From 3848da7c50a0a4e3556162e86ebe200fea0f200e Mon Sep 17 00:00:00 2001
From: Felix Erben <dc-erbe1@tesseract-login1.ib0.sgi.cluster.dirac.ed.ac.uk>
Date: Mon, 8 Jul 2019 17:43:14 +0100
Subject: [PATCH] added nucleon module (non-distillation)

---
 Hadrons/Modules.hpp                      | 139 ++++++------
 Hadrons/Modules/MContraction/Nucleon.cc  |  35 +++
 Hadrons/Modules/MContraction/Nucleon.hpp | 168 ++++++++++++++
 Hadrons/modules.inc                      | 266 ++++++++++++-----------
 4 files changed, 407 insertions(+), 201 deletions(-)
 create mode 100644 Hadrons/Modules/MContraction/Nucleon.cc
 create mode 100644 Hadrons/Modules/MContraction/Nucleon.hpp

diff --git a/Hadrons/Modules.hpp b/Hadrons/Modules.hpp
index 4a62cf02..07d24378 100644
--- a/Hadrons/Modules.hpp
+++ b/Hadrons/Modules.hpp
@@ -1,80 +1,81 @@
-#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/SeqGamma.hpp>
-#include <Hadrons/Modules/MSource/SeqAslash.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/StoutSmearing3D.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/MDistil/LapEvec.hpp>
-#include <Hadrons/Modules/MDistil/DistilVectors.hpp>
-#include <Hadrons/Modules/MDistil/Noises.hpp>
-#include <Hadrons/Modules/MDistil/BC2.hpp>
-#include <Hadrons/Modules/MDistil/Perambulator.hpp>
-#include <Hadrons/Modules/MDistil/PerambFromSolve.hpp>
-#include <Hadrons/Modules/MDistil/BContraction.hpp>
-#include <Hadrons/Modules/MDistil/Baryon2pt.hpp>
-#include <Hadrons/Modules/MDistil/g5_multiply.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/TrKinetic.hpp>
 #include <Hadrons/Modules/MScalarSUN/StochFreeField.hpp>
 #include <Hadrons/Modules/MScalarSUN/TwoPointNPR.hpp>
+#include <Hadrons/Modules/MScalarSUN/Grad.hpp>
+#include <Hadrons/Modules/MScalarSUN/TransProj.hpp>
 #include <Hadrons/Modules/MScalarSUN/Div.hpp>
 #include <Hadrons/Modules/MScalarSUN/TrMag.hpp>
+#include <Hadrons/Modules/MScalarSUN/Utils.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/MNoise/FullVolumeSpinColorDiagonal.hpp>
+#include <Hadrons/Modules/MNoise/TimeDilutedSpinColorDiagonal.hpp>
+#include <Hadrons/Modules/MScalar/FreeProp.hpp>
+#include <Hadrons/Modules/MScalar/Scalar.hpp>
+#include <Hadrons/Modules/MScalar/ChargedProp.hpp>
 #include <Hadrons/Modules/MIO/LoadPerambulator.hpp>
+#include <Hadrons/Modules/MIO/LoadEigenPack.hpp>
 #include <Hadrons/Modules/MIO/LoadA2AVectors.hpp>
-#include <Hadrons/Modules/MIO/LoadCosmHol.hpp>
 #include <Hadrons/Modules/MIO/LoadCoarseEigenPack.hpp>
+#include <Hadrons/Modules/MIO/LoadCosmHol.hpp>
 #include <Hadrons/Modules/MIO/LoadBinary.hpp>
+#include <Hadrons/Modules/MIO/LoadNersc.hpp>
+#include <Hadrons/Modules/MSink/Smear.hpp>
+#include <Hadrons/Modules/MSink/Point.hpp>
+#include <Hadrons/Modules/MFermion/FreeProp.hpp>
+#include <Hadrons/Modules/MFermion/GaugeProp.hpp>
+#include <Hadrons/Modules/MFermion/EMLepton.hpp>
+#include <Hadrons/Modules/MGauge/FundtoHirep.hpp>
+#include <Hadrons/Modules/MGauge/Random.hpp>
+#include <Hadrons/Modules/MGauge/StoutSmearing.hpp>
+#include <Hadrons/Modules/MGauge/Unit.hpp>
+#include <Hadrons/Modules/MGauge/GaugeFix.hpp>
+#include <Hadrons/Modules/MGauge/StoutSmearing3D.hpp>
+#include <Hadrons/Modules/MGauge/StochEm.hpp>
+#include <Hadrons/Modules/MGauge/Electrify.hpp>
+#include <Hadrons/Modules/MGauge/UnitEm.hpp>
+#include <Hadrons/Modules/MUtilities/RandomVectors.hpp>
+#include <Hadrons/Modules/MUtilities/PrecisionCast.hpp>
+#include <Hadrons/Modules/MDistil/Noises.hpp>
+#include <Hadrons/Modules/MDistil/Perambulator.hpp>
+#include <Hadrons/Modules/MDistil/BC2.hpp>
+#include <Hadrons/Modules/MDistil/g5_multiply.hpp>
+#include <Hadrons/Modules/MDistil/PerambFromSolve.hpp>
+#include <Hadrons/Modules/MDistil/Baryon2pt.hpp>
+#include <Hadrons/Modules/MDistil/LapEvec.hpp>
+#include <Hadrons/Modules/MDistil/BContraction.hpp>
+#include <Hadrons/Modules/MDistil/DistilVectors.hpp>
+#include <Hadrons/Modules/MSource/SeqConserved.hpp>
+#include <Hadrons/Modules/MSource/SeqAslash.hpp>
+#include <Hadrons/Modules/MSource/Z2.hpp>
+#include <Hadrons/Modules/MSource/Wall.hpp>
+#include <Hadrons/Modules/MSource/SeqGamma.hpp>
+#include <Hadrons/Modules/MSource/Point.hpp>
+#include <Hadrons/Modules/MSource/Momentum.hpp>
+#include <Hadrons/Modules/MContraction/WeakMesonDecayKl2.hpp>
+#include <Hadrons/Modules/MContraction/Nucleon.hpp>
+#include <Hadrons/Modules/MContraction/A2AAslashField.hpp>
+#include <Hadrons/Modules/MContraction/WeakEye3pt.hpp>
+#include <Hadrons/Modules/MContraction/WeakNonEye3pt.hpp>
+#include <Hadrons/Modules/MContraction/Baryon.hpp>
+#include <Hadrons/Modules/MContraction/Meson.hpp>
+#include <Hadrons/Modules/MContraction/A2ALoop.hpp>
+#include <Hadrons/Modules/MContraction/Gamma3pt.hpp>
+#include <Hadrons/Modules/MContraction/DiscLoop.hpp>
+#include <Hadrons/Modules/MContraction/A2AMesonField.hpp>
+#include <Hadrons/Modules/MAction/WilsonClover.hpp>
+#include <Hadrons/Modules/MAction/ScaledDWF.hpp>
+#include <Hadrons/Modules/MAction/MobiusDWF.hpp>
+#include <Hadrons/Modules/MAction/Wilson.hpp>
+#include <Hadrons/Modules/MAction/DWF.hpp>
+#include <Hadrons/Modules/MAction/ZMobiusDWF.hpp>
+#include <Hadrons/Modules/MSolver/RBPrecCG.hpp>
+#include <Hadrons/Modules/MSolver/LocalCoherenceLanczos.hpp>
+#include <Hadrons/Modules/MSolver/A2AVectors.hpp>
+#include <Hadrons/Modules/MSolver/MixedPrecisionRBPrecCG.hpp>
+#include <Hadrons/Modules/MSolver/Guesser.hpp>
+#include <Hadrons/Modules/MSolver/A2AAslashVectors.hpp>
+#include <Hadrons/Modules/MNPR/FourQuark.hpp>
+#include <Hadrons/Modules/MNPR/Bilinear.hpp>
+#include <Hadrons/Modules/MNPR/Amputate.hpp>
diff --git a/Hadrons/Modules/MContraction/Nucleon.cc b/Hadrons/Modules/MContraction/Nucleon.cc
new file mode 100644
index 00000000..304ff07a
--- /dev/null
+++ b/Hadrons/Modules/MContraction/Nucleon.cc
@@ -0,0 +1,35 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: Hadrons/Modules/MContraction/Nucleon.cc
+
+Copyright (C) 2015-2019
+
+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 <Hadrons/Modules/MContraction/Nucleon.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MContraction;
+
+template class Grid::Hadrons::MContraction::TNucleon<FIMPL,FIMPL,FIMPL>;
+
diff --git a/Hadrons/Modules/MContraction/Nucleon.hpp b/Hadrons/Modules/MContraction/Nucleon.hpp
new file mode 100644
index 00000000..d2a5129d
--- /dev/null
+++ b/Hadrons/Modules/MContraction/Nucleon.hpp
@@ -0,0 +1,168 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: Hadrons/Modules/MContraction/Nucleon.hpp
+
+Copyright (C) 2015-2019
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+Author: Felix Erben <felix.erben@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_MContraction_Nucleon_hpp_
+#define Hadrons_MContraction_Nucleon_hpp_
+
+#include <Hadrons/Global.hpp>
+#include <Hadrons/Module.hpp>
+#include <Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                               Nucleon                                       *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MContraction)
+
+class NucleonPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(NucleonPar,
+                                    std::string, q1,
+                                    std::string, q2,
+                                    std::string, q3,
+                                    std::string, output);
+};
+
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+class TNucleon: public Module<NucleonPar>
+{
+public:
+    FERM_TYPE_ALIASES(FImpl1, 1);
+    FERM_TYPE_ALIASES(FImpl2, 2);
+    FERM_TYPE_ALIASES(FImpl3, 3);
+    class Result: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(Result,
+                                        std::vector<std::vector<std::vector<Complex>>>, corr);
+    };
+public:
+    // constructor
+    TNucleon(const std::string name);
+    // destructor
+    virtual ~TNucleon(void) {};
+    // 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_TMP(Nucleon, ARG(TNucleon<FIMPL, FIMPL, FIMPL>), MContraction);
+
+/******************************************************************************
+ *                         TNucleon implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+TNucleon<FImpl1, FImpl2, FImpl3>::TNucleon(const std::string name)
+: Module<NucleonPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+std::vector<std::string> TNucleon<FImpl1, FImpl2, FImpl3>::getInput(void)
+{
+    std::vector<std::string> input = {par().q1, par().q2, par().q3};
+    
+    return input;
+}
+
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+std::vector<std::string> TNucleon<FImpl1, FImpl2, FImpl3>::getOutput(void)
+{
+    std::vector<std::string> out = {};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+void TNucleon<FImpl1, FImpl2, FImpl3>::setup(void)
+{
+    envTmpLat(LatticeComplex, "c");
+    envTmpLat(LatticeComplex, "diquark");
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+void TNucleon<FImpl1, FImpl2, FImpl3>::execute(void)
+{
+    LOG(Message) << "Computing nucleon contractions '" << getName() << "' using"
+                 << " quarks '" << par().q1 << "', '" << par().q2 << "', and '"
+                 << par().q3 << "'" << std::endl;
+    
+    auto       &q1 = envGet(PropagatorField1, par().q1);
+    auto       &q2 = envGet(PropagatorField2, par().q2);
+    auto       &q3 = envGet(PropagatorField3, par().q2);
+    envGetTmp(LatticeComplex, c);
+    //envGetTmp(LatticeComplex, quark2);
+    //envGetTmp(LatticeComplex, quark3);
+    envGetTmp(LatticeComplex, diquark);
+    Result     result;
+   
+    // C = i gamma_2 gamma_4 => C gamma_5 = - i gamma_1 gamma_3  
+    Gamma Cg5(Gamma::Algebra::SigmaXZ);
+    Gamma g4(Gamma::Algebra::GammaT);
+
+    std::vector<std::vector<int>> epsilon = {{0,1,2},{1,2,0},{2,0,1},{0,2,1},{2,1,0},{1,0,2}};
+    std::vector<int> epsilon_sgn = {1,1,1,-1,-1,-1};
+    for (int ie_src=0; ie_src < 6 ; ie_src++){
+       int c1_src = epsilon[ie_src][0];
+       int c2_src = epsilon[ie_src][1];
+       int c3_src = epsilon[ie_src][2];
+      for (int ie_snk=0; ie_snk < 6 ; ie_snk++){
+         int c1_snk = epsilon[ie_snk][0];
+         int c2_snk = epsilon[ie_snk][1];
+         int c3_snk = epsilon[ie_snk][2];
+         auto f1 = peekColour(q1,c1_snk,c1_src);
+         auto f2 = peekColour(q2,c2_snk,c2_src);
+         auto f3 = peekColour(q3,c3_snk,c3_src);
+         diquark = trace(f2 * Cg5 * f3);
+           //diquark = q2()()(c2,1) * Cg5 * q3()()(c3,2);
+         auto temp = Cg5 * f1 * diquark;
+         auto g4_temp = g4 * temp; 
+         int parity = 1;
+         c += epsilon_sgn[ie_src] * epsilon_sgn[ie_snk] * 0.5 * (double)parity * trace(temp + g4_temp);
+      }
+    }
+
+    // saveResult(par().output, "meson", result);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_MContraction_Nucleon_hpp_
diff --git a/Hadrons/modules.inc b/Hadrons/modules.inc
index 5cb77b9e..aa6d3af8 100644
--- a/Hadrons/modules.inc
+++ b/Hadrons/modules.inc
@@ -1,161 +1,163 @@
 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/MScalarSUN/Grad.cc \
+  Modules/MScalarSUN/TwoPointNPR.cc \
+  Modules/MScalarSUN/Div.cc \
+  Modules/MScalarSUN/TrMag.cc \
+  Modules/MScalarSUN/TransProj.cc \
+  Modules/MScalarSUN/TwoPoint.cc \
+  Modules/MScalarSUN/TrKinetic.cc \
+  Modules/MScalarSUN/TrPhi.cc \
+  Modules/MScalarSUN/EMT.cc \
+  Modules/MScalarSUN/StochFreeField.cc \
+  Modules/MNoise/FullVolumeSpinColorDiagonal.cc \
+  Modules/MNoise/TimeDilutedSpinColorDiagonal.cc \
+  Modules/MScalar/FreeProp.cc \
+  Modules/MScalar/ChargedProp.cc \
+  Modules/MIO/LoadBinary.cc \
+  Modules/MIO/LoadCosmHol.cc \
+  Modules/MIO/LoadCoarseEigenPack.cc \
+  Modules/MIO/LoadNersc.cc \
+  Modules/MIO/LoadEigenPack.cc \
+  Modules/MIO/LoadA2AVectors.cc \
+  Modules/MIO/LoadPerambulator.cc \
+  Modules/MSink/Smear.cc \
+  Modules/MSink/Point.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/Z2.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/Random.cc \
+  Modules/MGauge/StoutSmearing3D.cc \
+  Modules/MGauge/StochEm.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/StoutSmearing3D.cc \
+  Modules/MGauge/UnitEm.cc \
   Modules/MGauge/FundtoHirep.cc \
   Modules/MGauge/GaugeFix.cc \
-  Modules/MNoise/FullVolumeSpinColorDiagonal.cc \
-  Modules/MNoise/TimeDilutedSpinColorDiagonal.cc \
   Modules/MUtilities/RandomVectors.cc \
   Modules/MUtilities/PrecisionCast.cc \
-  Modules/MScalar/FreeProp.cc \
-  Modules/MScalar/ChargedProp.cc \
-  Modules/MDistil/DistilVectors.cc \
-  Modules/MDistil/g5_multiply.cc \
-  Modules/MDistil/BC2.cc \
-  Modules/MDistil/Noises.cc \
-  Modules/MDistil/BContraction.cc \
-  Modules/MDistil/LapEvec.cc \
-  Modules/MDistil/Baryon2pt.cc \
-  Modules/MDistil/Perambulator.cc \
   Modules/MDistil/PerambFromSolve.cc \
-  Modules/MNPR/Amputate.cc \
-  Modules/MNPR/Bilinear.cc \
-  Modules/MNPR/FourQuark.cc \
-  Modules/MAction/Wilson.cc \
+  Modules/MDistil/g5_multiply.cc \
+  Modules/MDistil/LapEvec.cc \
+  Modules/MDistil/Perambulator.cc \
+  Modules/MDistil/Noises.cc \
+  Modules/MDistil/DistilVectors.cc \
+  Modules/MDistil/BContraction.cc \
+  Modules/MDistil/Baryon2pt.cc \
+  Modules/MDistil/BC2.cc \
+  Modules/MSource/Momentum.cc \
+  Modules/MSource/SeqAslash.cc \
+  Modules/MSource/Z2.cc \
+  Modules/MSource/Point.cc \
+  Modules/MSource/SeqGamma.cc \
+  Modules/MSource/Wall.cc \
+  Modules/MSource/SeqConserved.cc \
+  Modules/MContraction/WeakEye3pt.cc \
+  Modules/MContraction/Meson.cc \
+  Modules/MContraction/A2AAslashField.cc \
+  Modules/MContraction/Baryon.cc \
+  Modules/MContraction/Nucleon.cc \
+  Modules/MContraction/WeakNonEye3pt.cc \
+  Modules/MContraction/DiscLoop.cc \
+  Modules/MContraction/WeakMesonDecayKl2.cc \
+  Modules/MContraction/A2AMesonField.cc \
+  Modules/MContraction/A2ALoop.cc \
+  Modules/MContraction/Gamma3pt.cc \
   Modules/MAction/MobiusDWF.cc \
-  Modules/MAction/ZMobiusDWF.cc \
   Modules/MAction/WilsonClover.cc \
+  Modules/MAction/Wilson.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/LoadPerambulator.cc \
-  Modules/MIO/LoadNersc.cc \
-  Modules/MIO/LoadCoarseEigenPack.cc \
-  Modules/MIO/LoadCosmHol.cc \
-  Modules/MIO/LoadA2AVectors.cc
+  Modules/MAction/ZMobiusDWF.cc \
+  Modules/MSolver/A2AVectors.cc \
+  Modules/MSolver/RBPrecCG.cc \
+  Modules/MSolver/LocalCoherenceLanczos.cc \
+  Modules/MSolver/MixedPrecisionRBPrecCG.cc \
+  Modules/MSolver/A2AAslashVectors.cc \
+  Modules/MNPR/Bilinear.cc \
+  Modules/MNPR/FourQuark.cc \
+  Modules/MNPR/Amputate.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/SeqGamma.hpp \
-  Modules/MSource/SeqAslash.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/StoutSmearing3D.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/MDistil/LapEvec.hpp \
-  Modules/MDistil/DistilVectors.hpp \
-  Modules/MDistil/Noises.hpp \
-  Modules/MDistil/BC2.hpp \
-  Modules/MDistil/Perambulator.hpp \
-  Modules/MDistil/PerambFromSolve.hpp \
-  Modules/MDistil/BContraction.hpp \
-  Modules/MDistil/Baryon2pt.hpp \
-  Modules/MDistil/g5_multiply.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/TrKinetic.hpp \
   Modules/MScalarSUN/StochFreeField.hpp \
   Modules/MScalarSUN/TwoPointNPR.hpp \
+  Modules/MScalarSUN/Grad.hpp \
+  Modules/MScalarSUN/TransProj.hpp \
   Modules/MScalarSUN/Div.hpp \
   Modules/MScalarSUN/TrMag.hpp \
+  Modules/MScalarSUN/Utils.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/MNoise/FullVolumeSpinColorDiagonal.hpp \
+  Modules/MNoise/TimeDilutedSpinColorDiagonal.hpp \
+  Modules/MScalar/FreeProp.hpp \
+  Modules/MScalar/Scalar.hpp \
+  Modules/MScalar/ChargedProp.hpp \
   Modules/MIO/LoadPerambulator.hpp \
+  Modules/MIO/LoadEigenPack.hpp \
   Modules/MIO/LoadA2AVectors.hpp \
-  Modules/MIO/LoadCosmHol.hpp \
   Modules/MIO/LoadCoarseEigenPack.hpp \
-  Modules/MIO/LoadBinary.hpp
+  Modules/MIO/LoadCosmHol.hpp \
+  Modules/MIO/LoadBinary.hpp \
+  Modules/MIO/LoadNersc.hpp \
+  Modules/MSink/Smear.hpp \
+  Modules/MSink/Point.hpp \
+  Modules/MFermion/FreeProp.hpp \
+  Modules/MFermion/GaugeProp.hpp \
+  Modules/MFermion/EMLepton.hpp \
+  Modules/MGauge/FundtoHirep.hpp \
+  Modules/MGauge/Random.hpp \
+  Modules/MGauge/StoutSmearing.hpp \
+  Modules/MGauge/Unit.hpp \
+  Modules/MGauge/GaugeFix.hpp \
+  Modules/MGauge/StoutSmearing3D.hpp \
+  Modules/MGauge/StochEm.hpp \
+  Modules/MGauge/Electrify.hpp \
+  Modules/MGauge/UnitEm.hpp \
+  Modules/MUtilities/RandomVectors.hpp \
+  Modules/MUtilities/PrecisionCast.hpp \
+  Modules/MDistil/Noises.hpp \
+  Modules/MDistil/Perambulator.hpp \
+  Modules/MDistil/BC2.hpp \
+  Modules/MDistil/g5_multiply.hpp \
+  Modules/MDistil/PerambFromSolve.hpp \
+  Modules/MDistil/Baryon2pt.hpp \
+  Modules/MDistil/LapEvec.hpp \
+  Modules/MDistil/BContraction.hpp \
+  Modules/MDistil/DistilVectors.hpp \
+  Modules/MSource/SeqConserved.hpp \
+  Modules/MSource/SeqAslash.hpp \
+  Modules/MSource/Z2.hpp \
+  Modules/MSource/Wall.hpp \
+  Modules/MSource/SeqGamma.hpp \
+  Modules/MSource/Point.hpp \
+  Modules/MSource/Momentum.hpp \
+  Modules/MContraction/WeakMesonDecayKl2.hpp \
+  Modules/MContraction/Nucleon.hpp \
+  Modules/MContraction/A2AAslashField.hpp \
+  Modules/MContraction/WeakEye3pt.hpp \
+  Modules/MContraction/WeakNonEye3pt.hpp \
+  Modules/MContraction/Baryon.hpp \
+  Modules/MContraction/Meson.hpp \
+  Modules/MContraction/A2ALoop.hpp \
+  Modules/MContraction/Gamma3pt.hpp \
+  Modules/MContraction/DiscLoop.hpp \
+  Modules/MContraction/A2AMesonField.hpp \
+  Modules/MAction/WilsonClover.hpp \
+  Modules/MAction/ScaledDWF.hpp \
+  Modules/MAction/MobiusDWF.hpp \
+  Modules/MAction/Wilson.hpp \
+  Modules/MAction/DWF.hpp \
+  Modules/MAction/ZMobiusDWF.hpp \
+  Modules/MSolver/RBPrecCG.hpp \
+  Modules/MSolver/LocalCoherenceLanczos.hpp \
+  Modules/MSolver/A2AVectors.hpp \
+  Modules/MSolver/MixedPrecisionRBPrecCG.hpp \
+  Modules/MSolver/Guesser.hpp \
+  Modules/MSolver/A2AAslashVectors.hpp \
+  Modules/MNPR/FourQuark.hpp \
+  Modules/MNPR/Bilinear.hpp \
+  Modules/MNPR/Amputate.hpp