From ce29b18dc9971dac36e20ddfb4ef35ea748500a0 Mon Sep 17 00:00:00 2001
From: fionnoh <fionnoh@gmail.com>
Date: Thu, 27 Jun 2019 13:46:06 +0800
Subject: [PATCH] New modules for loading in MFs as diskvectors and producing
 propagaotrs from 4 quark contractions

---
 Hadrons/Modules.hpp                           | 120 ++++-----
 .../MContraction/A2AFourQuarkContraction.cc   |   7 +
 .../MContraction/A2AFourQuarkContraction.hpp  | 105 ++++++++
 .../Modules/MIO/LoadA2AMatrixDiskVector.cc    |   7 +
 .../Modules/MIO/LoadA2AMatrixDiskVector.hpp   | 115 +++++++++
 Hadrons/modules.inc                           | 232 +++++++++---------
 6 files changed, 413 insertions(+), 173 deletions(-)
 create mode 100644 Hadrons/Modules/MContraction/A2AFourQuarkContraction.cc
 create mode 100644 Hadrons/Modules/MContraction/A2AFourQuarkContraction.hpp
 create mode 100644 Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.cc
 create mode 100644 Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.hpp

diff --git a/Hadrons/Modules.hpp b/Hadrons/Modules.hpp
index 898cb532..4d5e9db4 100644
--- a/Hadrons/Modules.hpp
+++ b/Hadrons/Modules.hpp
@@ -1,69 +1,71 @@
-#include <Hadrons/Modules/MContraction/WeakEye3pt.hpp>
-#include <Hadrons/Modules/MContraction/Baryon.hpp>
-#include <Hadrons/Modules/MContraction/A2AAslashField.hpp>
-#include <Hadrons/Modules/MContraction/A2ALoop.hpp>
-#include <Hadrons/Modules/MContraction/A2AMesonField.hpp>
-#include <Hadrons/Modules/MContraction/Meson.hpp>
-#include <Hadrons/Modules/MContraction/DiscLoop.hpp>
-#include <Hadrons/Modules/MContraction/Gamma3pt.hpp>
-#include <Hadrons/Modules/MContraction/WeakMesonDecayKl2.hpp>
-#include <Hadrons/Modules/MContraction/WeakNonEye3pt.hpp>
-#include <Hadrons/Modules/MFermion/FreeProp.hpp>
-#include <Hadrons/Modules/MFermion/GaugeProp.hpp>
-#include <Hadrons/Modules/MFermion/EMLepton.hpp>
+#include <Hadrons/Modules/MSource/Momentum.hpp>
+#include <Hadrons/Modules/MSource/SeqConserved.hpp>
 #include <Hadrons/Modules/MSource/SeqGamma.hpp>
 #include <Hadrons/Modules/MSource/SeqAslash.hpp>
+#include <Hadrons/Modules/MSource/Z2.hpp>
 #include <Hadrons/Modules/MSource/Point.hpp>
 #include <Hadrons/Modules/MSource/Wall.hpp>
-#include <Hadrons/Modules/MSource/Z2.hpp>
-#include <Hadrons/Modules/MSource/SeqConserved.hpp>
-#include <Hadrons/Modules/MSource/Momentum.hpp>
 #include <Hadrons/Modules/MSink/Smear.hpp>
 #include <Hadrons/Modules/MSink/Point.hpp>
-#include <Hadrons/Modules/MSolver/MixedPrecisionRBPrecCG.hpp>
-#include <Hadrons/Modules/MSolver/LocalCoherenceLanczos.hpp>
-#include <Hadrons/Modules/MSolver/A2AAslashVectors.hpp>
-#include <Hadrons/Modules/MSolver/Guesser.hpp>
-#include <Hadrons/Modules/MSolver/RBPrecCG.hpp>
-#include <Hadrons/Modules/MSolver/A2AVectors.hpp>
-#include <Hadrons/Modules/MGauge/UnitEm.hpp>
-#include <Hadrons/Modules/MGauge/StoutSmearing.hpp>
-#include <Hadrons/Modules/MGauge/Unit.hpp>
-#include <Hadrons/Modules/MGauge/Random.hpp>
-#include <Hadrons/Modules/MGauge/GaugeFix.hpp>
-#include <Hadrons/Modules/MGauge/FundtoHirep.hpp>
-#include <Hadrons/Modules/MGauge/StochEm.hpp>
-#include <Hadrons/Modules/MGauge/Electrify.hpp>
-#include <Hadrons/Modules/MNoise/TimeDilutedSpinColorDiagonal.hpp>
-#include <Hadrons/Modules/MNoise/FullVolumeSpinColorDiagonal.hpp>
-#include <Hadrons/Modules/MUtilities/PrecisionCast.hpp>
-#include <Hadrons/Modules/MUtilities/RandomVectors.hpp>
-#include <Hadrons/Modules/MScalar/FreeProp.hpp>
-#include <Hadrons/Modules/MScalar/Scalar.hpp>
-#include <Hadrons/Modules/MScalar/ChargedProp.hpp>
-#include <Hadrons/Modules/MNPR/Bilinear.hpp>
-#include <Hadrons/Modules/MNPR/Amputate.hpp>
-#include <Hadrons/Modules/MNPR/FourQuark.hpp>
-#include <Hadrons/Modules/MAction/DWF.hpp>
-#include <Hadrons/Modules/MAction/MobiusDWF.hpp>
-#include <Hadrons/Modules/MAction/Wilson.hpp>
-#include <Hadrons/Modules/MAction/WilsonClover.hpp>
-#include <Hadrons/Modules/MAction/ZMobiusDWF.hpp>
-#include <Hadrons/Modules/MAction/ScaledDWF.hpp>
-#include <Hadrons/Modules/MScalarSUN/StochFreeField.hpp>
+#include <Hadrons/Modules/MIO/LoadCosmHol.hpp>
+#include <Hadrons/Modules/MIO/LoadBinary.hpp>
+#include <Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.hpp>
+#include <Hadrons/Modules/MIO/LoadEigenPack.hpp>
+#include <Hadrons/Modules/MIO/LoadCoarseEigenPack.hpp>
+#include <Hadrons/Modules/MIO/LoadA2AVectors.hpp>
+#include <Hadrons/Modules/MIO/LoadNersc.hpp>
+#include <Hadrons/Modules/MScalarSUN/Utils.hpp>
+#include <Hadrons/Modules/MScalarSUN/Grad.hpp>
+#include <Hadrons/Modules/MScalarSUN/TrPhi.hpp>
 #include <Hadrons/Modules/MScalarSUN/TwoPointNPR.hpp>
+#include <Hadrons/Modules/MScalarSUN/TwoPoint.hpp>
+#include <Hadrons/Modules/MScalarSUN/TransProj.hpp>
+#include <Hadrons/Modules/MScalarSUN/TrKinetic.hpp>
+#include <Hadrons/Modules/MScalarSUN/StochFreeField.hpp>
 #include <Hadrons/Modules/MScalarSUN/Div.hpp>
 #include <Hadrons/Modules/MScalarSUN/TrMag.hpp>
 #include <Hadrons/Modules/MScalarSUN/EMT.hpp>
-#include <Hadrons/Modules/MScalarSUN/TwoPoint.hpp>
-#include <Hadrons/Modules/MScalarSUN/TrPhi.hpp>
-#include <Hadrons/Modules/MScalarSUN/Utils.hpp>
-#include <Hadrons/Modules/MScalarSUN/TransProj.hpp>
-#include <Hadrons/Modules/MScalarSUN/Grad.hpp>
-#include <Hadrons/Modules/MScalarSUN/TrKinetic.hpp>
-#include <Hadrons/Modules/MIO/LoadEigenPack.hpp>
-#include <Hadrons/Modules/MIO/LoadNersc.hpp>
-#include <Hadrons/Modules/MIO/LoadA2AVectors.hpp>
-#include <Hadrons/Modules/MIO/LoadCosmHol.hpp>
-#include <Hadrons/Modules/MIO/LoadCoarseEigenPack.hpp>
-#include <Hadrons/Modules/MIO/LoadBinary.hpp>
+#include <Hadrons/Modules/MAction/ZMobiusDWF.hpp>
+#include <Hadrons/Modules/MAction/ScaledDWF.hpp>
+#include <Hadrons/Modules/MAction/Wilson.hpp>
+#include <Hadrons/Modules/MAction/WilsonClover.hpp>
+#include <Hadrons/Modules/MAction/MobiusDWF.hpp>
+#include <Hadrons/Modules/MAction/DWF.hpp>
+#include <Hadrons/Modules/MContraction/DiscLoop.hpp>
+#include <Hadrons/Modules/MContraction/WeakEye3pt.hpp>
+#include <Hadrons/Modules/MContraction/Meson.hpp>
+#include <Hadrons/Modules/MContraction/A2AMesonField.hpp>
+#include <Hadrons/Modules/MContraction/Gamma3pt.hpp>
+#include <Hadrons/Modules/MContraction/WeakNonEye3pt.hpp>
+#include <Hadrons/Modules/MContraction/Baryon.hpp>
+#include <Hadrons/Modules/MContraction/A2AFourQuarkContraction.hpp>
+#include <Hadrons/Modules/MContraction/A2ALoop.hpp>
+#include <Hadrons/Modules/MContraction/WeakMesonDecayKl2.hpp>
+#include <Hadrons/Modules/MContraction/A2AAslashField.hpp>
+#include <Hadrons/Modules/MScalar/Scalar.hpp>
+#include <Hadrons/Modules/MScalar/FreeProp.hpp>
+#include <Hadrons/Modules/MScalar/ChargedProp.hpp>
+#include <Hadrons/Modules/MNoise/FullVolumeSpinColorDiagonal.hpp>
+#include <Hadrons/Modules/MNoise/TimeDilutedSpinColorDiagonal.hpp>
+#include <Hadrons/Modules/MUtilities/RandomVectors.hpp>
+#include <Hadrons/Modules/MUtilities/PrecisionCast.hpp>
+#include <Hadrons/Modules/MFermion/FreeProp.hpp>
+#include <Hadrons/Modules/MFermion/EMLepton.hpp>
+#include <Hadrons/Modules/MFermion/GaugeProp.hpp>
+#include <Hadrons/Modules/MSolver/A2AAslashVectors.hpp>
+#include <Hadrons/Modules/MSolver/Guesser.hpp>
+#include <Hadrons/Modules/MSolver/A2AVectors.hpp>
+#include <Hadrons/Modules/MSolver/RBPrecCG.hpp>
+#include <Hadrons/Modules/MSolver/LocalCoherenceLanczos.hpp>
+#include <Hadrons/Modules/MSolver/MixedPrecisionRBPrecCG.hpp>
+#include <Hadrons/Modules/MNPR/FourQuark.hpp>
+#include <Hadrons/Modules/MNPR/Bilinear.hpp>
+#include <Hadrons/Modules/MNPR/Amputate.hpp>
+#include <Hadrons/Modules/MGauge/StoutSmearing.hpp>
+#include <Hadrons/Modules/MGauge/GaugeFix.hpp>
+#include <Hadrons/Modules/MGauge/StochEm.hpp>
+#include <Hadrons/Modules/MGauge/FundtoHirep.hpp>
+#include <Hadrons/Modules/MGauge/Unit.hpp>
+#include <Hadrons/Modules/MGauge/Random.hpp>
+#include <Hadrons/Modules/MGauge/UnitEm.hpp>
+#include <Hadrons/Modules/MGauge/Electrify.hpp>
diff --git a/Hadrons/Modules/MContraction/A2AFourQuarkContraction.cc b/Hadrons/Modules/MContraction/A2AFourQuarkContraction.cc
new file mode 100644
index 00000000..9afe12ba
--- /dev/null
+++ b/Hadrons/Modules/MContraction/A2AFourQuarkContraction.cc
@@ -0,0 +1,7 @@
+#include <Hadrons/Modules/MContraction/A2AFourQuarkContraction.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MContraction;
+
+template class Grid::Hadrons::MContraction::TA2AFourQuarkContraction<FIMPL>;
diff --git a/Hadrons/Modules/MContraction/A2AFourQuarkContraction.hpp b/Hadrons/Modules/MContraction/A2AFourQuarkContraction.hpp
new file mode 100644
index 00000000..f977caab
--- /dev/null
+++ b/Hadrons/Modules/MContraction/A2AFourQuarkContraction.hpp
@@ -0,0 +1,105 @@
+#ifndef Hadrons_MContraction_A2AFourQuarkContraction_hpp_
+#define Hadrons_MContraction_A2AFourQuarkContraction_hpp_
+
+#include <Hadrons/Global.hpp>
+#include <Hadrons/Module.hpp>
+#include <Hadrons/ModuleFactory.hpp>
+#include <Hadrons/DiskVector.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         A2AFourQuarkContraction                                 *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MContraction)
+
+class A2AFourQuarkContractionPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(A2AFourQuarkContractionPar,
+                                    std::string, v1,
+                                    std::string, v2,
+                                    std::string, mf12);
+};
+
+template <typename FImpl>
+class TA2AFourQuarkContraction: public Module<A2AFourQuarkContractionPar>
+{
+  public:
+    FERM_TYPE_ALIASES(FImpl, );
+    // constructor
+    TA2AFourQuarkContraction(const std::string name);
+    // destructor
+    virtual ~TA2AFourQuarkContraction(void) {};
+    // 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_TMP(A2AFourQuarkContraction, TA2AFourQuarkContraction<FIMPL>, MContraction);
+
+/******************************************************************************
+ *                 TA2AFourQuarkContraction implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TA2AFourQuarkContraction<FImpl>::TA2AFourQuarkContraction(const std::string name)
+: Module<A2AFourQuarkContractionPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TA2AFourQuarkContraction<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().v1, par().v2, par().mf12};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TA2AFourQuarkContraction<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TA2AFourQuarkContraction<FImpl>::setup(void)
+{
+    int nt = env().getDim(Tp);
+
+    envCreate(std::vector<PropagatorField>, getName(), 1, nt, envGetGrid(PropagatorField));
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TA2AFourQuarkContraction<FImpl>::execute(void)
+{
+    int nt = env().getDim(Tp);
+
+    auto &v1   = envGet(std::vector<FermionField>, par().v1);
+    auto &v2   = envGet(std::vector<FermionField>, par().v2);
+    auto &mf12 = envGet(EigenDiskVector<Complex>, par().mf12);
+
+    auto &wwvv = envGet(std::vector<PropagatorField>, getName());
+
+    for (int t = 0; t < nt; t++)
+    {
+        wwvv[t] = zero;
+    }
+
+    LOG(Message) << "Computing 4 quark contraction for: " << getName() << std::endl;
+    A2Autils<FImpl>::ContractWWVV(wwvv, mf12, &v1[0], &v2[0]);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MContraction_A2AFourQuarkContraction_hpp_
diff --git a/Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.cc b/Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.cc
new file mode 100644
index 00000000..696e159c
--- /dev/null
+++ b/Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.cc
@@ -0,0 +1,7 @@
+#include <Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MIO;
+
+template class Grid::Hadrons::MIO::TLoadA2AMatrixDiskVector<FIMPL>;
diff --git a/Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.hpp b/Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.hpp
new file mode 100644
index 00000000..d7799a37
--- /dev/null
+++ b/Hadrons/Modules/MIO/LoadA2AMatrixDiskVector.hpp
@@ -0,0 +1,115 @@
+#ifndef Hadrons_MIO_LoadA2AMatrixDiskVector_hpp_
+#define Hadrons_MIO_LoadA2AMatrixDiskVector_hpp_
+
+#include <Hadrons/Global.hpp>
+#include <Hadrons/Module.hpp>
+#include <Hadrons/ModuleFactory.hpp>
+#include <Hadrons/A2AMatrix.hpp>
+#include <Hadrons/DiskVector.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         LoadA2AMatrixDiskVector                                 *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MIO)
+
+class LoadA2AMatrixDiskVectorPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(LoadA2AMatrixDiskVectorPar,
+                                    std::string,  file,
+                                    std::string,  dataset,
+                                    std::string,  diskVectorDir,
+                                    int,  cacheSize);
+};
+
+template <typename FImpl>
+class TLoadA2AMatrixDiskVector: public Module<LoadA2AMatrixDiskVectorPar>
+{
+  public:
+    FERM_TYPE_ALIASES(FImpl, );
+    // constructor
+    TLoadA2AMatrixDiskVector(const std::string name);
+    // destructor
+    virtual ~TLoadA2AMatrixDiskVector(void) {};
+    // 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_TMP(LoadA2AMatrixDiskVector, TLoadA2AMatrixDiskVector<FIMPL>, MIO);
+
+/******************************************************************************
+ *                 TLoadA2AMatrixDiskVector implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TLoadA2AMatrixDiskVector<FImpl>::TLoadA2AMatrixDiskVector(const std::string name)
+: Module<LoadA2AMatrixDiskVectorPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TLoadA2AMatrixDiskVector<FImpl>::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TLoadA2AMatrixDiskVector<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TLoadA2AMatrixDiskVector<FImpl>::setup(void)
+{
+    int Ls = 1;
+
+    std::string dvDir = par().diskVectorDir;
+    std::string dataset = par().dataset;
+    std::string dvFile = dvDir + "/" + getName() + "." + std::to_string(vm().getTrajectory());
+
+    int nt = env().getDim(Tp);
+    int cacheSize = par().cacheSize;
+    bool clean = true;
+    GridBase *grid = envGetGrid(FermionField);
+
+    envCreate(EigenDiskVector<ComplexD>, getName(), Ls, dvFile, nt, cacheSize, clean, grid);
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TLoadA2AMatrixDiskVector<FImpl>::execute(void)
+{
+    int nt = env().getDim(Tp);
+    std::string file  = par().file;
+    std::string dataset  = par().dataset;
+    GridBase *grid = envGetGrid(FermionField);
+
+    auto &mesonFieldDV = envGet(EigenDiskVector<ComplexD>, getName());
+
+    int traj = vm().getTrajectory();
+    tokenReplace(file, "traj", traj);
+    LOG(Message) << "-- Loading '" << file << "'-- " << std::endl;
+    double t;
+    A2AMatrixIo<HADRONS_A2AM_IO_TYPE> mfIO(file, dataset, nt);
+    mfIO.load(mesonFieldDV, &t, grid);
+    LOG(Message) << "Read " << mfIO.getSize() << " bytes in " << t << " usec, " << mfIO.getSize() / t * 1.0e6 / 1024 / 1024 << " MB/s" << std::endl;
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MIO_LoadA2AMatrixDiskVector_hpp_
diff --git a/Hadrons/modules.inc b/Hadrons/modules.inc
index 3b9e6563..d607c4bc 100644
--- a/Hadrons/modules.inc
+++ b/Hadrons/modules.inc
@@ -1,139 +1,143 @@
 modules_cc =\
-  Modules/MContraction/Baryon.cc \
-  Modules/MContraction/Meson.cc \
-  Modules/MContraction/WeakMesonDecayKl2.cc \
-  Modules/MContraction/WeakEye3pt.cc \
-  Modules/MContraction/A2ALoop.cc \
-  Modules/MContraction/WeakNonEye3pt.cc \
-  Modules/MContraction/A2AAslashField.cc \
-  Modules/MContraction/A2AMesonField.cc \
-  Modules/MContraction/DiscLoop.cc \
-  Modules/MContraction/Gamma3pt.cc \
-  Modules/MFermion/FreeProp.cc \
-  Modules/MFermion/GaugeProp.cc \
-  Modules/MFermion/EMLepton.cc \
-  Modules/MSource/Momentum.cc \
-  Modules/MSource/Point.cc \
-  Modules/MSource/Wall.cc \
   Modules/MSource/SeqConserved.cc \
   Modules/MSource/SeqGamma.cc \
-  Modules/MSource/SeqAslash.cc \
+  Modules/MSource/Momentum.cc \
+  Modules/MSource/Point.cc \
   Modules/MSource/Z2.cc \
+  Modules/MSource/SeqAslash.cc \
+  Modules/MSource/Wall.cc \
   Modules/MSink/Point.cc \
   Modules/MSink/Smear.cc \
-  Modules/MSolver/A2AVectors.cc \
-  Modules/MSolver/A2AAslashVectors.cc \
-  Modules/MSolver/RBPrecCG.cc \
-  Modules/MSolver/MixedPrecisionRBPrecCG.cc \
-  Modules/MSolver/LocalCoherenceLanczos.cc \
-  Modules/MGauge/StoutSmearing.cc \
-  Modules/MGauge/Unit.cc \
-  Modules/MGauge/UnitEm.cc \
-  Modules/MGauge/StochEm.cc \
-  Modules/MGauge/Random.cc \
-  Modules/MGauge/Electrify.cc \
-  Modules/MGauge/FundtoHirep.cc \
-  Modules/MGauge/GaugeFix.cc \
-  Modules/MNoise/FullVolumeSpinColorDiagonal.cc \
+  Modules/MIO/LoadA2AMatrixDiskVector.cc \
+  Modules/MIO/LoadNersc.cc \
+  Modules/MIO/LoadEigenPack.cc \
+  Modules/MIO/LoadCosmHol.cc \
+  Modules/MIO/LoadA2AVectors.cc \
+  Modules/MIO/LoadCoarseEigenPack.cc \
+  Modules/MIO/LoadBinary.cc \
+  Modules/MScalarSUN/TwoPointNPR.cc \
+  Modules/MScalarSUN/TrPhi.cc \
+  Modules/MScalarSUN/StochFreeField.cc \
+  Modules/MScalarSUN/TrMag.cc \
+  Modules/MScalarSUN/Div.cc \
+  Modules/MScalarSUN/Grad.cc \
+  Modules/MScalarSUN/TwoPoint.cc \
+  Modules/MScalarSUN/EMT.cc \
+  Modules/MScalarSUN/TransProj.cc \
+  Modules/MScalarSUN/TrKinetic.cc \
+  Modules/MAction/DWF.cc \
+  Modules/MAction/MobiusDWF.cc \
+  Modules/MAction/ZMobiusDWF.cc \
+  Modules/MAction/Wilson.cc \
+  Modules/MAction/ScaledDWF.cc \
+  Modules/MAction/WilsonClover.cc \
+  Modules/MContraction/WeakEye3pt.cc \
+  Modules/MContraction/DiscLoop.cc \
+  Modules/MContraction/Baryon.cc \
+  Modules/MContraction/A2AMesonField.cc \
+  Modules/MContraction/Gamma3pt.cc \
+  Modules/MContraction/A2ALoop.cc \
+  Modules/MContraction/A2AAslashField.cc \
+  Modules/MContraction/Meson.cc \
+  Modules/MContraction/A2AFourQuarkContraction.cc \
+  Modules/MContraction/WeakMesonDecayKl2.cc \
+  Modules/MContraction/WeakNonEye3pt.cc \
+  Modules/MScalar/ChargedProp.cc \
+  Modules/MScalar/FreeProp.cc \
   Modules/MNoise/TimeDilutedSpinColorDiagonal.cc \
+  Modules/MNoise/FullVolumeSpinColorDiagonal.cc \
   Modules/MUtilities/RandomVectors.cc \
   Modules/MUtilities/PrecisionCast.cc \
-  Modules/MScalar/FreeProp.cc \
-  Modules/MScalar/ChargedProp.cc \
+  Modules/MFermion/EMLepton.cc \
+  Modules/MFermion/FreeProp.cc \
+  Modules/MFermion/GaugeProp.cc \
+  Modules/MSolver/RBPrecCG.cc \
+  Modules/MSolver/LocalCoherenceLanczos.cc \
+  Modules/MSolver/MixedPrecisionRBPrecCG.cc \
+  Modules/MSolver/A2AVectors.cc \
+  Modules/MSolver/A2AAslashVectors.cc \
   Modules/MNPR/Amputate.cc \
   Modules/MNPR/Bilinear.cc \
   Modules/MNPR/FourQuark.cc \
-  Modules/MAction/Wilson.cc \
-  Modules/MAction/MobiusDWF.cc \
-  Modules/MAction/ZMobiusDWF.cc \
-  Modules/MAction/WilsonClover.cc \
-  Modules/MAction/DWF.cc \
-  Modules/MAction/ScaledDWF.cc \
-  Modules/MScalarSUN/TrPhi.cc \
-  Modules/MScalarSUN/Grad.cc \
-  Modules/MScalarSUN/TrMag.cc \
-  Modules/MScalarSUN/TrKinetic.cc \
-  Modules/MScalarSUN/EMT.cc \
-  Modules/MScalarSUN/TransProj.cc \
-  Modules/MScalarSUN/StochFreeField.cc \
-  Modules/MScalarSUN/TwoPoint.cc \
-  Modules/MScalarSUN/TwoPointNPR.cc \
-  Modules/MScalarSUN/Div.cc \
-  Modules/MIO/LoadEigenPack.cc \
-  Modules/MIO/LoadBinary.cc \
-  Modules/MIO/LoadNersc.cc \
-  Modules/MIO/LoadCoarseEigenPack.cc \
-  Modules/MIO/LoadCosmHol.cc \
-  Modules/MIO/LoadA2AVectors.cc
+  Modules/MGauge/Unit.cc \
+  Modules/MGauge/Electrify.cc \
+  Modules/MGauge/Random.cc \
+  Modules/MGauge/GaugeFix.cc \
+  Modules/MGauge/UnitEm.cc \
+  Modules/MGauge/StochEm.cc \
+  Modules/MGauge/FundtoHirep.cc \
+  Modules/MGauge/StoutSmearing.cc
 
 modules_hpp =\
-  Modules/MContraction/WeakEye3pt.hpp \
-  Modules/MContraction/Baryon.hpp \
-  Modules/MContraction/A2AAslashField.hpp \
-  Modules/MContraction/A2ALoop.hpp \
-  Modules/MContraction/A2AMesonField.hpp \
-  Modules/MContraction/Meson.hpp \
-  Modules/MContraction/DiscLoop.hpp \
-  Modules/MContraction/Gamma3pt.hpp \
-  Modules/MContraction/WeakMesonDecayKl2.hpp \
-  Modules/MContraction/WeakNonEye3pt.hpp \
-  Modules/MFermion/FreeProp.hpp \
-  Modules/MFermion/GaugeProp.hpp \
-  Modules/MFermion/EMLepton.hpp \
+  Modules/MSource/Momentum.hpp \
+  Modules/MSource/SeqConserved.hpp \
   Modules/MSource/SeqGamma.hpp \
   Modules/MSource/SeqAslash.hpp \
+  Modules/MSource/Z2.hpp \
   Modules/MSource/Point.hpp \
   Modules/MSource/Wall.hpp \
-  Modules/MSource/Z2.hpp \
-  Modules/MSource/SeqConserved.hpp \
-  Modules/MSource/Momentum.hpp \
   Modules/MSink/Smear.hpp \
   Modules/MSink/Point.hpp \
-  Modules/MSolver/MixedPrecisionRBPrecCG.hpp \
-  Modules/MSolver/LocalCoherenceLanczos.hpp \
-  Modules/MSolver/A2AAslashVectors.hpp \
-  Modules/MSolver/Guesser.hpp \
-  Modules/MSolver/RBPrecCG.hpp \
-  Modules/MSolver/A2AVectors.hpp \
-  Modules/MGauge/UnitEm.hpp \
-  Modules/MGauge/StoutSmearing.hpp \
-  Modules/MGauge/Unit.hpp \
-  Modules/MGauge/Random.hpp \
-  Modules/MGauge/GaugeFix.hpp \
-  Modules/MGauge/FundtoHirep.hpp \
-  Modules/MGauge/StochEm.hpp \
-  Modules/MGauge/Electrify.hpp \
-  Modules/MNoise/TimeDilutedSpinColorDiagonal.hpp \
-  Modules/MNoise/FullVolumeSpinColorDiagonal.hpp \
-  Modules/MUtilities/PrecisionCast.hpp \
-  Modules/MUtilities/RandomVectors.hpp \
-  Modules/MScalar/FreeProp.hpp \
-  Modules/MScalar/Scalar.hpp \
-  Modules/MScalar/ChargedProp.hpp \
-  Modules/MNPR/Bilinear.hpp \
-  Modules/MNPR/Amputate.hpp \
-  Modules/MNPR/FourQuark.hpp \
-  Modules/MAction/DWF.hpp \
-  Modules/MAction/MobiusDWF.hpp \
-  Modules/MAction/Wilson.hpp \
-  Modules/MAction/WilsonClover.hpp \
-  Modules/MAction/ZMobiusDWF.hpp \
-  Modules/MAction/ScaledDWF.hpp \
-  Modules/MScalarSUN/StochFreeField.hpp \
+  Modules/MIO/LoadCosmHol.hpp \
+  Modules/MIO/LoadBinary.hpp \
+  Modules/MIO/LoadA2AMatrixDiskVector.hpp \
+  Modules/MIO/LoadEigenPack.hpp \
+  Modules/MIO/LoadCoarseEigenPack.hpp \
+  Modules/MIO/LoadA2AVectors.hpp \
+  Modules/MIO/LoadNersc.hpp \
+  Modules/MScalarSUN/Utils.hpp \
+  Modules/MScalarSUN/Grad.hpp \
+  Modules/MScalarSUN/TrPhi.hpp \
   Modules/MScalarSUN/TwoPointNPR.hpp \
+  Modules/MScalarSUN/TwoPoint.hpp \
+  Modules/MScalarSUN/TransProj.hpp \
+  Modules/MScalarSUN/TrKinetic.hpp \
+  Modules/MScalarSUN/StochFreeField.hpp \
   Modules/MScalarSUN/Div.hpp \
   Modules/MScalarSUN/TrMag.hpp \
   Modules/MScalarSUN/EMT.hpp \
-  Modules/MScalarSUN/TwoPoint.hpp \
-  Modules/MScalarSUN/TrPhi.hpp \
-  Modules/MScalarSUN/Utils.hpp \
-  Modules/MScalarSUN/TransProj.hpp \
-  Modules/MScalarSUN/Grad.hpp \
-  Modules/MScalarSUN/TrKinetic.hpp \
-  Modules/MIO/LoadEigenPack.hpp \
-  Modules/MIO/LoadNersc.hpp \
-  Modules/MIO/LoadA2AVectors.hpp \
-  Modules/MIO/LoadCosmHol.hpp \
-  Modules/MIO/LoadCoarseEigenPack.hpp \
-  Modules/MIO/LoadBinary.hpp
+  Modules/MAction/ZMobiusDWF.hpp \
+  Modules/MAction/ScaledDWF.hpp \
+  Modules/MAction/Wilson.hpp \
+  Modules/MAction/WilsonClover.hpp \
+  Modules/MAction/MobiusDWF.hpp \
+  Modules/MAction/DWF.hpp \
+  Modules/MContraction/DiscLoop.hpp \
+  Modules/MContraction/WeakEye3pt.hpp \
+  Modules/MContraction/Meson.hpp \
+  Modules/MContraction/A2AMesonField.hpp \
+  Modules/MContraction/Gamma3pt.hpp \
+  Modules/MContraction/WeakNonEye3pt.hpp \
+  Modules/MContraction/Baryon.hpp \
+  Modules/MContraction/A2AFourQuarkContraction.hpp \
+  Modules/MContraction/A2ALoop.hpp \
+  Modules/MContraction/WeakMesonDecayKl2.hpp \
+  Modules/MContraction/A2AAslashField.hpp \
+  Modules/MScalar/Scalar.hpp \
+  Modules/MScalar/FreeProp.hpp \
+  Modules/MScalar/ChargedProp.hpp \
+  Modules/MNoise/FullVolumeSpinColorDiagonal.hpp \
+  Modules/MNoise/TimeDilutedSpinColorDiagonal.hpp \
+  Modules/MUtilities/RandomVectors.hpp \
+  Modules/MUtilities/PrecisionCast.hpp \
+  Modules/MFermion/FreeProp.hpp \
+  Modules/MFermion/EMLepton.hpp \
+  Modules/MFermion/GaugeProp.hpp \
+  Modules/MSolver/A2AAslashVectors.hpp \
+  Modules/MSolver/Guesser.hpp \
+  Modules/MSolver/A2AVectors.hpp \
+  Modules/MSolver/RBPrecCG.hpp \
+  Modules/MSolver/LocalCoherenceLanczos.hpp \
+  Modules/MSolver/MixedPrecisionRBPrecCG.hpp \
+  Modules/MNPR/FourQuark.hpp \
+  Modules/MNPR/Bilinear.hpp \
+  Modules/MNPR/Amputate.hpp \
+  Modules/MGauge/StoutSmearing.hpp \
+  Modules/MGauge/GaugeFix.hpp \
+  Modules/MGauge/StochEm.hpp \
+  Modules/MGauge/FundtoHirep.hpp \
+  Modules/MGauge/Unit.hpp \
+  Modules/MGauge/Random.hpp \
+  Modules/MGauge/UnitEm.hpp \
+  Modules/MGauge/Electrify.hpp