Committing incomplete work for parameter file I/O.

MacroMagic.h is central. Guido and I plan to move
over to generating virtual (XML, JSON, YAML, text, binary) encoding
from macro based system.

lib/AlignedAllocator.h

@@ -1,6 +1,13 @@
 #ifndef GRID_ALIGNED_ALLOCATOR_H
 #define GRID_ALIGNED_ALLOCATOR_H
 
+#ifdef HAVE_MALLOC_MALLOC_H
+#include <malloc/malloc.h>
+#endif
+#ifdef HAVE_MALLOC_H
+#include <malloc.h>
+#endif
+
 #include <immintrin.h>
 #ifdef HAVE_MM_MALLOC_H
 #include <mm_malloc.h>

lib/Config.h.in

@@ -1,4 +1,4 @@
-/* lib/GridConfig.h.in.  Generated from configure.ac by autoheader.  */
+/* lib/Config.h.in.  Generated from configure.ac by autoheader.  */
 
 /* AVX Intrinsics */
 #undef AVX1

lib/Grid.h

@@ -6,95 +6,48 @@
 //  Copyright (c) 2014 University of Edinburgh. All rights reserved.
 //
 
-
 #ifndef GRID_H
 #define GRID_H
 
+///////////////////
+// Std C++ dependencies
+///////////////////
 #include <cassert>
-
 #include <complex>
 #include <vector>
-
 #include <iostream>
 #include <iomanip>
 #include <random>
 #include <functional>
-
 #include <stdio.h>
 #include <stdlib.h>
-#include <sys/time.h>
 #include <stdio.h>
 #include <signal.h>
+#include <ctime>
+#include <sys/time.h>
+#include <chrono>
 
-#ifndef MAX
+///////////////////
-#define MAX(x,y) ((x)>(y)?(x):(y))
+// Grid headers
-#define MIN(x,y) ((x)>(y)?(y):(x))
+///////////////////
-#endif
+#include <MacroMagic.h>
-
+#include <Config.h>
-#define strong_inline __attribute__((always_inline)) inline
+#include <Timer.h>
-
+#include <Log.h>
-#include <GridConfig.h>
-
-#include <GridTime.h>
-#include <GridLog.h>
-
-////////////////////////////////////////////////////////////
-// Tunable header includes
-////////////////////////////////////////////////////////////
-
-#ifdef HAVE_MALLOC_MALLOC_H
-#include <malloc/malloc.h>
-#endif
-#ifdef HAVE_MALLOC_H
-#include <malloc.h>
-#endif
-
 #include <AlignedAllocator.h>
-
 #include <Simd.h>
 #include <Threads.h>
-
+#include <Communicator.h> 
-#include <Communicator.h> // subdir aggregate
+#include <Cartesian.h>    
-#include <Cartesian.h> // subdir aggregate
+#include <Tensors.h>      
-#include <Tensors.h>   // subdir aggregate
+#include <Lattice.h>      
-#include <Lattice.h>   // subdir aggregate
+#include <Cshift.h>       
-#include <Cshift.h>    // subdir aggregate
+#include <Stencil.h>      
-#include <Stencil.h>   // subdir aggregate
+#include <Algorithms.h>   
-#include <Algorithms.h>// subdir aggregate
-
 #include <qcd/QCD.h>
 #include <parallelIO/NerscIO.h>
 
-namespace Grid {
+#include <Init.h>
 
-  void Grid_init(int *argc,char ***argv);
-  void Grid_finalize(void);
-  // internal, controled with --handle
-  void Grid_sa_signal_handler(int sig,siginfo_t *si,void * ptr);
-  void Grid_debug_handler_init(void);
-  void Grid_quiesce_nodes(void);
-  void Grid_unquiesce_nodes(void);
-
-  // C++11 time facilities better?
-  double usecond(void);
-
-  const std::vector<int> GridDefaultSimd(int dims,int nsimd);
-  const std::vector<int> &GridDefaultLatt(void);
-  const std::vector<int> &GridDefaultMpi(void);
-  const int              &GridThreads(void)  ;
-  void                 GridSetThreads(int t) ;
-
-  // Common parsing chores
-  std::string GridCmdOptionPayload(char ** begin, char ** end, const std::string & option);
-  bool        GridCmdOptionExists(char** begin, char** end, const std::string& option);
-  std::string GridCmdVectorIntToString(const std::vector<int> & vec);
-
-  void GridParseLayout(char **argv,int argc,
-		       std::vector<int> &latt,
-		       std::vector<int> &simd,
-		       std::vector<int> &mpi);
-
-
-};
 
 #endif

lib/Init.h

@@ -0,0 +1,32 @@
+#ifndef GRID_INIT_H
+#define GRID_INIT_H
+
+namespace Grid {
+
+  void Grid_init(int *argc,char ***argv);
+  void Grid_finalize(void);
+  // internal, controled with --handle
+  void Grid_sa_signal_handler(int sig,siginfo_t *si,void * ptr);
+  void Grid_debug_handler_init(void);
+  void Grid_quiesce_nodes(void);
+  void Grid_unquiesce_nodes(void);
+
+  const std::vector<int> GridDefaultSimd(int dims,int nsimd);
+  const std::vector<int> &GridDefaultLatt(void);
+  const std::vector<int> &GridDefaultMpi(void);
+  const int              &GridThreads(void)  ;
+  void                    GridSetThreads(int t) ;
+
+  // Common parsing chores
+  std::string GridCmdOptionPayload(char ** begin, char ** end, const std::string & option);
+  bool        GridCmdOptionExists(char** begin, char** end, const std::string& option);
+  std::string GridCmdVectorIntToString(const std::vector<int> & vec);
+
+  void GridParseLayout(char **argv,int argc,
+		       std::vector<int> &latt,
+		       std::vector<int> &simd,
+		       std::vector<int> &mpi);
+
+
+};
+#endif

lib/Log.cc

@@ -40,7 +40,7 @@ void Grid_quiesce_nodes(void)
   int me;
   MPI_Comm_rank(MPI_COMM_WORLD,&me);
   if ( me ) { 
-    std::cout<<GridLogMessage.setstate(std::ios::badbit);
+    std::cout.setstate(std::ios::badbit);
   }
 #endif
 }
@@ -48,7 +48,7 @@ void Grid_quiesce_nodes(void)
 void Grid_unquiesce_nodes(void)
 {
 #ifdef GRID_COMMS_MPI
-    std::cout<<GridLogMessage.clear();
+    std::cout.clear();
 #endif
 }
 

lib/MacroMagic.h

@@ -0,0 +1,78 @@
+#ifndef GRID_MACRO_MAGIC_H
+#define GRID_MACRO_MAGIC_H
+
+#define strong_inline __attribute__((always_inline)) inline
+
+#ifndef MAX
+#define MAX(x,y) ((x)>(y)?(x):(y))
+#define MIN(x,y) ((x)>(y)?(y):(x))
+#endif
+
+#define GRID_MACRO_FIRST(a, ...) a
+#define GRID_MACRO_SECOND(a, b, ...) b
+
+#define GRID_MACRO_EMPTY()
+
+#define GRID_MACRO_EVAL(...)     GRID_MACRO_EVAL1024(__VA_ARGS__)
+#define GRID_MACRO_EVAL1024(...) GRID_MACRO_EVAL512(GRID_MACRO_EVAL512(__VA_ARGS__))
+#define GRID_MACRO_EVAL512(...)  GRID_MACRO_EVAL256(GRID_MACRO_EVAL256(__VA_ARGS__))
+#define GRID_MACRO_EVAL256(...)  GRID_MACRO_EVAL128(GRID_MACRO_EVAL128(__VA_ARGS__))
+#define GRID_MACRO_EVAL128(...)  GRID_MACRO_EVAL64(GRID_MACRO_EVAL64(__VA_ARGS__))
+#define GRID_MACRO_EVAL64(...)   GRID_MACRO_EVAL32(GRID_MACRO_EVAL32(__VA_ARGS__))
+#define GRID_MACRO_EVAL32(...)   GRID_MACRO_EVAL16(GRID_MACRO_EVAL16(__VA_ARGS__))
+#define GRID_MACRO_EVAL16(...)   GRID_MACRO_EVAL8(GRID_MACRO_EVAL8(__VA_ARGS__))
+#define GRID_MACRO_EVAL8(...)    GRID_MACRO_EVAL4(GRID_MACRO_EVAL4(__VA_ARGS__))
+#define GRID_MACRO_EVAL4(...)    GRID_MACRO_EVAL2(GRID_MACRO_EVAL2(__VA_ARGS__))
+#define GRID_MACRO_EVAL2(...)    GRID_MACRO_EVAL1(GRID_MACRO_EVAL1(__VA_ARGS__))
+#define GRID_MACRO_EVAL1(...) __VA_ARGS__
+
+#define GRID_MACRO_DEFER1(m) m GRID_MACRO_EMPTY()
+#define GRID_MACRO_DEFER2(m) m GRID_MACRO_EMPTY GRID_MACRO_EMPTY()()
+#define GRID_MACRO_DEFER3(m) m GRID_MACRO_EMPTY GRID_MACRO_EMPTY GRID_MACRO_EMPTY()()()
+#define GRID_MACRO_DEFER4(m) m GRID_MACRO_EMPTY GRID_MACRO_EMPTY GRID_MACRO_EMPTY GRID_MACRO_EMPTY()()()()
+
+#define GRID_MACRO_IS_PROBE(...) GRID_MACRO_SECOND(__VA_ARGS__, 0)
+#define GRID_MACRO_PROBE() ~, 1
+
+#define GRID_MACRO_CAT(a,b) a ## b
+
+#define GRID_MACRO_NOT(x) GRID_MACRO_IS_PROBE(GRID_MACRO_CAT(_GRID_MACRO_NOT_, x))
+#define _GRID_MACRO_NOT_0 GRID_MACRO_PROBE()
+
+#define GRID_MACRO_BOOL(x) GRID_MACRO_NOT(GRID_MACRO_NOT(x))
+
+#define GRID_MACRO_IF_ELSE(condition) _GRID_MACRO_IF_ELSE(GRID_MACRO_BOOL(condition))
+#define _GRID_MACRO_IF_ELSE(condition) GRID_MACRO_CAT(_GRID_MACRO_IF_, condition)
+
+#define _GRID_MACRO_IF_1(...) __VA_ARGS__ _GRID_MACRO_IF_1_ELSE
+#define _GRID_MACRO_IF_0(...)             _GRID_MACRO_IF_0_ELSE
+
+#define _GRID_MACRO_IF_1_ELSE(...)
+#define _GRID_MACRO_IF_0_ELSE(...) __VA_ARGS__
+
+#define GRID_MACRO_HAS_ARGS(...) GRID_MACRO_BOOL(GRID_MACRO_FIRST(_GRID_MACRO_END_OF_ARGUMENTS_ __VA_ARGS__)())
+#define _GRID_MACRO_END_OF_ARGUMENTS_() 0
+
+#define GRID_MACRO_MAP(m, first, second, ...)   \
+  m(first,second)                           \
+  GRID_MACRO_IF_ELSE(GRID_MACRO_HAS_ARGS(__VA_ARGS__))(				       \
+				 GRID_MACRO_DEFER4(_GRID_MACRO_MAP)()(m, __VA_ARGS__)   \
+				     )(                                 \
+				       /* Do nothing, just terminate */ \
+									)
+#define _GRID_MACRO_MAP() GRID_MACRO_MAP
+
+#define GRID_MACRO_MEMBER(A,B)        A B;
+
+#define GRID_MACRO_OS_WRITE_MEMBER(A,B) os<< #A <<" "#B <<" = "<< obj. B <<" ; " <<std::endl;
+
+#define GRID_DECL_CLASS_MEMBERS(cname,...)		\
+  GRID_MACRO_EVAL(GRID_MACRO_MAP(GRID_MACRO_MEMBER,__VA_ARGS__))		\
+  friend std::ostream & operator << (std::ostream &os, const cname &obj ) {	\
+    os<<"class "<<#cname<<" {"<<std::endl;\
+    GRID_MACRO_EVAL(GRID_MACRO_MAP(GRID_MACRO_OS_WRITE_MEMBER,__VA_ARGS__))	\
+      os<<"}";								\
+    return os;\
+  };  
+
+#endif

lib/Make.inc

@@ -1,4 +1,4 @@
 
-HFILES=./algorithms/approx/bigfloat.h ./algorithms/approx/bigfloat_double.h ./algorithms/approx/Chebyshev.h ./algorithms/approx/MultiShiftFunction.h ./algorithms/approx/Remez.h ./algorithms/approx/Zolotarev.h ./algorithms/CoarsenedMatrix.h ./algorithms/iterative/AdefGeneric.h ./algorithms/iterative/BfmHDCG.h ./algorithms/iterative/ConjugateGradient.h ./algorithms/iterative/ConjugateGradientMultiShift.h ./algorithms/iterative/ConjugateResidual.h ./algorithms/iterative/GeneralisedMinimumResidual.h ./algorithms/iterative/gmres.h ./algorithms/iterative/NormalEquations.h ./algorithms/iterative/PrecConjugateResidual.h ./algorithms/iterative/PrecGeneralisedConjugateResidual.h ./algorithms/iterative/SchurRedBlack.h ./algorithms/LinearOperator.h ./algorithms/Preconditioner.h ./algorithms/SparseMatrix.h ./Algorithms.h ./AlignedAllocator.h ./cartesian/Cartesian_base.h ./cartesian/Cartesian_full.h ./cartesian/Cartesian_red_black.h ./Cartesian.h ./communicator/Communicator_base.h ./Communicator.h ./cshift/Cshift_common.h ./cshift/Cshift_mpi.h ./cshift/Cshift_none.h ./Cshift.h ./Grid.h ./GridConfig.h ./GridLog.h ./GridTime.h ./lattice/Lattice_arith.h ./lattice/Lattice_base.h ./lattice/Lattice_comparison.h ./lattice/Lattice_comparison_utils.h ./lattice/Lattice_conformable.h ./lattice/Lattice_coordinate.h ./lattice/Lattice_ET.h ./lattice/Lattice_local.h ./lattice/Lattice_overload.h ./lattice/Lattice_peekpoke.h ./lattice/Lattice_reality.h ./lattice/Lattice_reduction.h ./lattice/Lattice_rng.h ./lattice/Lattice_trace.h ./lattice/Lattice_transfer.h ./lattice/Lattice_transpose.h ./lattice/Lattice_unary.h ./lattice/Lattice_where.h ./Lattice.h ./Old/Tensor_peek.h ./Old/Tensor_poke.h ./parallelIO/NerscIO.h ./qcd/action/ActionBase.h ./qcd/action/Actions.h ./qcd/action/DiffAction.h ./qcd/action/fermion/CayleyFermion5D.h ./qcd/action/fermion/ContinuedFractionFermion5D.h ./qcd/action/fermion/DomainWallFermion.h ./qcd/action/fermion/FermionOperator.h ./qcd/action/fermion/g5HermitianLinop.h ./qcd/action/fermion/MobiusFermion.h ./qcd/action/fermion/MobiusZolotarevFermion.h ./qcd/action/fermion/OverlapWilsonCayleyTanhFermion.h ./qcd/action/fermion/OverlapWilsonCayleyZolotarevFermion.h ./qcd/action/fermion/OverlapWilsonContfracTanhFermion.h ./qcd/action/fermion/OverlapWilsonContfracZolotarevFermion.h ./qcd/action/fermion/OverlapWilsonPartialFractionTanhFermion.h ./qcd/action/fermion/OverlapWilsonPartialFractionZolotarevFermion.h ./qcd/action/fermion/PartialFractionFermion5D.h ./qcd/action/fermion/ScaledShamirFermion.h ./qcd/action/fermion/ShamirZolotarevFermion.h ./qcd/action/fermion/WilsonCompressor.h ./qcd/action/fermion/WilsonFermion.h ./qcd/action/fermion/WilsonFermion5D.h ./qcd/action/fermion/WilsonKernels.h ./qcd/action/gauge/WilsonGaugeAction.h ./qcd/hmc/HMC.h ./qcd/hmc/integrators/Integrator.h ./qcd/hmc/integrators/Integrator_algorithm.h ./qcd/hmc/integrators/Integrator_base.h ./qcd/QCD.h ./qcd/spin/Dirac.h ./qcd/spin/TwoSpinor.h ./qcd/utils/CovariantCshift.h ./qcd/utils/LinalgUtils.h ./qcd/utils/SpaceTimeGrid.h ./qcd/utils/SUn.h ./qcd/utils/WilsonLoops.h ./simd/Grid_avx.h ./simd/Grid_avx512.h ./simd/Grid_empty.h ./simd/Grid_neon.h ./simd/Grid_qpx.h ./simd/Grid_sse4.h ./simd/Grid_vector_types.h ./simd/Grid_vector_unops.h ./Simd.h ./stencil/Lebesgue.h ./Stencil.h ./tensors/Tensor_arith.h ./tensors/Tensor_arith_add.h ./tensors/Tensor_arith_mac.h ./tensors/Tensor_arith_mul.h ./tensors/Tensor_arith_scalar.h ./tensors/Tensor_arith_sub.h ./tensors/Tensor_class.h ./tensors/Tensor_determinant.h ./tensors/Tensor_exp.h ./tensors/Tensor_extract_merge.h ./tensors/Tensor_index.h ./tensors/Tensor_inner.h ./tensors/Tensor_logical.h ./tensors/Tensor_outer.h ./tensors/Tensor_reality.h ./tensors/Tensor_Ta.h ./tensors/Tensor_trace.h ./tensors/Tensor_traits.h ./tensors/Tensor_transpose.h ./tensors/Tensor_unary.h ./Tensors.h ./Threads.h
+HFILES=./algorithms/approx/bigfloat.h ./algorithms/approx/bigfloat_double.h ./algorithms/approx/Chebyshev.h ./algorithms/approx/MultiShiftFunction.h ./algorithms/approx/Remez.h ./algorithms/approx/Zolotarev.h ./algorithms/CoarsenedMatrix.h ./algorithms/iterative/AdefGeneric.h ./algorithms/iterative/BfmHDCG.h ./algorithms/iterative/ConjugateGradient.h ./algorithms/iterative/ConjugateGradientMultiShift.h ./algorithms/iterative/ConjugateResidual.h ./algorithms/iterative/GeneralisedMinimumResidual.h ./algorithms/iterative/gmres.h ./algorithms/iterative/NormalEquations.h ./algorithms/iterative/PrecConjugateResidual.h ./algorithms/iterative/PrecGeneralisedConjugateResidual.h ./algorithms/iterative/SchurRedBlack.h ./algorithms/LinearOperator.h ./algorithms/Preconditioner.h ./algorithms/SparseMatrix.h ./Algorithms.h ./AlignedAllocator.h ./cartesian/Cartesian_base.h ./cartesian/Cartesian_full.h ./cartesian/Cartesian_red_black.h ./Cartesian.h ./communicator/Communicator_base.h ./Communicator.h ./Config.h ./cshift/Cshift_common.h ./cshift/Cshift_mpi.h ./cshift/Cshift_none.h ./Cshift.h ./Grid.h ./Init.h ./lattice/Lattice_arith.h ./lattice/Lattice_base.h ./lattice/Lattice_comparison.h ./lattice/Lattice_comparison_utils.h ./lattice/Lattice_conformable.h ./lattice/Lattice_coordinate.h ./lattice/Lattice_ET.h ./lattice/Lattice_local.h ./lattice/Lattice_overload.h ./lattice/Lattice_peekpoke.h ./lattice/Lattice_reality.h ./lattice/Lattice_reduction.h ./lattice/Lattice_rng.h ./lattice/Lattice_trace.h ./lattice/Lattice_transfer.h ./lattice/Lattice_transpose.h ./lattice/Lattice_unary.h ./lattice/Lattice_where.h ./Lattice.h ./Log.h ./MacroMagic.h ./Old/Tensor_peek.h ./Old/Tensor_poke.h ./parallelIO/NerscIO.h ./qcd/action/ActionBase.h ./qcd/action/Actions.h ./qcd/action/DiffAction.h ./qcd/action/fermion/CayleyFermion5D.h ./qcd/action/fermion/ContinuedFractionFermion5D.h ./qcd/action/fermion/DomainWallFermion.h ./qcd/action/fermion/FermionOperator.h ./qcd/action/fermion/g5HermitianLinop.h ./qcd/action/fermion/MobiusFermion.h ./qcd/action/fermion/MobiusZolotarevFermion.h ./qcd/action/fermion/OverlapWilsonCayleyTanhFermion.h ./qcd/action/fermion/OverlapWilsonCayleyZolotarevFermion.h ./qcd/action/fermion/OverlapWilsonContfracTanhFermion.h ./qcd/action/fermion/OverlapWilsonContfracZolotarevFermion.h ./qcd/action/fermion/OverlapWilsonPartialFractionTanhFermion.h ./qcd/action/fermion/OverlapWilsonPartialFractionZolotarevFermion.h ./qcd/action/fermion/PartialFractionFermion5D.h ./qcd/action/fermion/ScaledShamirFermion.h ./qcd/action/fermion/ShamirZolotarevFermion.h ./qcd/action/fermion/WilsonCompressor.h ./qcd/action/fermion/WilsonFermion.h ./qcd/action/fermion/WilsonFermion5D.h ./qcd/action/fermion/WilsonKernels.h ./qcd/action/gauge/WilsonGaugeAction.h ./qcd/action/pseudofermion/TwoFlavour.h ./qcd/hmc/HMC.h ./qcd/hmc/integrators/Integrator.h ./qcd/hmc/integrators/Integrator_algorithm.h ./qcd/hmc/integrators/Integrator_base.h ./qcd/QCD.h ./qcd/spin/Dirac.h ./qcd/spin/TwoSpinor.h ./qcd/utils/CovariantCshift.h ./qcd/utils/LinalgUtils.h ./qcd/utils/SpaceTimeGrid.h ./qcd/utils/SUn.h ./qcd/utils/WilsonLoops.h ./simd/Grid_avx.h ./simd/Grid_avx512.h ./simd/Grid_empty.h ./simd/Grid_neon.h ./simd/Grid_qpx.h ./simd/Grid_sse4.h ./simd/Grid_vector_types.h ./simd/Grid_vector_unops.h ./Simd.h ./stencil/Lebesgue.h ./Stencil.h ./tensors/Tensor_arith.h ./tensors/Tensor_arith_add.h ./tensors/Tensor_arith_mac.h ./tensors/Tensor_arith_mul.h ./tensors/Tensor_arith_scalar.h ./tensors/Tensor_arith_sub.h ./tensors/Tensor_class.h ./tensors/Tensor_determinant.h ./tensors/Tensor_exp.h ./tensors/Tensor_extract_merge.h ./tensors/Tensor_index.h ./tensors/Tensor_inner.h ./tensors/Tensor_logical.h ./tensors/Tensor_outer.h ./tensors/Tensor_reality.h ./tensors/Tensor_Ta.h ./tensors/Tensor_trace.h ./tensors/Tensor_traits.h ./tensors/Tensor_transpose.h ./tensors/Tensor_unary.h ./Tensors.h ./Threads.h ./Timer.h
 
-CCFILES=./algorithms/approx/MultiShiftFunction.cc ./algorithms/approx/Remez.cc ./algorithms/approx/Zolotarev.cc ./GridInit.cc ./GridLog.cc ./qcd/action/fermion/CayleyFermion5D.cc ./qcd/action/fermion/ContinuedFractionFermion5D.cc ./qcd/action/fermion/PartialFractionFermion5D.cc ./qcd/action/fermion/WilsonFermion.cc ./qcd/action/fermion/WilsonFermion5D.cc ./qcd/action/fermion/WilsonKernels.cc ./qcd/action/fermion/WilsonKernelsHand.cc ./qcd/hmc/HMC.cc ./qcd/hmc/integrators/Integrator.cc ./qcd/spin/Dirac.cc ./qcd/utils/SpaceTimeGrid.cc ./stencil/Lebesgue.cc ./stencil/Stencil_common.cc
+CCFILES=./algorithms/approx/MultiShiftFunction.cc ./algorithms/approx/Remez.cc ./algorithms/approx/Zolotarev.cc ./Init.cc ./Log.cc ./qcd/action/fermion/CayleyFermion5D.cc ./qcd/action/fermion/ContinuedFractionFermion5D.cc ./qcd/action/fermion/PartialFractionFermion5D.cc ./qcd/action/fermion/WilsonFermion.cc ./qcd/action/fermion/WilsonFermion5D.cc ./qcd/action/fermion/WilsonKernels.cc ./qcd/action/fermion/WilsonKernelsHand.cc ./qcd/hmc/HMC.cc ./qcd/hmc/integrators/Integrator.cc ./qcd/spin/Dirac.cc ./qcd/utils/SpaceTimeGrid.cc ./stencil/Lebesgue.cc ./stencil/Stencil_common.cc

lib/Timer.h

@@ -1,9 +1,17 @@
 #ifndef GRID_TIME_H
 #define GRID_TIME_H
-namespace Grid {
+
-  // Dress the output; use std::chrono
+#include <sys/time.h>
-#include <chrono>
 #include <ctime>
+#include <chrono>
+
+namespace Grid {
+
+
+  // Dress the output; use std::chrono
+
+// C++11 time facilities better?
+double usecond(void);
 
 typedef  std::chrono::system_clock          GridClock;
 typedef  std::chrono::time_point<GridClock> GridTimePoint;

lib/algorithms/approx/MultiShiftFunction.h

@@ -1,6 +1,8 @@
 #ifndef MULTI_SHIFT_FUNCTION
 #define MULTI_SHIFT_FUNCTION
+
 namespace Grid {
+
 class MultiShiftFunction {
 public:
   int order;

lib/pugixml/README.md

@@ -0,0 +1,44 @@
+pugixml [![Build Status](https://travis-ci.org/zeux/pugixml.svg?branch=master)](https://travis-ci.org/zeux/pugixml) [![Build status](https://ci.appveyor.com/api/projects/status/9hdks1doqvq8pwe7/branch/master?svg=true)](https://ci.appveyor.com/project/zeux/pugixml)
+=======
+
+pugixml is a C++ XML processing library, which consists of a DOM-like interface with rich traversal/modification
+capabilities, an extremely fast XML parser which constructs the DOM tree from an XML file/buffer, and an XPath 1.0
+implementation for complex data-driven tree queries. Full Unicode support is also available, with Unicode interface
+variants and conversions between different Unicode encodings (which happen automatically during parsing/saving).
+
+pugixml is used by a lot of projects, both open-source and proprietary, for performance and easy-to-use interface.
+
+## Documentation
+
+Documentation for the current release of pugixml is available on-line as two separate documents:
+
+* [Quick-start guide](http://pugixml.org/docs/quickstart.html), that aims to provide enough information to start using the library;
+* [Complete reference manual](http://pugixml.org/docs/manual.html), that describes all features of the library in detail.
+
+You’re advised to start with the quick-start guide; however, many important library features are either not described in it at all or only mentioned briefly; if you require more information you should read the complete manual.
+
+## License
+This library is available to anybody free of charge, under the terms of MIT License:
+
+Copyright (c) 2006-2015 Arseny Kapoulkine
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

lib/pugixml/pugiconfig.hpp

@@ -0,0 +1,71 @@
+/**
+ * pugixml parser - version 1.6
+ * --------------------------------------------------------
+ * Copyright (C) 2006-2015, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
+ * Report bugs and download new versions at http://pugixml.org/
+ *
+ * This library is distributed under the MIT License. See notice at the end
+ * of this file.
+ *
+ * This work is based on the pugxml parser, which is:
+ * Copyright (C) 2003, by Kristen Wegner (kristen@tima.net)
+ */
+
+#ifndef HEADER_PUGICONFIG_HPP
+#define HEADER_PUGICONFIG_HPP
+
+// Uncomment this to enable wchar_t mode
+// #define PUGIXML_WCHAR_MODE
+
+// Uncomment this to disable XPath
+// #define PUGIXML_NO_XPATH
+
+// Uncomment this to disable STL
+// #define PUGIXML_NO_STL
+
+// Uncomment this to disable exceptions
+// #define PUGIXML_NO_EXCEPTIONS
+
+// Set this to control attributes for public classes/functions, i.e.:
+// #define PUGIXML_API __declspec(dllexport) // to export all public symbols from DLL
+// #define PUGIXML_CLASS __declspec(dllimport) // to import all classes from DLL
+// #define PUGIXML_FUNCTION __fastcall // to set calling conventions to all public functions to fastcall
+// In absence of PUGIXML_CLASS/PUGIXML_FUNCTION definitions PUGIXML_API is used instead
+
+// Tune these constants to adjust memory-related behavior
+// #define PUGIXML_MEMORY_PAGE_SIZE 32768
+// #define PUGIXML_MEMORY_OUTPUT_STACK 10240
+// #define PUGIXML_MEMORY_XPATH_PAGE_SIZE 4096
+
+// Uncomment this to switch to header-only version
+// #define PUGIXML_HEADER_ONLY
+
+// Uncomment this to enable long long support
+// #define PUGIXML_HAS_LONG_LONG
+
+#endif
+
+/**
+ * Copyright (c) 2006-2015 Arseny Kapoulkine
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */

lib/pugixml/readme.txt

@@ -0,0 +1,52 @@
+pugixml 1.6 - an XML processing library
+
+Copyright (C) 2006-2015, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
+Report bugs and download new versions at http://pugixml.org/
+
+This is the distribution of pugixml, which is a C++ XML processing library,
+which consists of a DOM-like interface with rich traversal/modification
+capabilities, an extremely fast XML parser which constructs the DOM tree from
+an XML file/buffer, and an XPath 1.0 implementation for complex data-driven
+tree queries. Full Unicode support is also available, with Unicode interface
+variants and conversions between different Unicode encodings (which happen
+automatically during parsing/saving).
+
+The distribution contains the following folders:
+
+	contrib/ - various contributions to pugixml
+
+	docs/ - documentation
+		docs/samples - pugixml usage examples
+		docs/quickstart.html - quick start guide
+		docs/manual.html - complete manual
+
+	scripts/ - project files for IDE/build systems
+
+	src/ - header and source files
+
+	readme.txt - this file.
+
+This library is distributed under the MIT License:
+
+Copyright (c) 2006-2015 Arseny Kapoulkine
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

lib/qcd/action/ActionBase.h

@@ -7,14 +7,30 @@ template<class GaugeField>
 class Action { 
 
  public:
-  virtual void  init(const GaugeField &U, GridParallelRNG& pRNG) = 0;
+  virtual void  init (const GaugeField &U, GridParallelRNG& pRNG) = 0;  // 
-  virtual RealD S(const GaugeField &U)                           = 0;  // evaluate the action
+  virtual RealD S    (const GaugeField &U)                        = 0;  // evaluate the action
   virtual void  deriv(const GaugeField &U,GaugeField & dSdU )     = 0;  // evaluate the action derivative
-  //virtual void  refresh(const GaugeField & ) {}                ; 
+  virtual void  refresh(const GaugeField & ) {};                        // Default to no-op for actions with no internal fields
   // Boundary conditions?
   // Heatbath?
   virtual ~Action() {};
 };
 
+// Could derive PseudoFermion action with a PF field, FermionField, and a Grid; implement refresh
+template<class GaugeField, class FermionField>
+class PseudoFermionAction : public Action<GaugeField> {
+ public:
+  FermionField Phi;
+  GridParallelRNG &pRNG;
+  GridBase &Grid;
+
+  PseudoFermionAction(GridBase &_Grid,GridParallelRNG &_pRNG) : Grid(_Grid), Phi(&_Grid), pRNG(_pRNG) {
+  };
+
+  virtual void refresh(const GaugeField &gauge) {
+    gaussian(Phi,pRNG);
+  };
+
+};
 }}
 #endif

lib/qcd/action/fermion/WilsonFermion5D.cc

@@ -149,6 +149,7 @@ PARALLEL_FOR_LOOP
     ////////////////////////////
     // spin trace outer product
     ////////////////////////////
+// FIXME : need to sum over fifth direction.
     tmp = TraceIndex<SpinIndex>(outerProduct(Btilde,A)); // ordering here
     PokeIndex<LorentzIndex>(mat,tmp,mu);
 

lib/qcd/hmc/HMC.cc

@@ -17,8 +17,5 @@ namespace Grid{
 	  
       }
 
-
-   
-
   }
 }

lib/qcd/hmc/HMC.h

@@ -27,13 +27,22 @@ namespace Grid{
     
     template <class Algorithm> 
     class HybridMonteCarlo{
+
       const HMCparameters Params;
-      GridSerialRNG sRNG;
+
+      GridSerialRNG sRNG; // Fixme: need a RNG management strategy.
+
       Integrator<Algorithm>& MD;
 
+      /////////////////////////////////////////////////////////
+      // Metropolis step
+      /////////////////////////////////////////////////////////
       bool metropolis_test(const RealD DeltaH){
+
 	RealD rn_test;
+
 	RealD prob = std::exp(-DeltaH);
+
 	random(sRNG,rn_test);
       
 	std::cout<<GridLogMessage<< "--------------------------------------------\n";
@@ -47,11 +56,16 @@ namespace Grid{
 	  std::cout<<GridLogMessage <<"-- REJECTED\n";
 	  return false;
 	}
+
       }
 
+      /////////////////////////////////////////////////////////
+      // Evolution
+      /////////////////////////////////////////////////////////
       RealD evolve_step(LatticeLorentzColourMatrix& U){
 
 	MD.init(U); // set U and initialize P and phi's 
+
 	RealD H0 = MD.S(U); // initial state action  
 	std::cout<<GridLogMessage<<"Total H before = "<< H0 << "\n";
 
@@ -64,13 +78,17 @@ namespace Grid{
       }
       
     public:
-    HybridMonteCarlo(HMCparameters Pms, 
+
-		     Integrator<Algorithm>& MolDyn):
+      /////////////////////////////////////////
-      Params(Pms),MD(MolDyn){
+      // Constructor
-	//FIXME
+      /////////////////////////////////////////
-	// initialize RNGs also with seed
+      HybridMonteCarlo(HMCparameters Pms,  Integrator<Algorithm>& MolDyn): Params(Pms),MD(MolDyn) {
+
+	//FIXME...  initialize RNGs also with seed ; RNG management strategy
 	sRNG.SeedRandomDevice();
+
       }
+
       ~HybridMonteCarlo(){};
 
 
@@ -95,7 +113,8 @@ namespace Grid{
 	  DeltaH = evolve_step(Ucopy);
 		
 	  if(metropolis_test(DeltaH)) Uin = Ucopy;
-	  //need sync?
+	  //need sync? // Query Guido on this comment
+
 	}
       }
     };

tests/Make.inc

@@ -1,5 +1,5 @@
 
-bin_PROGRAMS = Test_GaugeAction Test_cayley_cg Test_cayley_coarsen_support Test_cayley_even_odd Test_cayley_ldop_cr Test_cf_coarsen_support Test_cf_cr_unprec Test_contfrac_cg Test_contfrac_even_odd Test_cshift Test_cshift_red_black Test_dwf_cg_prec Test_dwf_cg_schur Test_dwf_cg_unprec Test_dwf_cr_unprec Test_dwf_even_odd Test_dwf_fpgcr Test_dwf_hdcr Test_gamma Test_hmc_WilsonGauge Test_lie_generators Test_main Test_multishift_sqrt Test_nersc_io Test_quenched_update Test_remez Test_rng Test_rng_fixed Test_simd Test_stencil Test_wilson_cg_prec Test_wilson_cg_schur Test_wilson_cg_unprec Test_wilson_cr_unprec Test_wilson_even_odd Test_wilson_force Test_wilson_force_phiMphi
+bin_PROGRAMS = Test_GaugeAction Test_cayley_cg Test_cayley_coarsen_support Test_cayley_even_odd Test_cayley_ldop_cr Test_cf_coarsen_support Test_cf_cr_unprec Test_contfrac_cg Test_contfrac_even_odd Test_cshift Test_cshift_red_black Test_dwf_cg_prec Test_dwf_cg_schur Test_dwf_cg_unprec Test_dwf_cr_unprec Test_dwf_even_odd Test_dwf_fpgcr Test_dwf_hdcr Test_gamma Test_hmc_WilsonGauge Test_lie_generators Test_main Test_multishift_sqrt Test_nersc_io Test_quenched_update Test_remez Test_rng Test_rng_fixed Test_simd Test_stencil Test_wilson_cg_prec Test_wilson_cg_schur Test_wilson_cg_unprec Test_wilson_cr_unprec Test_wilson_even_odd Test_wilson_force Test_wilson_force_phiMdagMphi Test_wilson_force_phiMphi
 
 
 Test_GaugeAction_SOURCES=Test_GaugeAction.cc
@@ -146,6 +146,10 @@ Test_wilson_force_SOURCES=Test_wilson_force.cc
 Test_wilson_force_LDADD=-lGrid
 
 
+Test_wilson_force_phiMdagMphi_SOURCES=Test_wilson_force_phiMdagMphi.cc
+Test_wilson_force_phiMdagMphi_LDADD=-lGrid
+
+
 Test_wilson_force_phiMphi_SOURCES=Test_wilson_force_phiMphi.cc
 Test_wilson_force_phiMphi_LDADD=-lGrid