScalarImplCR>, MSource);
 
 /******************************************************************************
  *                       TZ2 template implementation                          *
@@ -91,6 +95,7 @@ MODULE_REGISTER_NS(Z2, TZ2<FIMPL>, MSource);
 template <typename FImpl>
 TZ2<FImpl>::TZ2(const std::string name)
 : Module<Z2Par>(name)
+, tName_ (name + "_t")
 {}
 
 // dependencies/products ///////////////////////////////////////////////////////
@@ -114,29 +119,36 @@ std::vector<std::string> TZ2<FImpl>::getOutput(void)
 template <typename FImpl>
 void TZ2<FImpl>::setup(void)
 {
-    env().template registerLattice<PropagatorField>(getName());
+    envCreateLat(PropagatorField, getName());
+    envCacheLat(Lattice<iScalar<vInteger>>, tName_);
+    envTmpLat(LatticeComplex, "eta");
 }
 
 // execution ///////////////////////////////////////////////////////////////////
 template <typename FImpl>
 void TZ2<FImpl>::execute(void)
 {
-    Lattice<iScalar<vInteger>> t(env().getGrid());
-    LatticeComplex             eta(env().getGrid());
-    Complex                    shift(1., 1.);
-    
     if (par().tA == par().tB)
     {
         LOG(Message) << "Generating Z_2 wall source at t= " << par().tA
-        << std::endl;
+                     << std::endl;
     }
     else
     {
         LOG(Message) << "Generating Z_2 band for " << par().tA << " <= t <= "
-        << par().tB << std::endl;
+                     << par().tB << std::endl;
     }
-    PropagatorField &src = *env().template createLattice<PropagatorField>(getName());
-    LatticeCoordinate(t, Tp);
+    
+    auto    &src = envGet(PropagatorField, getName());
+    auto    &t   = envGet(Lattice<iScalar<vInteger>>, tName_);
+    Complex shift(1., 1.);
+
+    if (!hasT_)
+    {
+        LatticeCoordinate(t, Tp);
+        hasT_ = true;
+    }
+    envGetTmp(LatticeComplex, eta);
     bernoulli(*env().get4dRng(), eta);
     eta = (2.*eta - shift)*(1./::sqrt(2.));
     eta = where((t >= par().tA) and (t <= par().tB), eta, 0.*eta);
@@ -148,4 +160,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons_Z2_hpp_
+#endif // Hadrons_MSource_Z2_hpp_

extras/Hadrons/Modules/MUtilities/TestSeqConserved.hpp

@@ -0,0 +1,186 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MUtilities/TestSeqConserved.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MUtilities_TestSeqConserved_hpp_
+#define Hadrons_MUtilities_TestSeqConserved_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/*
+  Ward Identity contractions using sequential propagators.
+ -----------------------------
+ 
+ * options:
+ - q:      point source propagator, 5D if available (string)
+ - qSeq:   result of sequential insertion of conserved current using q (string)
+ - action: action used for computation of q (string)
+ - origin: string giving point source origin of q (string)
+ - t_J:    time at which sequential current is inserted (int)
+ - mu:     Lorentz index of current inserted (int)
+ - curr:   current type, e.g. vector/axial (Current)
+*/
+
+/******************************************************************************
+ *                            TestSeqConserved                                *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MUtilities)
+
+class TestSeqConservedPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(TestSeqConservedPar,
+                                    std::string,  q,
+                                    std::string,  qSeq,
+                                    std::string,  action,
+                                    std::string,  origin,
+                                    unsigned int, t_J,
+                                    unsigned int, mu,
+                                    Current,      curr);
+};
+
+template <typename FImpl>
+class TTestSeqConserved: public Module<TestSeqConservedPar>
+{
+public:
+    FERM_TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TTestSeqConserved(const std::string name);
+    // destructor
+    virtual ~TTestSeqConserved(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(TestSeqConserved, TTestSeqConserved<FIMPL>, MUtilities);
+
+/******************************************************************************
+ *                     TTestSeqConserved implementation                       *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TTestSeqConserved<FImpl>::TTestSeqConserved(const std::string name)
+: Module<TestSeqConservedPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TTestSeqConserved<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().q, par().qSeq, par().action};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TTestSeqConserved<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TTestSeqConserved<FImpl>::setup(void)
+{
+    auto Ls = env().getObjectLs(par().q);
+    if (Ls != env().getObjectLs(par().action))
+    {
+        HADRON_ERROR(Size, "Ls mismatch between quark action and propagator");
+    }
+    envTmpLat(PropagatorField, "tmp");
+    envTmpLat(LatticeComplex, "c");
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TTestSeqConserved<FImpl>::execute(void)
+{
+    // Check sequential insertion of current gives same result as conserved 
+    // current sink upon contraction. Assume q uses a point source.
+
+    auto                  &q    = envGet(PropagatorField, par().q);
+    auto                  &qSeq = envGet(PropagatorField, par().qSeq);
+    auto                  &act  = envGet(FMat, par().action);
+    Gamma                 g5(Gamma::Algebra::Gamma5);
+    Gamma::Algebra        gA = (par().curr == Current::Axial) ?
+                                  Gamma::Algebra::Gamma5 :
+                                  Gamma::Algebra::Identity;
+    Gamma                 g(gA);
+    SitePropagator        qSite;
+    Complex               test_S, test_V, check_S, check_V;
+    std::vector<TComplex> check_buf;
+    std::vector<int>      siteCoord;
+
+    envGetTmp(PropagatorField, tmp);
+    envGetTmp(LatticeComplex, c);
+    siteCoord = strToVec<int>(par().origin);
+    peekSite(qSite, qSeq, siteCoord);
+    test_S = trace(qSite*g);
+    test_V = trace(qSite*g*Gamma::gmu[par().mu]);
+    act.ContractConservedCurrent(q, q, tmp, par().curr, par().mu);
+    c = trace(tmp*g);
+    sliceSum(c, check_buf, Tp);
+    check_S = TensorRemove(check_buf[par().t_J]);
+
+    c = trace(tmp*g*Gamma::gmu[par().mu]);
+    sliceSum(c, check_buf, Tp);
+    check_V = TensorRemove(check_buf[par().t_J]);
+
+    LOG(Message) << "Test S  = " << abs(test_S)   << std::endl;
+    LOG(Message) << "Test V  = " << abs(test_V) << std::endl;
+    LOG(Message) << "Check S = " << abs(check_S) << std::endl;
+    LOG(Message) << "Check V = " << abs(check_V) << std::endl;
+
+    // Check difference = 0
+    check_S -= test_S;
+    check_V -= test_V;
+
+    LOG(Message) << "Consistency check for sequential conserved " 
+                 << par().curr << " current insertion: " << std::endl; 
+    LOG(Message) << "Diff S  = " << abs(check_S) << std::endl;
+    LOG(Message) << "Diff V  = " << abs(check_V) << std::endl;
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_TestSeqConserved_hpp_

extras/Hadrons/Modules/MUtilities/TestSeqGamma.hpp

@@ -0,0 +1,150 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MUtilities/TestSeqGamma.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Lanny91 <andrew.lawson@gmail.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_MUtilities_TestSeqGamma_hpp_
+#define Hadrons_MUtilities_TestSeqGamma_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                              TestSeqGamma                                  *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MUtilities)
+
+class TestSeqGammaPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(TestSeqGammaPar,
+                                    std::string,    q,
+                                    std::string,    qSeq,
+                                    std::string,    origin,
+                                    Gamma::Algebra, gamma,
+                                    unsigned int,   t_g);
+};
+
+template <typename FImpl>
+class TTestSeqGamma: public Module<TestSeqGammaPar>
+{
+public:
+    FERM_TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TTestSeqGamma(const std::string name);
+    // destructor
+    virtual ~TTestSeqGamma(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+protected:
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(TestSeqGamma, TTestSeqGamma<FIMPL>, MUtilities);
+
+/******************************************************************************
+ *                      TTestSeqGamma implementation                          *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TTestSeqGamma<FImpl>::TTestSeqGamma(const std::string name)
+: Module<TestSeqGammaPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TTestSeqGamma<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().q, par().qSeq};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TTestSeqGamma<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TTestSeqGamma<FImpl>::setup(void)
+{
+    envTmpLat(LatticeComplex, "c");
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TTestSeqGamma<FImpl>::execute(void)
+{
+    auto                  &q    = envGet(PropagatorField, par().q);
+    auto                  &qSeq = envGet(PropagatorField, par().qSeq);
+    Gamma                 g5(Gamma::Algebra::Gamma5);
+    Gamma                 g(par().gamma);
+    SitePropagator        qSite;
+    Complex               test, check;
+    std::vector<TComplex> check_buf;
+    std::vector<int>      siteCoord;
+
+    // Check sequential insertion of gamma matrix gives same result as 
+    // insertion of gamma at sink upon contraction. Assume q uses a point 
+    // source.
+    
+    envGetTmp(LatticeComplex, c);
+    siteCoord = strToVec<int>(par().origin);
+    peekSite(qSite, qSeq, siteCoord);
+    test = trace(g*qSite);
+
+    c = trace(adj(g)*g5*adj(q)*g5*g*q);
+    sliceSum(c, check_buf, Tp);
+    check = TensorRemove(check_buf[par().t_g]);
+
+    LOG(Message) << "Seq Result = " << abs(test)  << std::endl;
+    LOG(Message) << "Reference  = " << abs(check) << std::endl;
+
+    // Check difference = 0
+    check -= test;
+
+    LOG(Message) << "Consistency check for sequential " << par().gamma  
+                 << " insertion = " << abs(check) << std::endl;
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_TestSeqGamma_hpp_

extras/Hadrons/Modules/templates/Module_in_NS.hpp.template

@@ -1,5 +1,5 @@
-#ifndef Hadrons____FILEBASENAME____hpp_
-#define Hadrons____FILEBASENAME____hpp_
+#ifndef Hadrons____NAMESPACE_______FILEBASENAME____hpp_
+#define Hadrons____NAMESPACE_______FILEBASENAME____hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -41,4 +41,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons____FILEBASENAME____hpp_
+#endif // Hadrons____NAMESPACE_______FILEBASENAME____hpp_

extras/Hadrons/Modules/templates/Module_tmp_in_NS.hpp.template

@@ -1,5 +1,5 @@
-#ifndef Hadrons____FILEBASENAME____hpp_
-#define Hadrons____FILEBASENAME____hpp_
+#ifndef Hadrons____NAMESPACE_______FILEBASENAME____hpp_
+#define Hadrons____NAMESPACE_______FILEBASENAME____hpp_
 
 #include <Grid/Hadrons/Global.hpp>
 #include <Grid/Hadrons/Module.hpp>
@@ -82,4 +82,4 @@ END_MODULE_NAMESPACE
 
 END_HADRONS_NAMESPACE
 
-#endif // Hadrons____FILEBASENAME____hpp_
+#endif // Hadrons____NAMESPACE_______FILEBASENAME____hpp_

extras/Hadrons/VirtualMachine.cc

@@ -0,0 +1,622 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/VirtualMachine.cc
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/VirtualMachine.hpp>
+#include <Grid/Hadrons/GeneticScheduler.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace Hadrons;
+
+/******************************************************************************
+ *                      VirtualMachine implementation                         *
+ ******************************************************************************/
+// trajectory counter //////////////////////////////////////////////////////////
+void VirtualMachine::setTrajectory(const unsigned int traj)
+{
+    traj_ = traj;
+}
+
+unsigned int VirtualMachine::getTrajectory(void) const
+{
+    return traj_;
+}
+
+// module management ///////////////////////////////////////////////////////////
+void VirtualMachine::pushModule(VirtualMachine::ModPt &pt)
+{
+    std::string name = pt->getName();
+    
+    if (!hasModule(name))
+    {
+        std::vector<unsigned int> inputAddress;
+        unsigned int              address;
+        ModuleInfo                m;
+        
+        // module registration -------------------------------------------------
+        m.data = std::move(pt);
+        m.type = typeIdPt(*m.data.get());
+        m.name = name;
+        // input dependencies
+        for (auto &in: m.data->getInput())
+        {
+            if (!env().hasObject(in))
+            {
+                // if object does not exist, add it with no creator module
+                env().addObject(in , -1);
+            }
+            m.input.push_back(env().getObjectAddress(in));
+        }
+        // reference dependencies
+        for (auto &ref: m.data->getReference())
+        {
+            if (!env().hasObject(ref))
+            {
+                // if object does not exist, add it with no creator module
+                env().addObject(ref , -1);
+            }
+            m.input.push_back(env().getObjectAddress(ref));
+        }
+        auto inCopy = m.input;
+        // if module has inputs with references, they need to be added as
+        // an input
+        for (auto &in: inCopy)
+        {
+            int inm = env().getObjectModule(in);
+
+            if (inm > 0)
+            {
+                if (getModule(inm)->getReference().size() > 0)
+                {
+                    for (auto &rin: getModule(inm)->getReference())
+                    {
+                        m.input.push_back(env().getObjectAddress(rin));
+                    }
+                }
+            }
+        }
+        module_.push_back(std::move(m));
+        address              = static_cast<unsigned int>(module_.size() - 1);
+        moduleAddress_[name] = address;
+        // connecting outputs to potential inputs ------------------------------
+        for (auto &out: getModule(address)->getOutput())
+        {
+            if (!env().hasObject(out))
+            {
+                // output does not exists, add it
+                env().addObject(out, address);
+            }
+            else
+            {
+                if (env().getObjectModule(env().getObjectAddress(out)) < 0)
+                {
+                    // output exists but without creator, correct it
+                    env().setObjectModule(env().getObjectAddress(out), address);
+                }
+                else
+                {
+                    // output already fully registered, error
+                    HADRON_ERROR(Definition, "object '" + out
+                                 + "' is already produced by module '"
+                                 + module_[env().getObjectModule(out)].name
+                                 + "' (while pushing module '" + name + "')");
+                }
+                if (getModule(address)->getReference().size() > 0)
+                {
+                    // module has references, dependency should be propagated
+                    // to children modules; find module with `out` as an input
+                    // and add references to their input
+                    auto pred = [this, out](const ModuleInfo &n)
+                    {
+                        auto &in = n.input;
+                        auto it  = std::find(in.begin(), in.end(), 
+                                             env().getObjectAddress(out));
+                        
+                        return (it != in.end());
+                    };
+                    auto it = std::find_if(module_.begin(), module_.end(), pred);
+                    while (it != module_.end())
+                    {
+                        for (auto &ref: getModule(address)->getReference())
+                        {
+                            it->input.push_back(env().getObjectAddress(ref));
+                        }
+                        it = std::find_if(++it, module_.end(), pred);
+                    }   
+                }
+            }
+        }
+        graphOutdated_         = true;
+        memoryProfileOutdated_ = true;
+    }
+    else
+    {
+        HADRON_ERROR(Definition, "module '" + name + "' already exists");
+    }
+}
+
+unsigned int VirtualMachine::getNModule(void) const
+{
+    return module_.size();
+}
+
+void VirtualMachine::createModule(const std::string name, const std::string type,
+                                  XmlReader &reader)
+{
+    auto &factory = ModuleFactory::getInstance();
+    auto pt       = factory.create(type, name);
+    
+    pt->parseParameters(reader, "options");
+    pushModule(pt);
+}
+
+ModuleBase * VirtualMachine::getModule(const unsigned int address) const
+{
+    if (hasModule(address))
+    {
+        return module_[address].data.get();
+    }
+    else
+    {
+        HADRON_ERROR(Definition, "no module with address " + std::to_string(address));
+    }
+}
+
+ModuleBase * VirtualMachine::getModule(const std::string name) const
+{
+    return getModule(getModuleAddress(name));
+}
+
+unsigned int VirtualMachine::getModuleAddress(const std::string name) const
+{
+    if (hasModule(name))
+    {
+        return moduleAddress_.at(name);
+    }
+    else
+    {
+        HADRON_ERROR(Definition, "no module with name '" + name + "'");
+    }
+}
+
+std::string VirtualMachine::getModuleName(const unsigned int address) const
+{
+    if (hasModule(address))
+    {
+        return module_[address].name;
+    }
+    else
+    {
+        HADRON_ERROR(Definition, "no module with address " + std::to_string(address));
+    }
+}
+
+std::string VirtualMachine::getModuleType(const unsigned int address) const
+{
+    if (hasModule(address))
+    {
+        return typeName(module_[address].type);
+    }
+    else
+    {
+        HADRON_ERROR(Definition, "no module with address " + std::to_string(address));
+    }
+}
+
+std::string VirtualMachine::getModuleType(const std::string name) const
+{
+    return getModuleType(getModuleAddress(name));
+}
+
+std::string VirtualMachine::getModuleNamespace(const unsigned int address) const
+{
+    std::string type = getModuleType(address), ns;
+    
+    auto pos2 = type.rfind("::");
+    auto pos1 = type.rfind("::", pos2 - 2);
+    
+    return type.substr(pos1 + 2, pos2 - pos1 - 2);
+}
+
+std::string VirtualMachine::getModuleNamespace(const std::string name) const
+{
+    return getModuleNamespace(getModuleAddress(name));
+}
+
+bool VirtualMachine::hasModule(const unsigned int address) const
+{
+    return (address < module_.size());
+}
+
+bool VirtualMachine::hasModule(const std::string name) const
+{
+    return (moduleAddress_.find(name) != moduleAddress_.end());
+}
+
+// print VM content ////////////////////////////////////////////////////////////
+void VirtualMachine::printContent(void) const
+{
+    LOG(Debug) << "Modules: " << std::endl;
+    for (unsigned int i = 0; i < module_.size(); ++i)
+    {
+        LOG(Debug) << std::setw(4) << i << ": "
+                   << getModuleName(i) << std::endl;
+    }
+}
+
+// module graph ////////////////////////////////////////////////////////////////
+Graph<unsigned int> VirtualMachine::getModuleGraph(void)
+{
+    if (graphOutdated_)
+    {
+        makeModuleGraph();
+        graphOutdated_ = false;
+    }
+
+    return graph_;
+}
+
+void VirtualMachine::makeModuleGraph(void)
+{
+    Graph<unsigned int> graph;
+    
+    // create vertices
+    for (unsigned int m = 0; m < module_.size(); ++m)
+    {
+        graph.addVertex(m);
+    }
+    // create edges
+    for (unsigned int m = 0; m < module_.size(); ++m)
+    {
+        for (auto &in: module_[m].input)
+        {
+            graph.addEdge(env().getObjectModule(in), m);
+        }
+    }
+    graph_ = graph;
+}
+
+// memory profile //////////////////////////////////////////////////////////////
+const VirtualMachine::MemoryProfile & VirtualMachine::getMemoryProfile(void)
+{
+    if (memoryProfileOutdated_)
+    {
+        makeMemoryProfile();
+        memoryProfileOutdated_ = false;
+    }
+
+    return profile_;
+}
+
+void VirtualMachine::makeMemoryProfile(void)
+{
+    bool protect = env().objectsProtected();
+    bool hmsg    = HadronsLogMessage.isActive();
+    bool gmsg    = GridLogMessage.isActive();
+    bool err     = HadronsLogError.isActive();
+    auto program = getModuleGraph().topoSort();
+
+    resetProfile();
+    profile_.module.resize(getNModule());
+    env().protectObjects(false);
+    GridLogMessage.Active(false);
+    HadronsLogMessage.Active(false);
+    HadronsLogError.Active(false);
+    for (auto it = program.rbegin(); it != program.rend(); ++it) 
+    {
+        auto a = *it;
+
+        if (profile_.module[a].empty())
+        {
+            LOG(Debug) << "Profiling memory for module '" << module_[a].name
+                       << "' (" << a << ")..." << std::endl;
+            memoryProfile(a);
+            env().freeAll();
+        }
+    }
+    env().protectObjects(protect);
+    GridLogMessage.Active(gmsg);
+    HadronsLogMessage.Active(hmsg);
+    HadronsLogError.Active(err);
+    LOG(Debug) << "Memory profile:" << std::endl;
+    LOG(Debug) << "----------------" << std::endl;
+    for (unsigned int a = 0; a < profile_.module.size(); ++a)
+    {
+        LOG(Debug) << getModuleName(a) << " (" << a << ")" << std::endl;
+        for (auto &o: profile_.module[a])
+        {
+            LOG(Debug) << "|__ " << env().getObjectName(o.first) << " ("
+                       << sizeString(o.second) << ")" << std::endl;
+        }
+        LOG(Debug) << std::endl;
+    }
+    LOG(Debug) << "----------------" << std::endl;
+}
+
+void VirtualMachine::resetProfile(void)
+{
+    profile_.module.clear();
+    profile_.object.clear();
+}
+
+void VirtualMachine::resizeProfile(void)
+{
+    if (env().getMaxAddress() > profile_.object.size())
+    {
+        MemoryPrint empty;
+
+        empty.size   = 0;
+        empty.module = -1;
+        profile_.object.resize(env().getMaxAddress(), empty);
+    }
+}
+
+void VirtualMachine::updateProfile(const unsigned int address)
+{
+    resizeProfile();
+    for (unsigned int a = 0; a < env().getMaxAddress(); ++a)
+    {
+        if (env().hasCreatedObject(a) and (profile_.object[a].module == -1))
+        {
+            profile_.object[a].size     = env().getObjectSize(a);
+            profile_.object[a].storage  = env().getObjectStorage(a);
+            profile_.object[a].module   = address;
+            profile_.module[address][a] = profile_.object[a].size;
+            if (env().getObjectModule(a) < 0)
+            {
+                env().setObjectModule(a, address);
+            }
+        }
+    }
+}
+
+void VirtualMachine::cleanEnvironment(void)
+{
+    resizeProfile();
+    for (unsigned int a = 0; a < env().getMaxAddress(); ++a)
+    {
+        if (env().hasCreatedObject(a) and (profile_.object[a].module == -1))
+        {
+            env().freeObject(a);
+        }
+    }
+}
+
+void VirtualMachine::memoryProfile(const unsigned int address)
+{
+    auto m = getModule(address);
+
+    LOG(Debug) << "Setting up module '" << m->getName() 
+               << "' (" << address << ")..." << std::endl;
+    try
+    {
+        m->setup();
+        updateProfile(address);
+    }
+    catch (Exceptions::Definition &)
+    {
+        cleanEnvironment();
+        for (auto &in: m->getInput())
+        {
+            memoryProfile(env().getObjectModule(in));
+        }
+        for (auto &ref: m->getReference())
+        {
+            memoryProfile(env().getObjectModule(ref));
+        }
+        m->setup();
+        updateProfile(address);
+    }
+}
+
+void VirtualMachine::memoryProfile(const std::string name)
+{
+    memoryProfile(getModuleAddress(name));
+}
+
+// garbage collector ///////////////////////////////////////////////////////////
+VirtualMachine::GarbageSchedule 
+VirtualMachine::makeGarbageSchedule(const Program &p) const
+{
+    GarbageSchedule freeProg;
+    
+    freeProg.resize(p.size());
+    for (unsigned int a = 0; a < env().getMaxAddress(); ++a)
+    {
+        if (env().getObjectStorage(a) == Environment::Storage::temporary)
+        {
+            auto it = std::find(p.begin(), p.end(), env().getObjectModule(a));
+
+            if (it != p.end())
+            {
+                freeProg[std::distance(p.begin(), it)].insert(a);
+            }
+        }
+        else if (env().getObjectStorage(a) == Environment::Storage::object)
+        {
+            auto pred = [a, this](const unsigned int b)
+            {
+                auto &in = module_[b].input;
+                auto it  = std::find(in.begin(), in.end(), a);
+                
+                return (it != in.end()) or (b == env().getObjectModule(a));
+            };
+            auto it = std::find_if(p.rbegin(), p.rend(), pred);
+            if (it != p.rend())
+            {
+                freeProg[std::distance(it, p.rend()) - 1].insert(a);
+            }
+        }
+    }
+
+    return freeProg;
+}
+
+// high-water memory function //////////////////////////////////////////////////
+VirtualMachine::Size VirtualMachine::memoryNeeded(const Program &p)
+{
+    const MemoryProfile &profile = getMemoryProfile();
+    GarbageSchedule     freep    = makeGarbageSchedule(p);
+    Size                current = 0, max = 0;
+
+    for (unsigned int i = 0; i < p.size(); ++i)
+    {
+        for (auto &o: profile.module[p[i]])
+        {
+            current += o.second;
+        }
+        max = std::max(current, max);
+        for (auto &o: freep[i])
+        {
+            current -= profile.object[o].size;
+        }
+    }
+
+    return max;
+}
+
+// genetic scheduler ///////////////////////////////////////////////////////////
+VirtualMachine::Program VirtualMachine::schedule(const GeneticPar &par)
+{
+    typedef GeneticScheduler<Size, unsigned int> Scheduler;
+
+    auto graph = getModuleGraph();
+
+    //constrained topological sort using a genetic algorithm
+    LOG(Message) << "Scheduling computation..." << std::endl;
+    LOG(Message) << "               #module= " << graph.size() << std::endl;
+    LOG(Message) << "       population size= " << par.popSize << std::endl;
+    LOG(Message) << "       max. generation= " << par.maxGen << std::endl;
+    LOG(Message) << "  max. cst. generation= " << par.maxCstGen << std::endl;
+    LOG(Message) << "         mutation rate= " << par.mutationRate << std::endl;
+    
+    unsigned int          k = 0, gen, prevPeak, nCstPeak = 0;
+    std::random_device    rd;
+    Scheduler::Parameters gpar;
+    
+    gpar.popSize      = par.popSize;
+    gpar.mutationRate = par.mutationRate;
+    gpar.seed         = rd();
+    CartesianCommunicator::BroadcastWorld(0, &(gpar.seed), sizeof(gpar.seed));
+    Scheduler::ObjFunc memPeak = [this](const Program &p)->Size
+    {
+        return memoryNeeded(p);
+    };
+    Scheduler scheduler(graph, memPeak, gpar);
+    gen = 0;
+    do
+    {
+        LOG(Debug) << "Generation " << gen << ":" << std::endl;
+        scheduler.nextGeneration();
+        if (gen != 0)
+        {
+            if (prevPeak == scheduler.getMinValue())
+            {
+                nCstPeak++;
+            }
+            else
+            {
+                nCstPeak = 0;
+            }
+        }
+        
+        prevPeak = scheduler.getMinValue();
+        if (gen % 10 == 0)
+        {
+            LOG(Iterative) << "Generation " << gen << ": "
+                           << sizeString(scheduler.getMinValue()) << std::endl;
+        }
+        
+        gen++;
+    } while ((gen < par.maxGen) and (nCstPeak < par.maxCstGen));
+    
+    return scheduler.getMinSchedule();
+}
+
+// general execution ///////////////////////////////////////////////////////////
+#define BIG_SEP "==============="
+#define SEP     "---------------"
+#define MEM_MSG(size) sizeString(size)
+
+void VirtualMachine::executeProgram(const Program &p) const
+{
+    Size            memPeak = 0, sizeBefore, sizeAfter;
+    GarbageSchedule freeProg;
+    
+    // build garbage collection schedule
+    LOG(Debug) << "Building garbage collection schedule..." << std::endl;
+    freeProg = makeGarbageSchedule(p);
+
+    // program execution
+    LOG(Debug) << "Executing program..." << std::endl;
+    for (unsigned int i = 0; i < p.size(); ++i)
+    {
+        // execute module
+        LOG(Message) << SEP << " Measurement step " << i + 1 << "/"
+                     << p.size() << " (module '" << module_[p[i]].name
+                     << "') " << SEP << std::endl;
+        (*module_[p[i]].data)();
+        sizeBefore = env().getTotalSize();
+        // print used memory after execution
+        LOG(Message) << "Allocated objects: " << MEM_MSG(sizeBefore)
+                     << std::endl;
+        if (sizeBefore > memPeak)
+        {
+            memPeak = sizeBefore;
+        }
+        // garbage collection for step i
+        LOG(Message) << "Garbage collection..." << std::endl;
+        for (auto &j: freeProg[i])
+        {
+            env().freeObject(j);
+        }
+        // print used memory after garbage collection if necessary
+        sizeAfter = env().getTotalSize();
+        if (sizeBefore != sizeAfter)
+        {
+            LOG(Message) << "Allocated objects: " << MEM_MSG(sizeAfter)
+                            << std::endl;
+        }
+        else
+        {
+            LOG(Message) << "Nothing to free" << std::endl;
+        }
+    }
+}
+
+void VirtualMachine::executeProgram(const std::vector<std::string> &p) const
+{
+    Program pAddress;
+    
+    for (auto &n: p)
+    {
+        pAddress.push_back(getModuleAddress(n));
+    }
+    executeProgram(pAddress);
+}

extras/Hadrons/VirtualMachine.hpp

@@ -0,0 +1,207 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/VirtualMachine.hpp
+
+Copyright (C) 2015-2018
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_VirtualMachine_hpp_
+#define Hadrons_VirtualMachine_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Graph.hpp>
+#include <Grid/Hadrons/Environment.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+#define DEFINE_VM_ALIAS \
+inline VirtualMachine & vm(void) const\
+{\
+    return VirtualMachine::getInstance();\
+}
+
+/******************************************************************************
+ *                   Virtual machine for module execution                     *
+ ******************************************************************************/
+// forward declaration of Module
+class ModuleBase;
+
+class VirtualMachine
+{
+    SINGLETON_DEFCTOR(VirtualMachine);
+public:
+    typedef SITE_SIZE_TYPE                      Size;
+    typedef std::unique_ptr<ModuleBase>         ModPt;
+    typedef std::vector<std::set<unsigned int>> GarbageSchedule;
+    typedef std::vector<unsigned int>           Program;
+    struct MemoryPrint
+    {
+        Size                 size;
+        Environment::Storage storage;
+        int                  module;
+    };
+    struct MemoryProfile
+    {
+        std::vector<std::map<unsigned int, Size>> module;
+        std::vector<MemoryPrint>                  object;
+    };
+    class GeneticPar: Serializable
+    {
+    public:
+        GeneticPar(void):
+            popSize{20}, maxGen{1000}, maxCstGen{100}, mutationRate{.1} {};
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(GeneticPar,
+                                        unsigned int, popSize,
+                                        unsigned int, maxGen,
+                                        unsigned int, maxCstGen,
+                                        double      , mutationRate);
+    };
+private:
+    struct ModuleInfo
+    {
+        const std::type_info      *type{nullptr};
+        std::string               name;
+        ModPt                     data{nullptr};
+        std::vector<unsigned int> input;
+        size_t                    maxAllocated;
+    };
+public:
+    // trajectory counter
+    void                setTrajectory(const unsigned int traj);
+    unsigned int        getTrajectory(void) const;
+    // module management
+    void                pushModule(ModPt &pt);
+    template <typename M>
+    void                createModule(const std::string name);
+    template <typename M>
+    void                createModule(const std::string name,
+                                         const typename M::Par &par);
+    void                createModule(const std::string name,
+                                         const std::string type,
+                                         XmlReader &reader);
+    unsigned int        getNModule(void) const;
+    ModuleBase *        getModule(const unsigned int address) const;
+    ModuleBase *        getModule(const std::string name) const;
+    template <typename M>
+    M *                 getModule(const unsigned int address) const;
+    template <typename M>
+    M *                 getModule(const std::string name) const;
+    unsigned int        getModuleAddress(const std::string name) const;
+    std::string         getModuleName(const unsigned int address) const;
+    std::string         getModuleType(const unsigned int address) const;
+    std::string         getModuleType(const std::string name) const;
+    std::string         getModuleNamespace(const unsigned int address) const;
+    std::string         getModuleNamespace(const std::string name) const;
+    bool                hasModule(const unsigned int address) const;
+    bool                hasModule(const std::string name) const;
+    // print VM content
+    void                printContent(void) const;
+    // module graph (could be a const reference if topoSort was const)
+    Graph<unsigned int> getModuleGraph(void);
+    // memory profile
+    const MemoryProfile &getMemoryProfile(void);
+    // garbage collector
+    GarbageSchedule     makeGarbageSchedule(const Program &p) const;
+    // high-water memory function
+    Size                memoryNeeded(const Program &p);
+    // genetic scheduler
+    Program             schedule(const GeneticPar &par);
+    // general execution
+    void                executeProgram(const Program &p) const;
+    void                executeProgram(const std::vector<std::string> &p) const;
+private:
+    // environment shortcut
+    DEFINE_ENV_ALIAS;
+    // module graph
+    void makeModuleGraph(void);
+    // memory profile
+    void makeMemoryProfile(void);
+    void resetProfile(void);
+    void resizeProfile(void);
+    void updateProfile(const unsigned int address);
+    void cleanEnvironment(void);
+    void memoryProfile(const std::string name);
+    void memoryProfile(const unsigned int address);
+private:
+    // general
+    unsigned int                        traj_;
+    // module and related maps
+    std::vector<ModuleInfo>             module_;
+    std::map<std::string, unsigned int> moduleAddress_;
+    std::string                         currentModule_{""};
+    // module graph
+    bool                                graphOutdated_{true};
+    Graph<unsigned int>                 graph_;
+    // memory profile
+    bool                                memoryProfileOutdated_{true};
+    MemoryProfile                       profile_;
+};
+
+/******************************************************************************
+ *                   VirtualMachine template implementation                   *
+ ******************************************************************************/
+// module management ///////////////////////////////////////////////////////////
+template <typename M>
+void VirtualMachine::createModule(const std::string name)
+{
+    ModPt pt(new M(name));
+    
+    pushModule(pt);
+}
+
+template <typename M>
+void VirtualMachine::createModule(const std::string name,
+                               const typename M::Par &par)
+{
+    ModPt pt(new M(name));
+    
+    static_cast<M *>(pt.get())->setPar(par);
+    pushModule(pt);
+}
+
+template <typename M>
+M * VirtualMachine::getModule(const unsigned int address) const
+{
+    if (auto *pt = dynamic_cast<M *>(getModule(address)))
+    {
+        return pt;
+    }
+    else
+    {
+        HADRON_ERROR(Definition, "module '" + module_[address].name
+                     + "' does not have type " + typeid(M).name()
+                     + "(has type: " + getModuleType(address) + ")");
+    }
+}
+
+template <typename M>
+M * VirtualMachine::getModule(const std::string name) const
+{
+    return getModule<M>(getModuleAddress(name));
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_VirtualMachine_hpp_

extras/Hadrons/modules.inc

@@ -1,30 +1,52 @@
 modules_cc =\
+  Modules/MScalar/ChargedProp.cc \
+  Modules/MScalar/FreeProp.cc \
   Modules/MContraction/WeakHamiltonianEye.cc \
-  Modules/MContraction/WeakHamiltonianNonEye.cc \
   Modules/MContraction/WeakNeutral4ptDisc.cc \
-  Modules/MGauge/Load.cc \
+  Modules/MContraction/WeakHamiltonianNonEye.cc \
+  Modules/MGauge/Unit.cc \
+  Modules/MGauge/StochEm.cc \
   Modules/MGauge/Random.cc \
-  Modules/MGauge/Unit.cc
+  Modules/MGauge/FundtoHirep.cc \
+  Modules/MScalar/FreeProp.cc \
+  Modules/MScalar/ChargedProp.cc \
+  Modules/MIO/LoadNersc.cc
 
 modules_hpp =\
-  Modules/MAction/DWF.hpp \
-  Modules/MAction/Wilson.hpp \
   Modules/MContraction/Baryon.hpp \
-  Modules/MContraction/DiscLoop.hpp \
-  Modules/MContraction/Gamma3pt.hpp \
   Modules/MContraction/Meson.hpp \
   Modules/MContraction/WeakHamiltonian.hpp \
-  Modules/MContraction/WeakHamiltonianEye.hpp \
   Modules/MContraction/WeakHamiltonianNonEye.hpp \
+  Modules/MContraction/DiscLoop.hpp \
   Modules/MContraction/WeakNeutral4ptDisc.hpp \
-  Modules/MGauge/Load.hpp \
-  Modules/MGauge/Random.hpp \
-  Modules/MGauge/Unit.hpp \
-  Modules/MLoop/NoiseLoop.hpp \
-  Modules/MSolver/RBPrecCG.hpp \
-  Modules/MSource/Point.hpp \
+  Modules/MContraction/Gamma3pt.hpp \
+  Modules/MContraction/WardIdentity.hpp \
+  Modules/MContraction/WeakHamiltonianEye.hpp \
+  Modules/MFermion/GaugeProp.hpp \
   Modules/MSource/SeqGamma.hpp \
+  Modules/MSource/Point.hpp \
   Modules/MSource/Wall.hpp \
   Modules/MSource/Z2.hpp \
-  Modules/Quark.hpp
+  Modules/MSource/SeqConserved.hpp \
+  Modules/MSink/Smear.hpp \
+  Modules/MSink/Point.hpp \
+  Modules/MSolver/RBPrecCG.hpp \
+  Modules/MGauge/Unit.hpp \
+  Modules/MGauge/Random.hpp \
+  Modules/MGauge/StochEm.hpp \
+  Modules/MGauge/FundtoHirep.hpp \
+  Modules/MUtilities/TestSeqGamma.hpp \
+  Modules/MUtilities/TestSeqConserved.hpp \
+  Modules/MLoop/NoiseLoop.hpp \
+  Modules/MScalar/FreeProp.hpp \
+  Modules/MScalar/Scalar.hpp \
+  Modules/MScalar/ChargedProp.hpp \
+  Modules/MAction/DWF.hpp \
+  Modules/MAction/Wilson.hpp \
+  Modules/MAction/WilsonClover.hpp \
+  Modules/MScalarSUN/TrMag.hpp \
+  Modules/MScalarSUN/TwoPoint.hpp \
+  Modules/MScalarSUN/TrPhi.hpp \
+  Modules/MIO/LoadNersc.hpp \
+  Modules/MIO/LoadBinary.hpp
 

extras/qed-fvol/Global.cc

@@ -0,0 +1,11 @@
+#include <qed-fvol/Global.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace QedFVol;
+
+QedFVolLogger QedFVol::QedFVolLogError(1,"Error");
+QedFVolLogger QedFVol::QedFVolLogWarning(1,"Warning");
+QedFVolLogger QedFVol::QedFVolLogMessage(1,"Message");
+QedFVolLogger QedFVol::QedFVolLogIterative(1,"Iterative");
+QedFVolLogger QedFVol::QedFVolLogDebug(1,"Debug");

extras/qed-fvol/Global.hpp

@@ -0,0 +1,42 @@
+#ifndef QedFVol_Global_hpp_
+#define QedFVol_Global_hpp_
+
+#include <Grid/Grid.h>
+
+#define BEGIN_QEDFVOL_NAMESPACE \
+namespace Grid {\
+using namespace QCD;\
+namespace QedFVol {\
+using Grid::operator<<;
+#define END_QEDFVOL_NAMESPACE }}
+
+/* the 'using Grid::operator<<;' statement prevents a very nasty compilation
+ * error with GCC (clang compiles fine without it).
+ */
+
+BEGIN_QEDFVOL_NAMESPACE
+
+class QedFVolLogger: public Logger
+{
+public:
+    QedFVolLogger(int on, std::string nm): Logger("QedFVol", on, nm,
+                                                  GridLogColours, "BLACK"){};
+};
+
+#define LOG(channel) std::cout << QedFVolLog##channel
+#define QEDFVOL_ERROR(msg)\
+LOG(Error) << msg << " (" << __FUNCTION__ << " at " << __FILE__ << ":"\
+           << __LINE__ << ")" << std::endl;\
+abort();
+
+#define DEBUG_VAR(var) LOG(Debug) << #var << "= " << (var) << std::endl;
+
+extern QedFVolLogger QedFVolLogError;
+extern QedFVolLogger QedFVolLogWarning;
+extern QedFVolLogger QedFVolLogMessage;
+extern QedFVolLogger QedFVolLogIterative;
+extern QedFVolLogger QedFVolLogDebug;
+
+END_QEDFVOL_NAMESPACE
+
+#endif // QedFVol_Global_hpp_

extras/qed-fvol/Makefile.am

@@ -0,0 +1,9 @@
+AM_CXXFLAGS += -I$(top_srcdir)/extras
+
+bin_PROGRAMS = qed-fvol
+
+qed_fvol_SOURCES =   \
+    qed-fvol.cc      \
+    Global.cc
+
+qed_fvol_LDADD   = -lGrid

extras/qed-fvol/WilsonLoops.h

@@ -0,0 +1,265 @@
+#ifndef QEDFVOL_WILSONLOOPS_H
+#define QEDFVOL_WILSONLOOPS_H
+
+#include <Global.hpp>
+
+BEGIN_QEDFVOL_NAMESPACE
+
+template <class Gimpl> class NewWilsonLoops : public Gimpl {
+public:
+  INHERIT_GIMPL_TYPES(Gimpl);
+
+  typedef typename Gimpl::GaugeLinkField GaugeMat;
+  typedef typename Gimpl::GaugeField GaugeLorentz;
+
+  //////////////////////////////////////////////////
+  // directed plaquette oriented in mu,nu plane
+  //////////////////////////////////////////////////
+  static void dirPlaquette(GaugeMat &plaq, const std::vector<GaugeMat> &U,
+                           const int mu, const int nu) {
+    // Annoyingly, must use either scope resolution to find dependent base
+    // class,
+    // or this-> ; there is no "this" in a static method. This forces explicit
+    // Gimpl scope
+    // resolution throughout the usage in this file, and rather defeats the
+    // purpose of deriving
+    // from Gimpl.
+    plaq = Gimpl::CovShiftBackward(
+        U[mu], mu, Gimpl::CovShiftBackward(
+                       U[nu], nu, Gimpl::CovShiftForward(U[mu], mu, U[nu])));
+  }
+  //////////////////////////////////////////////////
+  // trace of directed plaquette oriented in mu,nu plane
+  //////////////////////////////////////////////////
+  static void traceDirPlaquette(LatticeComplex &plaq,
+                                const std::vector<GaugeMat> &U, const int mu,
+                                const int nu) {
+    GaugeMat sp(U[0]._grid);
+    dirPlaquette(sp, U, mu, nu);
+    plaq = trace(sp);
+  }
+  //////////////////////////////////////////////////
+  // sum over all planes of plaquette
+  //////////////////////////////////////////////////
+  static void sitePlaquette(LatticeComplex &Plaq,
+                            const std::vector<GaugeMat> &U) {
+    LatticeComplex sitePlaq(U[0]._grid);
+    Plaq = zero;
+    for (int mu = 1; mu < U[0]._grid->_ndimension; mu++) {
+      for (int nu = 0; nu < mu; nu++) {
+        traceDirPlaquette(sitePlaq, U, mu, nu);
+        Plaq = Plaq + sitePlaq;
+      }
+    }
+  }
+  //////////////////////////////////////////////////
+  // sum over all x,y,z,t and over all planes of plaquette
+  //////////////////////////////////////////////////
+  static Real sumPlaquette(const GaugeLorentz &Umu) {
+    std::vector<GaugeMat> U(4, Umu._grid);
+
+    for (int mu = 0; mu < Umu._grid->_ndimension; mu++) {
+      U[mu] = PeekIndex<LorentzIndex>(Umu, mu);
+    }
+
+    LatticeComplex Plaq(Umu._grid);
+
+    sitePlaquette(Plaq, U);
+
+    TComplex Tp = sum(Plaq);
+    Complex p = TensorRemove(Tp);
+    return p.real();
+  }
+  //////////////////////////////////////////////////
+  // average over all x,y,z,t and over all planes of plaquette
+  //////////////////////////////////////////////////
+  static Real avgPlaquette(const GaugeLorentz &Umu) {
+    int ndim = Umu._grid->_ndimension;
+    Real sumplaq = sumPlaquette(Umu);
+    Real vol = Umu._grid->gSites();
+    Real faces = (1.0 * ndim * (ndim - 1)) / 2.0;
+    return sumplaq / vol / faces / Nc; // Nc dependent... FIXME
+  }
+
+  //////////////////////////////////////////////////
+  // Wilson loop of size (R1, R2), oriented in mu,nu plane
+  //////////////////////////////////////////////////
+  static void wilsonLoop(GaugeMat &wl, const std::vector<GaugeMat> &U,
+                           const int Rmu, const int Rnu,
+                           const int mu, const int nu) {
+    wl = U[nu];
+
+    for(int i = 0; i < Rnu-1; i++){
+      wl = Gimpl::CovShiftForward(U[nu], nu, wl);
+    }
+
+    for(int i = 0; i < Rmu; i++){
+      wl = Gimpl::CovShiftForward(U[mu], mu, wl);
+    }
+
+    for(int i = 0; i < Rnu; i++){
+      wl = Gimpl::CovShiftBackward(U[nu], nu, wl);
+    }
+
+    for(int i = 0; i < Rmu; i++){
+      wl = Gimpl::CovShiftBackward(U[mu], mu, wl);
+    }
+  }
+  //////////////////////////////////////////////////
+  // trace of Wilson Loop oriented in mu,nu plane
+  //////////////////////////////////////////////////
+  static void traceWilsonLoop(LatticeComplex &wl,
+                                const std::vector<GaugeMat> &U,
+                                const int Rmu, const int Rnu,
+                                const int mu, const int nu) {
+    GaugeMat sp(U[0]._grid);
+    wilsonLoop(sp, U, Rmu, Rnu, mu, nu);
+    wl = trace(sp);
+  }
+  //////////////////////////////////////////////////
+  // sum over all planes of Wilson loop
+  //////////////////////////////////////////////////
+  static void siteWilsonLoop(LatticeComplex &Wl,
+                            const std::vector<GaugeMat> &U,
+                            const int R1, const int R2) {
+    LatticeComplex siteWl(U[0]._grid);
+    Wl = zero;
+    for (int mu = 1; mu < U[0]._grid->_ndimension; mu++) {
+      for (int nu = 0; nu < mu; nu++) {
+        traceWilsonLoop(siteWl, U, R1, R2, mu, nu);
+        Wl = Wl + siteWl;
+        traceWilsonLoop(siteWl, U, R2, R1, mu, nu);
+        Wl = Wl + siteWl;
+      }
+    }
+  }
+  //////////////////////////////////////////////////
+  // sum over planes of Wilson loop with length R1
+  // in the time direction
+  //////////////////////////////////////////////////
+  static void siteTimelikeWilsonLoop(LatticeComplex &Wl,
+                            const std::vector<GaugeMat> &U,
+                            const int R1, const int R2) {
+    LatticeComplex siteWl(U[0]._grid);
+
+    int ndim = U[0]._grid->_ndimension;
+
+    Wl = zero;
+    for (int nu = 0; nu < ndim - 1; nu++) {
+      traceWilsonLoop(siteWl, U, R1, R2, ndim-1, nu);
+      Wl = Wl + siteWl;
+    }
+  }
+  //////////////////////////////////////////////////
+  // sum Wilson loop over all planes orthogonal to the time direction
+  //////////////////////////////////////////////////
+  static void siteSpatialWilsonLoop(LatticeComplex &Wl,
+                            const std::vector<GaugeMat> &U,
+                            const int R1, const int R2) {
+    LatticeComplex siteWl(U[0]._grid);
+
+    Wl = zero;
+    for (int mu = 1; mu < U[0]._grid->_ndimension - 1; mu++) {
+      for (int nu = 0; nu < mu; nu++) {
+        traceWilsonLoop(siteWl, U, R1, R2, mu, nu);
+        Wl = Wl + siteWl;
+        traceWilsonLoop(siteWl, U, R2, R1, mu, nu);
+        Wl = Wl + siteWl;
+      }
+    }
+  }
+  //////////////////////////////////////////////////
+  // sum over all x,y,z,t and over all planes of Wilson loop
+  //////////////////////////////////////////////////
+  static Real sumWilsonLoop(const GaugeLorentz &Umu,
+                            const int R1, const int R2) {
+    std::vector<GaugeMat> U(4, Umu._grid);
+
+    for (int mu = 0; mu < Umu._grid->_ndimension; mu++) {
+      U[mu] = PeekIndex<LorentzIndex>(Umu, mu);
+    }
+
+    LatticeComplex Wl(Umu._grid);
+
+    siteWilsonLoop(Wl, U, R1, R2);
+
+    TComplex Tp = sum(Wl);
+    Complex p = TensorRemove(Tp);
+    return p.real();
+  }
+  //////////////////////////////////////////////////
+  // sum over all x,y,z,t and over all planes of timelike Wilson loop
+  //////////////////////////////////////////////////
+  static Real sumTimelikeWilsonLoop(const GaugeLorentz &Umu,
+                            const int R1, const int R2) {
+    std::vector<GaugeMat> U(4, Umu._grid);
+
+    for (int mu = 0; mu < Umu._grid->_ndimension; mu++) {
+      U[mu] = PeekIndex<LorentzIndex>(Umu, mu);
+    }
+
+    LatticeComplex Wl(Umu._grid);
+
+    siteTimelikeWilsonLoop(Wl, U, R1, R2);
+
+    TComplex Tp = sum(Wl);
+    Complex p = TensorRemove(Tp);
+    return p.real();
+  }
+  //////////////////////////////////////////////////
+  // sum over all x,y,z,t and over all planes of spatial Wilson loop
+  //////////////////////////////////////////////////
+  static Real sumSpatialWilsonLoop(const GaugeLorentz &Umu,
+                            const int R1, const int R2) {
+    std::vector<GaugeMat> U(4, Umu._grid);
+
+    for (int mu = 0; mu < Umu._grid->_ndimension; mu++) {
+      U[mu] = PeekIndex<LorentzIndex>(Umu, mu);
+    }
+
+    LatticeComplex Wl(Umu._grid);
+
+    siteSpatialWilsonLoop(Wl, U, R1, R2);
+
+    TComplex Tp = sum(Wl);
+    Complex p = TensorRemove(Tp);
+    return p.real();
+  }
+  //////////////////////////////////////////////////
+  // average over all x,y,z,t and over all planes of Wilson loop
+  //////////////////////////////////////////////////
+  static Real avgWilsonLoop(const GaugeLorentz &Umu,
+                            const int R1, const int R2) {
+    int ndim = Umu._grid->_ndimension;
+    Real sumWl = sumWilsonLoop(Umu, R1, R2);
+    Real vol = Umu._grid->gSites();
+    Real faces = 1.0 * ndim * (ndim - 1);
+    return sumWl / vol / faces / Nc; // Nc dependent... FIXME
+  }
+  //////////////////////////////////////////////////
+  // average over all x,y,z,t and over all planes of timelike Wilson loop
+  //////////////////////////////////////////////////
+  static Real avgTimelikeWilsonLoop(const GaugeLorentz &Umu,
+                            const int R1, const int R2) {
+    int ndim = Umu._grid->_ndimension;
+    Real sumWl = sumTimelikeWilsonLoop(Umu, R1, R2);
+    Real vol = Umu._grid->gSites();
+    Real faces = 1.0 * (ndim - 1);
+    return sumWl / vol / faces / Nc; // Nc dependent... FIXME
+  }
+  //////////////////////////////////////////////////
+  // average over all x,y,z,t and over all planes of spatial Wilson loop
+  //////////////////////////////////////////////////
+  static Real avgSpatialWilsonLoop(const GaugeLorentz &Umu,
+                            const int R1, const int R2) {
+    int ndim = Umu._grid->_ndimension;
+    Real sumWl = sumSpatialWilsonLoop(Umu, R1, R2);
+    Real vol = Umu._grid->gSites();
+    Real faces = 1.0 * (ndim - 1) * (ndim - 2);
+    return sumWl / vol / faces / Nc; // Nc dependent... FIXME
+  }
+};
+
+END_QEDFVOL_NAMESPACE
+
+#endif // QEDFVOL_WILSONLOOPS_H

extras/qed-fvol/qed-fvol.cc

@@ -0,0 +1,88 @@
+#include <Global.hpp>
+#include <WilsonLoops.h>
+
+using namespace Grid;
+using namespace QCD;
+using namespace QedFVol;
+
+typedef PeriodicGaugeImpl<QedGimplR>    QedPeriodicGimplR;
+typedef PhotonR::GaugeField             EmField;
+typedef PhotonR::GaugeLinkField         EmComp;
+
+const int NCONFIGS = 10;
+const int NWILSON = 10;
+
+int main(int argc, char *argv[])
+{
+    // parse command line
+    std::string parameterFileName;
+    
+    if (argc < 2)
+    {
+        std::cerr << "usage: " << argv[0] << " <parameter file> [Grid options]";
+        std::cerr << std::endl;
+        std::exit(EXIT_FAILURE);
+    }
+    parameterFileName = argv[1];
+    
+    // initialization
+    Grid_init(&argc, &argv);
+    QedFVolLogError.Active(GridLogError.isActive());
+    QedFVolLogWarning.Active(GridLogWarning.isActive());
+    QedFVolLogMessage.Active(GridLogMessage.isActive());
+    QedFVolLogIterative.Active(GridLogIterative.isActive());
+    QedFVolLogDebug.Active(GridLogDebug.isActive());
+    LOG(Message) << "Grid initialized" << std::endl;
+    
+    // QED stuff
+    std::vector<int> latt_size   = GridDefaultLatt();
+    std::vector<int> simd_layout = GridDefaultSimd(4, vComplex::Nsimd());
+    std::vector<int> mpi_layout  = GridDefaultMpi();
+    GridCartesian    grid(latt_size,simd_layout,mpi_layout);
+    GridParallelRNG  pRNG(&grid);
+    PhotonR          photon(PhotonR::Gauge::feynman,
+                            PhotonR::ZmScheme::qedL);
+    EmField          a(&grid);
+    EmField          expA(&grid);
+
+    Complex imag_unit(0, 1);
+
+    Real wlA;
+    std::vector<Real> logWlAvg(NWILSON, 0.0), logWlTime(NWILSON, 0.0), logWlSpace(NWILSON, 0.0);
+
+    pRNG.SeedRandomDevice();
+
+    LOG(Message) << "Wilson loop calculation beginning" << std::endl;
+    for(int ic = 0; ic < NCONFIGS; ic++){
+        LOG(Message) << "Configuration " << ic <<std::endl;
+        photon.StochasticField(a, pRNG);
+
+        // Exponentiate photon field
+        expA = exp(imag_unit*a);
+
+        // Calculate Wilson loops
+        for(int iw=1; iw<=NWILSON; iw++){
+            wlA = NewWilsonLoops<QedPeriodicGimplR>::avgWilsonLoop(expA, iw, iw) * 3;
+            logWlAvg[iw-1] -= 2*log(wlA);
+            wlA = NewWilsonLoops<QedPeriodicGimplR>::avgTimelikeWilsonLoop(expA, iw, iw) * 3;
+            logWlTime[iw-1] -= 2*log(wlA);
+            wlA = NewWilsonLoops<QedPeriodicGimplR>::avgSpatialWilsonLoop(expA, iw, iw) * 3;
+            logWlSpace[iw-1] -= 2*log(wlA);
+        }
+    }
+    LOG(Message) << "Wilson loop calculation completed" << std::endl;
+    
+    // Calculate Wilson loops
+    for(int iw=1; iw<=10; iw++){
+        LOG(Message) << iw << 'x' << iw << " Wilson loop" << std::endl;
+        LOG(Message) << "-2log(W) average: " << logWlAvg[iw-1]/NCONFIGS << std::endl;
+        LOG(Message) << "-2log(W) timelike: " << logWlTime[iw-1]/NCONFIGS << std::endl;
+        LOG(Message) << "-2log(W) spatial: " << logWlSpace[iw-1]/NCONFIGS << std::endl;
+    }
+
+    // epilogue
+    LOG(Message) << "Grid is finalizing now" << std::endl;
+    Grid_finalize();
+    
+    return EXIT_SUCCESS;
+}

lib/Grid.h

@@ -41,7 +41,9 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 #include <Grid/GridCore.h>
 #include <Grid/GridQCDcore.h>
 #include <Grid/qcd/action/Action.h>
+#include <Grid/qcd/utils/GaugeFix.h>
 #include <Grid/qcd/smearing/Smearing.h>
+#include <Grid/parallelIO/MetaData.h>
 #include <Grid/qcd/hmc/HMC_aggregate.h>
 
 #endif

lib/GridStd.h

@@ -7,6 +7,7 @@
 #include <cassert>
 #include <complex>
 #include <vector>
+#include <string>
 #include <iostream>
 #include <iomanip>
 #include <random>
@@ -18,6 +19,7 @@
 #include <ctime>
 #include <sys/time.h>
 #include <chrono>
+#include <zlib.h>
 
 ///////////////////
 // Grid config

lib/Makefile.am

@@ -1,28 +1,18 @@
 extra_sources=
 extra_headers=
-if BUILD_COMMS_MPI
-  extra_sources+=communicator/Communicator_mpi.cc
-  extra_sources+=communicator/Communicator_base.cc
-endif
 
 if BUILD_COMMS_MPI3
   extra_sources+=communicator/Communicator_mpi3.cc
   extra_sources+=communicator/Communicator_base.cc
-endif
-
-if BUILD_COMMS_MPI3L
-  extra_sources+=communicator/Communicator_mpi3_leader.cc
-  extra_sources+=communicator/Communicator_base.cc
-endif
-
-if BUILD_COMMS_SHMEM
-  extra_sources+=communicator/Communicator_shmem.cc
-  extra_sources+=communicator/Communicator_base.cc
+  extra_sources+=communicator/SharedMemoryMPI.cc
+  extra_sources+=communicator/SharedMemory.cc
 endif
 
 if BUILD_COMMS_NONE
   extra_sources+=communicator/Communicator_none.cc
   extra_sources+=communicator/Communicator_base.cc
+  extra_sources+=communicator/SharedMemoryNone.cc
+  extra_sources+=communicator/SharedMemory.cc
 endif
 
 if BUILD_HDF5

lib/algorithms/Algorithms.h

@@ -1,6 +1,6 @@
     /*************************************************************************************
 
-    Grid physics library, www.github.com/paboyle/Grid 
+    Grid physics library, www.github.com/paboyle/Grid
 
     Source file: ./lib/Algorithms.h
 
@@ -37,6 +37,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #include <Grid/algorithms/approx/Chebyshev.h>
 #include <Grid/algorithms/approx/Remez.h>
 #include <Grid/algorithms/approx/MultiShiftFunction.h>
+#include <Grid/algorithms/approx/Forecast.h>
 
 #include <Grid/algorithms/iterative/ConjugateGradient.h>
 #include <Grid/algorithms/iterative/ConjugateResidual.h>
@@ -44,30 +45,16 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #include <Grid/algorithms/iterative/SchurRedBlack.h>
 #include <Grid/algorithms/iterative/ConjugateGradientMultiShift.h>
 #include <Grid/algorithms/iterative/ConjugateGradientMixedPrec.h>
-
-// Lanczos support
-//#include <Grid/algorithms/iterative/MatrixUtils.h>
+#include <Grid/algorithms/iterative/BlockConjugateGradient.h>
+#include <Grid/algorithms/iterative/ConjugateGradientReliableUpdate.h>
 #include <Grid/algorithms/iterative/ImplicitlyRestartedLanczos.h>
 #include <Grid/algorithms/CoarsenedMatrix.h>
 #include <Grid/algorithms/FFT.h>
 
-// Eigen/lanczos
 // EigCg
-// MCR
 // Pcg
-// Multishift CG
 // Hdcg
 // GCR
 // etc..
 
-// integrator/Leapfrog
-// integrator/Omelyan
-// integrator/ForceGradient
-
-// montecarlo/hmc
-// montecarlo/rhmc
-// montecarlo/metropolis
-// etc...
-
-
 #endif

lib/algorithms/CoarsenedMatrix.h

@@ -103,29 +103,32 @@ namespace Grid {
     GridBase *CoarseGrid;
     GridBase *FineGrid;
     std::vector<Lattice<Fobj> > subspace;
+    int checkerboard;
 
-    Aggregation(GridBase *_CoarseGrid,GridBase *_FineGrid) : 
-      CoarseGrid(_CoarseGrid),
+  Aggregation(GridBase *_CoarseGrid,GridBase *_FineGrid,int _checkerboard) : 
+    CoarseGrid(_CoarseGrid),
       FineGrid(_FineGrid),
-      subspace(nbasis,_FineGrid)
+      subspace(nbasis,_FineGrid),
+      checkerboard(_checkerboard)
 	{
 	};
   
     void Orthogonalise(void){
       CoarseScalar InnerProd(CoarseGrid); 
+      std::cout << GridLogMessage <<" Gramm-Schmidt pass 1"<<std::endl;
       blockOrthogonalise(InnerProd,subspace);
+      std::cout << GridLogMessage <<" Gramm-Schmidt pass 2"<<std::endl;
+      blockOrthogonalise(InnerProd,subspace);
+      //      std::cout << GridLogMessage <<" Gramm-Schmidt checking orthogonality"<<std::endl;
+      //      CheckOrthogonal();
     } 
     void CheckOrthogonal(void){
       CoarseVector iProj(CoarseGrid); 
       CoarseVector eProj(CoarseGrid); 
-      Lattice<CComplex> pokey(CoarseGrid);
-
-      
       for(int i=0;i<nbasis;i++){
 	blockProject(iProj,subspace[i],subspace);
-
 	eProj=zero; 
-	for(int ss=0;ss<CoarseGrid->oSites();ss++){
+	parallel_for(int ss=0;ss<CoarseGrid->oSites();ss++){
 	  eProj._odata[ss](i)=CComplex(1.0);
 	}
 	eProj=eProj - iProj;
@@ -137,6 +140,7 @@ namespace Grid {
       blockProject(CoarseVec,FineVec,subspace);
     }
     void PromoteFromSubspace(const CoarseVector &CoarseVec,FineField &FineVec){
+      FineVec.checkerboard = subspace[0].checkerboard;
       blockPromote(CoarseVec,FineVec,subspace);
     }
     void CreateSubspaceRandom(GridParallelRNG &RNG){
@@ -147,6 +151,7 @@ namespace Grid {
       Orthogonalise();
     }
 
+    /*
     virtual void CreateSubspaceLanczos(GridParallelRNG  &RNG,LinearOperatorBase<FineField> &hermop,int nn=nbasis) 
     {
       // Run a Lanczos with sloppy convergence
@@ -195,7 +200,7 @@ namespace Grid {
 	  std::cout << GridLogMessage <<"subspace["<<b<<"] = "<<norm2(subspace[b])<<std::endl;
 	}
     }
-
+    */
     virtual void CreateSubspace(GridParallelRNG  &RNG,LinearOperatorBase<FineField> &hermop,int nn=nbasis) {
 
       RealD scale;

lib/algorithms/FFT.h

@@ -230,6 +230,7 @@ namespace Grid {
       // Barrel shift and collect global pencil
       std::vector<int> lcoor(Nd), gcoor(Nd);
       result = source;
+      int pc = processor_coor[dim];
       for(int p=0;p<processors[dim];p++) {
         PARALLEL_REGION
         {
@@ -240,7 +241,8 @@ namespace Grid {
           for(int idx=0;idx<sgrid->lSites();idx++) {
             sgrid->LocalIndexToLocalCoor(idx,cbuf);
             peekLocalSite(s,result,cbuf);
-            cbuf[dim]+=p*L;
+	    cbuf[dim]+=((pc+p) % processors[dim])*L;
+	    //            cbuf[dim]+=p*L;
             pokeLocalSite(s,pgbuf,cbuf);
           }
         }
@@ -278,7 +280,6 @@ namespace Grid {
       flops+= flops_call*NN;
       
       // writing out result
-      int pc = processor_coor[dim];
       PARALLEL_REGION
       {
         std::vector<int> clbuf(Nd), cgbuf(Nd);

lib/algorithms/LinearOperator.h

@@ -162,15 +162,10 @@ namespace Grid {
 	_Mat.M(in,out);
       }
       void HermOpAndNorm(const Field &in, Field &out,RealD &n1,RealD &n2){
-	ComplexD dot;
-
 	_Mat.M(in,out);
 	
-	dot= innerProduct(in,out);
-	n1=real(dot);
-
-	dot = innerProduct(out,out);
-	n2=real(dot);
+	ComplexD dot= innerProduct(in,out); n1=real(dot);
+	n2=norm2(out);
       }
       void HermOp(const Field &in, Field &out){
 	_Mat.M(in,out);
@@ -188,14 +183,16 @@ namespace Grid {
       virtual  RealD Mpc      (const Field &in, Field &out) =0;
       virtual  RealD MpcDag   (const Field &in, Field &out) =0;
       virtual void MpcDagMpc(const Field &in, Field &out,RealD &ni,RealD &no) {
-	Field tmp(in._grid);
+      Field tmp(in._grid);
+      tmp.checkerboard = in.checkerboard;
 	ni=Mpc(in,tmp);
 	no=MpcDag(tmp,out);
       }
-      void HermOpAndNorm(const Field &in, Field &out,RealD &n1,RealD &n2){
+      virtual void HermOpAndNorm(const Field &in, Field &out,RealD &n1,RealD &n2){
+      out.checkerboard = in.checkerboard;
 	MpcDagMpc(in,out,n1,n2);
       }
-      void HermOp(const Field &in, Field &out){
+      virtual void HermOp(const Field &in, Field &out){
 	RealD n1,n2;
 	HermOpAndNorm(in,out,n1,n2);
       }
@@ -212,7 +209,6 @@ namespace Grid {
       void OpDir  (const Field &in, Field &out,int dir,int disp) {
 	assert(0);
       }
-
     };
     template<class Matrix,class Field>
       class SchurDiagMooeeOperator :  public SchurOperatorBase<Field> {
@@ -221,13 +217,15 @@ namespace Grid {
     public:
       SchurDiagMooeeOperator (Matrix &Mat): _Mat(Mat){};
       virtual  RealD Mpc      (const Field &in, Field &out) {
-	Field tmp(in._grid);
-//	std::cout <<"grid pointers: in._grid="<< in._grid << " out._grid=" << out._grid << "  _Mat.Grid=" << _Mat.Grid() << " _Mat.RedBlackGrid=" << _Mat.RedBlackGrid() << std::endl;
+      Field tmp(in._grid);
+      tmp.checkerboard = !in.checkerboard;
+	//std::cout <<"grid pointers: in._grid="<< in._grid << " out._grid=" << out._grid << "  _Mat.Grid=" << _Mat.Grid() << " _Mat.RedBlackGrid=" << _Mat.RedBlackGrid() << std::endl;
 
 	_Mat.Meooe(in,tmp);
 	_Mat.MooeeInv(tmp,out);
 	_Mat.Meooe(out,tmp);
 
+      //std::cout << "cb in " << in.checkerboard << "  cb out " << out.checkerboard << std::endl;
 	_Mat.Mooee(in,out);
 	return axpy_norm(out,-1.0,tmp,out);
       }
@@ -270,7 +268,6 @@ namespace Grid {
 	return axpy_norm(out,-1.0,tmp,in);
       }
     };
-
     template<class Matrix,class Field>
       class SchurDiagTwoOperator :  public SchurOperatorBase<Field> {
     protected:
@@ -299,6 +296,59 @@ namespace Grid {
 	return axpy_norm(out,-1.0,tmp,in);
       }
     };
+    ///////////////////////////////////////////////////////////////////////////////////////////////////
+    // Left  handed Moo^-1 ; (Moo - Moe Mee^-1 Meo) psi = eta  -->  ( 1 - Moo^-1 Moe Mee^-1 Meo ) psi = Moo^-1 eta
+    // Right handed Moo^-1 ; (Moo - Moe Mee^-1 Meo) Moo^-1 Moo psi = eta  -->  ( 1 - Moe Mee^-1 Meo ) Moo^-1 phi=eta ; psi = Moo^-1 phi
+    ///////////////////////////////////////////////////////////////////////////////////////////////////
+    template<class Matrix,class Field> using SchurDiagOneRH = SchurDiagTwoOperator<Matrix,Field> ;
+    template<class Matrix,class Field> using SchurDiagOneLH = SchurDiagOneOperator<Matrix,Field> ;
+    ///////////////////////////////////////////////////////////////////////////////////////////////////
+    //  Staggered use
+    ///////////////////////////////////////////////////////////////////////////////////////////////////
+    template<class Matrix,class Field>
+      class SchurStaggeredOperator :  public SchurOperatorBase<Field> {
+    protected:
+      Matrix &_Mat;
+    public:
+      SchurStaggeredOperator (Matrix &Mat): _Mat(Mat){};
+      virtual void HermOpAndNorm(const Field &in, Field &out,RealD &n1,RealD &n2){
+	GridLogIterative.TimingMode(1);
+	std::cout << GridLogIterative << " HermOpAndNorm "<<std::endl;
+	n2 = Mpc(in,out);
+	std::cout << GridLogIterative << " HermOpAndNorm.Mpc "<<std::endl;
+	ComplexD dot= innerProduct(in,out);
+	std::cout << GridLogIterative << " HermOpAndNorm.innerProduct "<<std::endl;
+	n1 = real(dot);
+      }
+      virtual void HermOp(const Field &in, Field &out){
+	std::cout << GridLogIterative << " HermOp "<<std::endl;
+	Mpc(in,out);
+      }
+      virtual  RealD Mpc      (const Field &in, Field &out) {
+	Field tmp(in._grid);
+	Field tmp2(in._grid);
+
+	std::cout << GridLogIterative << " HermOp.Mpc "<<std::endl;
+	_Mat.Mooee(in,out);
+	_Mat.Mooee(out,tmp);
+	std::cout << GridLogIterative << " HermOp.MooeeMooee "<<std::endl;
+
+	_Mat.Meooe(in,out);
+	_Mat.Meooe(out,tmp2);
+	std::cout << GridLogIterative << " HermOp.MeooeMeooe "<<std::endl;
+
+	RealD nn=axpy_norm(out,-1.0,tmp2,tmp);
+	std::cout << GridLogIterative << " HermOp.axpy_norm "<<std::endl;
+	return nn;
+      }
+      virtual  RealD MpcDag   (const Field &in, Field &out){
+	return Mpc(in,out);
+      }
+      virtual void MpcDagMpc(const Field &in, Field &out,RealD &ni,RealD &no) {
+	assert(0);// Never need with staggered
+      }
+    };
+    template<class Matrix,class Field> using SchurStagOperator = SchurStaggeredOperator<Matrix,Field>;
 
 
     /////////////////////////////////////////////////////////////
@@ -314,6 +364,14 @@ namespace Grid {
       virtual void operator() (const Field &in, Field &out) = 0;
     };
 
+    template<class Field> class IdentityLinearFunction : public LinearFunction<Field> {
+    public:
+      void operator() (const Field &in, Field &out){
+	out = in;
+      };
+    };
+
+
     /////////////////////////////////////////////////////////////
     // Base classes for Multishift solvers for operators
     /////////////////////////////////////////////////////////////
@@ -336,6 +394,64 @@ namespace Grid {
      };
     */
 
+  ////////////////////////////////////////////////////////////////////////////////////////////
+  // Hermitian operator Linear function and operator function
+  ////////////////////////////////////////////////////////////////////////////////////////////
+    template<class Field>
+      class HermOpOperatorFunction : public OperatorFunction<Field> {
+      void operator() (LinearOperatorBase<Field> &Linop, const Field &in, Field &out) {
+	Linop.HermOp(in,out);
+      };
+    };
+
+    template<typename Field>
+      class PlainHermOp : public LinearFunction<Field> {
+    public:
+      LinearOperatorBase<Field> &_Linop;
+      
+      PlainHermOp(LinearOperatorBase<Field>& linop) : _Linop(linop) 
+      {}
+      
+      void operator()(const Field& in, Field& out) {
+	_Linop.HermOp(in,out);
+      }
+    };
+
+    template<typename Field>
+    class FunctionHermOp : public LinearFunction<Field> {
+    public:
+      OperatorFunction<Field>   & _poly;
+      LinearOperatorBase<Field> &_Linop;
+      
+      FunctionHermOp(OperatorFunction<Field> & poly,LinearOperatorBase<Field>& linop) 
+	: _poly(poly), _Linop(linop) {};
+      
+      void operator()(const Field& in, Field& out) {
+	_poly(_Linop,in,out);
+      }
+    };
+
+  template<class Field>
+  class Polynomial : public OperatorFunction<Field> {
+  private:
+    std::vector<RealD> Coeffs;
+  public:
+    Polynomial(std::vector<RealD> &_Coeffs) : Coeffs(_Coeffs) { };
+
+    // Implement the required interface
+    void operator() (LinearOperatorBase<Field> &Linop, const Field &in, Field &out) {
+
+      Field AtoN(in._grid);
+      Field Mtmp(in._grid);
+      AtoN = in;
+      out = AtoN*Coeffs[0];
+      for(int n=1;n<Coeffs.size();n++){
+	Mtmp = AtoN;
+	Linop.HermOp(Mtmp,AtoN);
+	out=out+AtoN*Coeffs[n];
+      }
+    };
+  };
 
 }
 

lib/algorithms/approx/Chebyshev.h

@@ -8,6 +8,7 @@
 
 Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 Author: paboyle <paboyle@ph.ed.ac.uk>
+Author: Christoph Lehner <clehner@bnl.gov>
 
     This program is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -33,41 +34,12 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 
 namespace Grid {
 
-  ////////////////////////////////////////////////////////////////////////////////////////////
-  // Simple general polynomial with user supplied coefficients
-  ////////////////////////////////////////////////////////////////////////////////////////////
-  template<class Field>
-  class HermOpOperatorFunction : public OperatorFunction<Field> {
-    void operator() (LinearOperatorBase<Field> &Linop, const Field &in, Field &out) {
-      Linop.HermOp(in,out);
-    };
-  };
-
-  template<class Field>
-  class Polynomial : public OperatorFunction<Field> {
-  private:
-    std::vector<RealD> Coeffs;
-  public:
-    Polynomial(std::vector<RealD> &_Coeffs) : Coeffs(_Coeffs) { };
-
-    // Implement the required interface
-    void operator() (LinearOperatorBase<Field> &Linop, const Field &in, Field &out) {
-
-      Field AtoN(in._grid);
-      Field Mtmp(in._grid);
-      AtoN = in;
-      out = AtoN*Coeffs[0];
-//            std::cout <<"Poly in " <<norm2(in)<<" size "<< Coeffs.size()<<std::endl;
-//            std::cout <<"Coeffs[0]= "<<Coeffs[0]<< " 0 " <<norm2(out)<<std::endl;
-      for(int n=1;n<Coeffs.size();n++){
-	Mtmp = AtoN;
-	Linop.HermOp(Mtmp,AtoN);
-	out=out+AtoN*Coeffs[n];
-//            std::cout <<"Coeffs "<<n<<"= "<< Coeffs[n]<< " 0 " <<std::endl;
-//		std::cout << n<<" " <<norm2(out)<<std::endl;
-      }
-    };
-  };
+struct ChebyParams : Serializable {
+  GRID_SERIALIZABLE_CLASS_MEMBERS(ChebyParams,
+				  RealD, alpha,  
+				  RealD, beta,   
+				  int, Npoly);
+};
 
   ////////////////////////////////////////////////////////////////////////////////////////////
   // Generic Chebyshev approximations
@@ -82,8 +54,10 @@ namespace Grid {
 
   public:
     void csv(std::ostream &out){
-	RealD diff = hi-lo;
-      for (RealD x=lo-0.2*diff; x<hi+0.2*diff; x+=(hi-lo)/1000) {
+      RealD diff = hi-lo;
+      RealD delta = (hi-lo)*1.0e-9;
+      for (RealD x=lo; x<hi; x+=delta) {
+	delta*=1.1;
 	RealD f = approx(x);
 	out<< x<<" "<<f<<std::endl;
       }
@@ -99,6 +73,7 @@ namespace Grid {
     };
 
     Chebyshev(){};
+    Chebyshev(ChebyParams p){ Init(p.alpha,p.beta,p.Npoly);};
     Chebyshev(RealD _lo,RealD _hi,int _order, RealD (* func)(RealD) ) {Init(_lo,_hi,_order,func);};
     Chebyshev(RealD _lo,RealD _hi,int _order) {Init(_lo,_hi,_order);};
 
@@ -193,6 +168,47 @@ namespace Grid {
       return sum;
     };
 
+    RealD approxD(RealD x)
+    {
+      RealD Un;
+      RealD Unm;
+      RealD Unp;
+      
+      RealD y=( x-0.5*(hi+lo))/(0.5*(hi-lo));
+      
+      RealD U0=1;
+      RealD U1=2*y;
+      
+      RealD sum;
+      sum = Coeffs[1]*U0;
+      sum+= Coeffs[2]*U1*2.0;
+      
+      Un =U1;
+      Unm=U0;
+      for(int i=2;i<order-1;i++){
+	Unp=2*y*Un-Unm;
+	Unm=Un;
+	Un =Unp;
+	sum+= Un*Coeffs[i+1]*(i+1.0);
+      }
+      return sum/(0.5*(hi-lo));
+    };
+    
+    RealD approxInv(RealD z, RealD x0, int maxiter, RealD resid) {
+      RealD x = x0;
+      RealD eps;
+      
+      int i;
+      for (i=0;i<maxiter;i++) {
+	eps = approx(x) - z;
+	if (fabs(eps / z) < resid)
+	  return x;
+	x = x - eps / approxD(x);
+      }
+      
+      return std::numeric_limits<double>::quiet_NaN();
+    }
+    
     // Implement the required interface
     void operator() (LinearOperatorBase<Field> &Linop, const Field &in, Field &out) {
 

lib/algorithms/approx/Forecast.h

@@ -0,0 +1,152 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid
+
+Source file: ./lib/algorithms/approx/Forecast.h
+
+Copyright (C) 2015
+
+Author: Peter Boyle <paboyle@ph.ed.ac.uk>
+Author: paboyle <paboyle@ph.ed.ac.uk>
+Author: David Murphy <dmurphy@phys.columbia.edu>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef INCLUDED_FORECAST_H
+#define INCLUDED_FORECAST_H
+
+namespace Grid {
+
+  // Abstract base class.
+  // Takes a matrix (Mat), a source (phi), and a vector of Fields (chi)
+  // and returns a forecasted solution to the system D*psi = phi (psi).
+  template<class Matrix, class Field>
+  class Forecast
+  {
+    public:
+      virtual Field operator()(Matrix &Mat, const Field& phi, const std::vector<Field>& chi) = 0;
+  };
+
+  // Implementation of Brower et al.'s chronological inverter (arXiv:hep-lat/9509012),
+  // used to forecast solutions across poles of the EOFA heatbath.
+  //
+  // Modified from CPS (cps_pp/src/util/dirac_op/d_op_base/comsrc/minresext.C)
+  template<class Matrix, class Field>
+  class ChronoForecast : public Forecast<Matrix,Field>
+  {
+    public:
+      Field operator()(Matrix &Mat, const Field& phi, const std::vector<Field>& prev_solns)
+      {
+        int degree = prev_solns.size();
+        Field chi(phi); // forecasted solution
+
+        // Trivial cases
+        if(degree == 0){ chi = zero; return chi; }
+        else if(degree == 1){ return prev_solns[0]; }
+
+        RealD dot;
+        ComplexD xp;
+        Field r(phi); // residual
+        Field Mv(phi);
+        std::vector<Field> v(prev_solns); // orthonormalized previous solutions
+        std::vector<Field> MdagMv(degree,phi);
+
+        // Array to hold the matrix elements
+        std::vector<std::vector<ComplexD>> G(degree, std::vector<ComplexD>(degree));
+
+        // Solution and source vectors
+        std::vector<ComplexD> a(degree);
+        std::vector<ComplexD> b(degree);
+
+        // Orthonormalize the vector basis
+        for(int i=0; i<degree; i++){
+          v[i] *= 1.0/std::sqrt(norm2(v[i]));
+          for(int j=i+1; j<degree; j++){ v[j] -= innerProduct(v[i],v[j]) * v[i]; }
+        }
+
+        // Perform sparse matrix multiplication and construct rhs
+        for(int i=0; i<degree; i++){
+          b[i] = innerProduct(v[i],phi);
+          Mat.M(v[i],Mv);
+          Mat.Mdag(Mv,MdagMv[i]);
+          G[i][i] = innerProduct(v[i],MdagMv[i]);
+        }
+
+        // Construct the matrix
+        for(int j=0; j<degree; j++){
+        for(int k=j+1; k<degree; k++){
+          G[j][k] = innerProduct(v[j],MdagMv[k]);
+          G[k][j] = std::conj(G[j][k]);
+        }}
+
+        // Gauss-Jordan elimination with partial pivoting
+        for(int i=0; i<degree; i++){
+
+          // Perform partial pivoting
+          int k = i;
+          for(int j=i+1; j<degree; j++){ if(std::abs(G[j][j]) > std::abs(G[k][k])){ k = j; } }
+          if(k != i){
+            xp = b[k];
+            b[k] = b[i];
+            b[i] = xp;
+            for(int j=0; j<degree; j++){
+              xp = G[k][j];
+              G[k][j] = G[i][j];
+              G[i][j] = xp;
+            }
+          }
+
+          // Convert matrix to upper triangular form
+          for(int j=i+1; j<degree; j++){
+            xp = G[j][i]/G[i][i];
+            b[j] -= xp * b[i];
+            for(int k=0; k<degree; k++){ G[j][k] -= xp*G[i][k]; }
+          }
+        }
+
+        // Use Gaussian elimination to solve equations and calculate initial guess
+        chi = zero;
+        r = phi;
+        for(int i=degree-1; i>=0; i--){
+          a[i] = 0.0;
+          for(int j=i+1; j<degree; j++){ a[i] += G[i][j] * a[j]; }
+          a[i] = (b[i]-a[i])/G[i][i];
+          chi += a[i]*v[i];
+          r -= a[i]*MdagMv[i];
+        }
+
+        RealD true_r(0.0);
+        ComplexD tmp;
+        for(int i=0; i<degree; i++){
+          tmp = -b[i];
+          for(int j=0; j<degree; j++){ tmp += G[i][j]*a[j]; }
+          tmp = std::conj(tmp)*tmp;
+          true_r += std::sqrt(tmp.real());
+        }
+
+        RealD error = std::sqrt(norm2(r)/norm2(phi));
+        std::cout << GridLogMessage << "ChronoForecast: |res|/|src| = " << error << std::endl;
+
+        return chi;
+      };
+  };
+
+}
+
+#endif

lib/algorithms/densematrix/DenseMatrix.h

@@ -1,137 +0,0 @@
-    /*************************************************************************************
-
-    Grid physics library, www.github.com/paboyle/Grid 
-
-    Source file: ./lib/algorithms/iterative/DenseMatrix.h
-
-    Copyright (C) 2015
-
-Author: Peter Boyle <paboyle@ph.ed.ac.uk>
-Author: paboyle <paboyle@ph.ed.ac.uk>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-    See the full license in the file "LICENSE" in the top level distribution directory
-    *************************************************************************************/
-    /*  END LEGAL */
-#ifndef GRID_DENSE_MATRIX_H
-#define GRID_DENSE_MATRIX_H
-
-namespace Grid {
-    /////////////////////////////////////////////////////////////
-    // Matrix untils
-    /////////////////////////////////////////////////////////////
-
-template<class T> using DenseVector = std::vector<T>;
-template<class T> using DenseMatrix = DenseVector<DenseVector<T> >;
-
-template<class T> void Size(DenseVector<T> & vec, int &N) 
-{ 
-  N= vec.size();
-}
-template<class T> void Size(DenseMatrix<T> & mat, int &N,int &M) 
-{ 
-  N= mat.size();
-  M= mat[0].size();
-}
-
-template<class T> void SizeSquare(DenseMatrix<T> & mat, int &N) 
-{ 
-  int M; Size(mat,N,M);
-  assert(N==M);
-}
-
-template<class T> void Resize(DenseVector<T > & mat, int N) { 
-  mat.resize(N);
-}
-template<class T> void Resize(DenseMatrix<T > & mat, int N, int M) { 
-  mat.resize(N);
-  for(int i=0;i<N;i++){
-    mat[i].resize(M);
-  }
-}
-template<class T> void Fill(DenseMatrix<T> & mat, T&val) { 
-  int N,M;
-  Size(mat,N,M);
-  for(int i=0;i<N;i++){
-  for(int j=0;j<M;j++){
-    mat[i][j] = val;
-  }}
-}
-
-/** Transpose of a matrix **/
-template<class T> DenseMatrix<T> Transpose(DenseMatrix<T> & mat){
-  int N,M;
-  Size(mat,N,M);
-  DenseMatrix<T> C; Resize(C,M,N);
-  for(int i=0;i<M;i++){
-  for(int j=0;j<N;j++){
-    C[i][j] = mat[j][i];
-  }} 
-  return C;
-}
-/** Set DenseMatrix to unit matrix **/
-template<class T> void Unity(DenseMatrix<T> &A){
-  int N;  SizeSquare(A,N);
-  for(int i=0;i<N;i++){
-    for(int j=0;j<N;j++){
-      if ( i==j ) A[i][j] = 1;
-      else        A[i][j] = 0;
-    } 
-  } 
-}
-
-/** Add C * I to matrix **/
-template<class T>
-void PlusUnit(DenseMatrix<T> & A,T c){
-  int dim;  SizeSquare(A,dim);
-  for(int i=0;i<dim;i++){A[i][i] = A[i][i] + c;} 
-}
-
-/** return the Hermitian conjugate of matrix **/
-template<class T>
-DenseMatrix<T> HermitianConj(DenseMatrix<T> &mat){
-
-  int dim; SizeSquare(mat,dim);
-
-  DenseMatrix<T> C; Resize(C,dim,dim);
-
-  for(int i=0;i<dim;i++){
-    for(int j=0;j<dim;j++){
-      C[i][j] = conj(mat[j][i]);
-    } 
-  } 
-  return C;
-}
-/**Get a square submatrix**/
-template <class T>
-DenseMatrix<T> GetSubMtx(DenseMatrix<T> &A,int row_st, int row_end, int col_st, int col_end)
-{
-  DenseMatrix<T> H; Resize(H,row_end - row_st,col_end-col_st);
-
-  for(int i = row_st; i<row_end; i++){
-  for(int j = col_st; j<col_end; j++){
-    H[i-row_st][j-col_st]=A[i][j];
-  }}
-  return H;
-}
-
-}
-
-#include "Householder.h"
-#include "Francis.h"
-
-#endif
-

lib/algorithms/densematrix/Francis.h

@@ -1,525 +0,0 @@
-    /*************************************************************************************
-
-    Grid physics library, www.github.com/paboyle/Grid 
-
-    Source file: ./lib/algorithms/iterative/Francis.h
-
-    Copyright (C) 2015
-
-Author: Peter Boyle <paboyle@ph.ed.ac.uk>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-    See the full license in the file "LICENSE" in the top level distribution directory
-    *************************************************************************************/
-    /*  END LEGAL */
-#ifndef FRANCIS_H
-#define FRANCIS_H
-
-#include <cstdlib>
-#include <string>
-#include <cmath>
-#include <iostream>
-#include <sstream>
-#include <stdexcept>
-#include <fstream>
-#include <complex>
-#include <algorithm>
-
-//#include <timer.h>
-//#include <lapacke.h>
-//#include <Eigen/Dense>
-
-namespace Grid {
-
-template <class T> int SymmEigensystem(DenseMatrix<T > &Ain, DenseVector<T> &evals, DenseMatrix<T> &evecs, RealD small);
-template <class T> int     Eigensystem(DenseMatrix<T > &Ain, DenseVector<T> &evals, DenseMatrix<T> &evecs, RealD small);
-
-/**
-  Find the eigenvalues of an upper hessenberg matrix using the Francis QR algorithm.
-H =
-      x  x  x  x  x  x  x  x  x
-      x  x  x  x  x  x  x  x  x
-      0  x  x  x  x  x  x  x  x
-      0  0  x  x  x  x  x  x  x
-      0  0  0  x  x  x  x  x  x
-      0  0  0  0  x  x  x  x  x
-      0  0  0  0  0  x  x  x  x
-      0  0  0  0  0  0  x  x  x
-      0  0  0  0  0  0  0  x  x
-Factorization is P T P^H where T is upper triangular (mod cc blocks) and P is orthagonal/unitary.
-**/
-template <class T>
-int QReigensystem(DenseMatrix<T> &Hin, DenseVector<T> &evals, DenseMatrix<T> &evecs, RealD small)
-{
-  DenseMatrix<T> H = Hin; 
-
-  int N ; SizeSquare(H,N);
-  int M = N;
-
-  Fill(evals,0);
-  Fill(evecs,0);
-
-  T s,t,x=0,y=0,z=0;
-  T u,d;
-  T apd,amd,bc;
-  DenseVector<T> p(N,0);
-  T nrm = Norm(H);    ///DenseMatrix Norm
-  int n, m;
-  int e = 0;
-  int it = 0;
-  int tot_it = 0;
-  int l = 0;
-  int r = 0;
-  DenseMatrix<T> P; Resize(P,N,N); Unity(P);
-  DenseVector<int> trows(N,0);
-
-  /// Check if the matrix is really hessenberg, if not abort
-  RealD sth = 0;
-  for(int j=0;j<N;j++){
-    for(int i=j+2;i<N;i++){
-      sth = abs(H[i][j]);
-      if(sth > small){
-	std::cout << "Non hessenberg H = " << sth << " > " << small << std::endl;
-	exit(1);
-      }
-    }
-  }
-
-  do{
-    std::cout << "Francis QR Step N = " << N << std::endl;
-    /** Check for convergence
-      x  x  x  x  x
-      0  x  x  x  x
-      0  0  x  x  x
-      0  0  x  x  x
-      0  0  0  0  x
-      for this matrix l = 4
-     **/
-    do{
-      l = Chop_subdiag(H,nrm,e,small);
-      r = 0;    ///May have converged on more than one eval
-      ///Single eval
-      if(l == N-1){
-        evals[e] = H[l][l];
-        N--; e++; r++; it = 0;
-      }
-      ///RealD eval
-      if(l == N-2){
-        trows[l+1] = 1;    ///Needed for UTSolve
-        apd = H[l][l] + H[l+1][l+1];
-        amd = H[l][l] - H[l+1][l+1];
-        bc =  (T)4.0*H[l+1][l]*H[l][l+1];
-        evals[e]   = (T)0.5*( apd + sqrt(amd*amd + bc) );
-        evals[e+1] = (T)0.5*( apd - sqrt(amd*amd + bc) );
-        N-=2; e+=2; r++; it = 0;
-      }
-    } while(r>0);
-
-    if(N ==0) break;
-
-    DenseVector<T > ck; Resize(ck,3);
-    DenseVector<T> v;   Resize(v,3);
-
-    for(int m = N-3; m >= l; m--){
-      ///Starting vector essentially random shift.
-      if(it%10 == 0 && N >= 3 && it > 0){
-        s = (T)1.618033989*( abs( H[N-1][N-2] ) + abs( H[N-2][N-3] ) );
-        t = (T)0.618033989*( abs( H[N-1][N-2] ) + abs( H[N-2][N-3] ) );
-        x = H[m][m]*H[m][m] + H[m][m+1]*H[m+1][m] - s*H[m][m] + t;
-        y = H[m+1][m]*(H[m][m] + H[m+1][m+1] - s);
-        z = H[m+1][m]*H[m+2][m+1];
-      }
-      ///Starting vector implicit Q theorem
-      else{
-        s = (H[N-2][N-2] + H[N-1][N-1]);
-        t = (H[N-2][N-2]*H[N-1][N-1] - H[N-2][N-1]*H[N-1][N-2]);
-        x = H[m][m]*H[m][m] + H[m][m+1]*H[m+1][m] - s*H[m][m] + t;
-        y = H[m+1][m]*(H[m][m] + H[m+1][m+1] - s);
-        z = H[m+1][m]*H[m+2][m+1];
-      }
-      ck[0] = x; ck[1] = y; ck[2] = z;
-
-      if(m == l) break;
-
-      /** Some stupid thing from numerical recipies, seems to work**/
-      // PAB.. for heaven's sake quote page, purpose, evidence it works.
-      //       what sort of comment is that!?!?!?
-      u=abs(H[m][m-1])*(abs(y)+abs(z));
-      d=abs(x)*(abs(H[m-1][m-1])+abs(H[m][m])+abs(H[m+1][m+1]));
-      if ((T)abs(u+d) == (T)abs(d) ){
-	l = m; break;
-      }
-
-      //if (u < small){l = m; break;}
-    }
-    if(it > 100000){
-     std::cout << "QReigensystem: bugger it got stuck after 100000 iterations" << std::endl;
-     std::cout << "got " << e << " evals " << l << " " << N << std::endl;
-      exit(1);
-    }
-    normalize(ck);    ///Normalization cancels in PHP anyway
-    T beta;
-    Householder_vector<T >(ck, 0, 2, v, beta);
-    Householder_mult<T >(H,v,beta,0,l,l+2,0);
-    Householder_mult<T >(H,v,beta,0,l,l+2,1);
-    ///Accumulate eigenvector
-    Householder_mult<T >(P,v,beta,0,l,l+2,1);
-    int sw = 0;      ///Are we on the last row?
-    for(int k=l;k<N-2;k++){
-      x = H[k+1][k];
-      y = H[k+2][k];
-      z = (T)0.0;
-      if(k+3 <= N-1){
-	z = H[k+3][k];
-      } else{
-	sw = 1; 
-	v[2] = (T)0.0;
-      }
-      ck[0] = x; ck[1] = y; ck[2] = z;
-      normalize(ck);
-      Householder_vector<T >(ck, 0, 2-sw, v, beta);
-      Householder_mult<T >(H,v, beta,0,k+1,k+3-sw,0);
-      Householder_mult<T >(H,v, beta,0,k+1,k+3-sw,1);
-      ///Accumulate eigenvector
-      Householder_mult<T >(P,v, beta,0,k+1,k+3-sw,1);
-    }
-    it++;
-    tot_it++;
-  }while(N > 1);
-  N = evals.size();
-  ///Annoying - UT solves in reverse order;
-  DenseVector<T> tmp; Resize(tmp,N);
-  for(int i=0;i<N;i++){
-    tmp[i] = evals[N-i-1];
-  } 
-  evals = tmp;
-  UTeigenvectors(H, trows, evals, evecs);
-  for(int i=0;i<evals.size();i++){evecs[i] = P*evecs[i]; normalize(evecs[i]);}
-  return tot_it;
-}
-
-template <class T>
-int my_Wilkinson(DenseMatrix<T> &Hin, DenseVector<T> &evals, DenseMatrix<T> &evecs, RealD small)
-{
-  /**
-  Find the eigenvalues of an upper Hessenberg matrix using the Wilkinson QR algorithm.
-  H =
-  x  x  0  0  0  0
-  x  x  x  0  0  0
-  0  x  x  x  0  0
-  0  0  x  x  x  0
-  0  0  0  x  x  x
-  0  0  0  0  x  x
-  Factorization is P T P^H where T is upper triangular (mod cc blocks) and P is orthagonal/unitary.  **/
-  return my_Wilkinson(Hin, evals, evecs, small, small);
-}
-
-template <class T>
-int my_Wilkinson(DenseMatrix<T> &Hin, DenseVector<T> &evals, DenseMatrix<T> &evecs, RealD small, RealD tol)
-{
-  int N; SizeSquare(Hin,N);
-  int M = N;
-
-  ///I don't want to modify the input but matricies must be passed by reference
-  //Scale a matrix by its "norm"
-  //RealD Hnorm = abs( Hin.LargestDiag() ); H =  H*(1.0/Hnorm);
-  DenseMatrix<T> H;  H = Hin;
-  
-  RealD Hnorm = abs(Norm(Hin));
-  H = H * (1.0 / Hnorm);
-
-  // TODO use openmp and memset
-  Fill(evals,0);
-  Fill(evecs,0);
-
-  T s, t, x = 0, y = 0, z = 0;
-  T u, d;
-  T apd, amd, bc;
-  DenseVector<T> p; Resize(p,N); Fill(p,0);
-
-  T nrm = Norm(H);    ///DenseMatrix Norm
-  int n, m;
-  int e = 0;
-  int it = 0;
-  int tot_it = 0;
-  int l = 0;
-  int r = 0;
-  DenseMatrix<T> P; Resize(P,N,N);
-  Unity(P);
-  DenseVector<int> trows(N, 0);
-  /// Check if the matrix is really symm tridiag
-  RealD sth = 0;
-  for(int j = 0; j < N; ++j)
-  {
-    for(int i = j + 2; i < N; ++i)
-    {
-      if(abs(H[i][j]) > tol || abs(H[j][i]) > tol)
-      {
-	std::cout << "Non Tridiagonal H(" << i << ","<< j << ") = |" << Real( real( H[j][i] ) ) << "| > " << tol << std::endl;
-	std::cout << "Warning tridiagonalize and call again" << std::endl;
-        // exit(1); // see what is going on
-        //return;
-      }
-    }
-  }
-
-  do{
-    do{
-      //Jasper
-      //Check if the subdiagonal term is small enough (<small)
-      //if true then it is converged.
-      //check start from H.dim - e - 1
-      //How to deal with more than 2 are converged?
-      //What if Chop_symm_subdiag return something int the middle?
-      //--------------
-      l = Chop_symm_subdiag(H,nrm, e, small);
-      r = 0;    ///May have converged on more than one eval
-      //Jasper
-      //In this case
-      // x  x  0  0  0  0
-      // x  x  x  0  0  0
-      // 0  x  x  x  0  0
-      // 0  0  x  x  x  0
-      // 0  0  0  x  x  0
-      // 0  0  0  0  0  x  <- l
-      //--------------
-      ///Single eval
-      if(l == N - 1)
-      {
-        evals[e] = H[l][l];
-        N--;
-        e++;
-        r++;
-        it = 0;
-      }
-      //Jasper
-      // x  x  0  0  0  0
-      // x  x  x  0  0  0
-      // 0  x  x  x  0  0
-      // 0  0  x  x  0  0
-      // 0  0  0  0  x  x  <- l
-      // 0  0  0  0  x  x
-      //--------------
-      ///RealD eval
-      if(l == N - 2)
-      {
-        trows[l + 1] = 1;    ///Needed for UTSolve
-        apd = H[l][l] + H[l + 1][ l + 1];
-        amd = H[l][l] - H[l + 1][l + 1];
-        bc =  (T) 4.0 * H[l + 1][l] * H[l][l + 1];
-        evals[e] = (T) 0.5 * (apd + sqrt(amd * amd + bc));
-        evals[e + 1] = (T) 0.5 * (apd - sqrt(amd * amd + bc));
-        N -= 2;
-        e += 2;
-        r++;
-        it = 0;
-      }
-    }while(r > 0);
-    //Jasper
-    //Already converged
-    //--------------
-    if(N == 0) break;
-
-    DenseVector<T> ck,v; Resize(ck,2); Resize(v,2);
-
-    for(int m = N - 3; m >= l; m--)
-    {
-      ///Starting vector essentially random shift.
-      if(it%10 == 0 && N >= 3 && it > 0)
-      {
-        t = abs(H[N - 1][N - 2]) + abs(H[N - 2][N - 3]);
-        x = H[m][m] - t;
-        z = H[m + 1][m];
-      } else {
-      ///Starting vector implicit Q theorem
-        d = (H[N - 2][N - 2] - H[N - 1][N - 1]) * (T) 0.5;
-        t =  H[N - 1][N - 1] - H[N - 1][N - 2] * H[N - 1][N - 2] 
-	  / (d + sign(d) * sqrt(d * d + H[N - 1][N - 2] * H[N - 1][N - 2]));
-        x = H[m][m] - t;
-        z = H[m + 1][m];
-      }
-      //Jasper
-      //why it is here????
-      //-----------------------
-      if(m == l)
-        break;
-
-      u = abs(H[m][m - 1]) * (abs(y) + abs(z));
-      d = abs(x) * (abs(H[m - 1][m - 1]) + abs(H[m][m]) + abs(H[m + 1][m + 1]));
-      if ((T)abs(u + d) == (T)abs(d))
-      {
-        l = m;
-        break;
-      }
-    }
-    //Jasper
-    if(it > 1000000)
-    {
-      std::cout << "Wilkinson: bugger it got stuck after 100000 iterations" << std::endl;
-      std::cout << "got " << e << " evals " << l << " " << N << std::endl;
-      exit(1);
-    }
-    //
-    T s, c;
-    Givens_calc<T>(x, z, c, s);
-    Givens_mult<T>(H, l, l + 1, c, -s, 0);
-    Givens_mult<T>(H, l, l + 1, c,  s, 1);
-    Givens_mult<T>(P, l, l + 1, c,  s, 1);
-    //
-    for(int k = l; k < N - 2; ++k)
-    {
-      x = H.A[k + 1][k];
-      z = H.A[k + 2][k];
-      Givens_calc<T>(x, z, c, s);
-      Givens_mult<T>(H, k + 1, k + 2, c, -s, 0);
-      Givens_mult<T>(H, k + 1, k + 2, c,  s, 1);
-      Givens_mult<T>(P, k + 1, k + 2, c,  s, 1);
-    }
-    it++;
-    tot_it++;
-  }while(N > 1);
-
-  N = evals.size();
-  ///Annoying - UT solves in reverse order;
-  DenseVector<T> tmp(N);
-  for(int i = 0; i < N; ++i)
-    tmp[i] = evals[N-i-1];
-  evals = tmp;
-  //
-  UTeigenvectors(H, trows, evals, evecs);
-  //UTSymmEigenvectors(H, trows, evals, evecs);
-  for(int i = 0; i < evals.size(); ++i)
-  {
-    evecs[i] = P * evecs[i];
-    normalize(evecs[i]);
-    evals[i] = evals[i] * Hnorm;
-  }
-  // // FIXME this is to test
-  // Hin.write("evecs3", evecs);
-  // Hin.write("evals3", evals);
-  // // check rsd
-  // for(int i = 0; i < M; i++) {
-  //   vector<T> Aevec = Hin * evecs[i];
-  //   RealD norm2(0.);
-  //   for(int j = 0; j < M; j++) {
-  //     norm2 += (Aevec[j] - evals[i] * evecs[i][j]) * (Aevec[j] - evals[i] * evecs[i][j]);
-  //   }
-  // }
-  return tot_it;
-}
-
-template <class T>
-void Hess(DenseMatrix<T > &A, DenseMatrix<T> &Q, int start){
-
-  /**
-  turn a matrix A =
-  x  x  x  x  x
-  x  x  x  x  x
-  x  x  x  x  x
-  x  x  x  x  x
-  x  x  x  x  x
-  into
-  x  x  x  x  x
-  x  x  x  x  x
-  0  x  x  x  x
-  0  0  x  x  x
-  0  0  0  x  x
-  with householder rotations
-  Slow.
-  */
-  int N ; SizeSquare(A,N);
-  DenseVector<T > p; Resize(p,N); Fill(p,0);
-
-  for(int k=start;k<N-2;k++){
-    //cerr << "hess" << k << std::endl;
-    DenseVector<T > ck,v; Resize(ck,N-k-1); Resize(v,N-k-1);
-    for(int i=k+1;i<N;i++){ck[i-k-1] = A(i,k);}  ///kth column
-    normalize(ck);    ///Normalization cancels in PHP anyway
-    T beta;
-    Householder_vector<T >(ck, 0, ck.size()-1, v, beta);  ///Householder vector
-    Householder_mult<T>(A,v,beta,start,k+1,N-1,0);  ///A -> PA
-    Householder_mult<T >(A,v,beta,start,k+1,N-1,1);  ///PA -> PAP^H
-    ///Accumulate eigenvector
-    Householder_mult<T >(Q,v,beta,start,k+1,N-1,1);  ///Q -> QP^H
-  }
-  /*for(int l=0;l<N-2;l++){
-    for(int k=l+2;k<N;k++){
-    A(0,k,l);
-    }
-    }*/
-}
-
-template <class T>
-void Tri(DenseMatrix<T > &A, DenseMatrix<T> &Q, int start){
-///Tridiagonalize a matrix
-  int N; SizeSquare(A,N);
-  Hess(A,Q,start);
-  /*for(int l=0;l<N-2;l++){
-    for(int k=l+2;k<N;k++){
-    A(0,l,k);
-    }
-    }*/
-}
-
-template <class T>
-void ForceTridiagonal(DenseMatrix<T> &A){
-///Tridiagonalize a matrix
-  int N ; SizeSquare(A,N);
-  for(int l=0;l<N-2;l++){
-    for(int k=l+2;k<N;k++){
-      A[l][k]=0;
-      A[k][l]=0;
-    }
-  }
-}
-
-template <class T>
-int my_SymmEigensystem(DenseMatrix<T > &Ain, DenseVector<T> &evals, DenseVector<DenseVector<T> > &evecs, RealD small){
-  ///Solve a symmetric eigensystem, not necessarily in tridiagonal form
-  int N; SizeSquare(Ain,N);
-  DenseMatrix<T > A; A = Ain;
-  DenseMatrix<T > Q; Resize(Q,N,N); Unity(Q);
-  Tri(A,Q,0);
-  int it = my_Wilkinson<T>(A, evals, evecs, small);
-  for(int k=0;k<N;k++){evecs[k] = Q*evecs[k];}
-  return it;
-}
-
-
-template <class T>
-int Wilkinson(DenseMatrix<T> &Ain, DenseVector<T> &evals, DenseVector<DenseVector<T> > &evecs, RealD small){
-  return my_Wilkinson(Ain, evals, evecs, small);
-}
-
-template <class T>
-int SymmEigensystem(DenseMatrix<T> &Ain, DenseVector<T> &evals, DenseVector<DenseVector<T> > &evecs, RealD small){
-  return my_SymmEigensystem(Ain, evals, evecs, small);
-}
-
-template <class T>
-int Eigensystem(DenseMatrix<T > &Ain, DenseVector<T> &evals, DenseVector<DenseVector<T> > &evecs, RealD small){
-///Solve a general eigensystem, not necessarily in tridiagonal form
-  int N = Ain.dim;
-  DenseMatrix<T > A(N); A = Ain;
-  DenseMatrix<T > Q(N);Q.Unity();
-  Hess(A,Q,0);
-  int it = QReigensystem<T>(A, evals, evecs, small);
-  for(int k=0;k<N;k++){evecs[k] = Q*evecs[k];}
-  return it;
-}
-
-}
-#endif