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	general baryons case added
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		@@ -7,7 +7,7 @@ Source file: Hadrons/Modules/MContraction/Baryon.hpp
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Copyright (C) 2015-2019
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Author: Antonin Portelli <antonin.portelli@me.com>
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Author: Lanny91 <andrew.lawson@gmail.com>
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Author: Felix Erben <felix.erben@ed.ac.uk>
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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@@ -62,7 +62,7 @@ public:
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    {
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    public:
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        GRID_SERIALIZABLE_CLASS_MEMBERS(Result,
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                                        std::vector<std::vector<std::vector<Complex>>>, corr);
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                                        std::vector<Complex>, corr);
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    };
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public:
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    // constructor
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@@ -112,13 +112,14 @@ template <typename FImpl1, typename FImpl2, typename FImpl3>
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void TBaryon<FImpl1, FImpl2, FImpl3>::setup(void)
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{
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    envTmpLat(LatticeComplex, "c");
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    envTmpLat(LatticeComplex, "diquark");
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}
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// execution ///////////////////////////////////////////////////////////////////
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template <typename FImpl1, typename FImpl2, typename FImpl3>
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void TBaryon<FImpl1, FImpl2, FImpl3>::execute(void)
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{
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    LOG(Message) << "Computing baryon contractions '" << getName() << "' using"
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    LOG(Message) << "Computing nucleon contractions '" << getName() << "' using"
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                 << " quarks '" << par().q1 << "', '" << par().q2 << "', and '"
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                 << par().q3 << "'" << std::endl;
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@@ -126,11 +127,116 @@ void TBaryon<FImpl1, FImpl2, FImpl3>::execute(void)
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    auto       &q2 = envGet(PropagatorField2, par().q2);
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    auto       &q3 = envGet(PropagatorField3, par().q2);
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    envGetTmp(LatticeComplex, c);
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    envGetTmp(LatticeComplex, diquark);
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    Result     result;
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    // FIXME: do contractions
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    // saveResult(par().output, "meson", result);
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    int nt = env().getDim(Tp);
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    result.corr.resize(nt);
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    std::vector<TComplex> buf;
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    // C = i gamma_2 gamma_4 => C gamma_5 = - i gamma_1 gamma_3  
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    Gamma GammaA(Gamma::Algebra::Identity); //Still hardcoded 1
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    Gamma GammaB(Gamma::Algebra::SigmaXZ); //Still hardcoded Cg5
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    Gamma g4(Gamma::Algebra::GammaT); //needed for parity P_\pm = 0.5*(1 \pm \gamma_4)
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    std::vector<std::vector<int>> epsilon = {{0,1,2},{1,2,0},{2,0,1},{0,2,1},{2,1,0},{1,0,2}};
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    std::vector<int> epsilon_sgn = {1,1,1,-1,-1,-1};
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    char left[] = "uud";
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    char right[] = "uud";
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    std::vector<int> wick_contraction = {0,0,0,0,0,0};
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    for (int ie=0; ie < 6 ; ie++)
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      if (left[0] == right[epsilon[ie][0]] && left[1] == right[epsilon[ie][1]] && left[2] == right[epsilon[ie][2]])
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        wick_contraction[ie]=1;
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    int parity = 1;
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    for (int ie_src=0; ie_src < 6 ; ie_src++){
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       int a_src = epsilon[ie_src][0]; //a
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       int b_src = epsilon[ie_src][1]; //b
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       int c_src = epsilon[ie_src][2]; //c
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      for (int ie_snk=0; ie_snk < 6 ; ie_snk++){
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         int a_snk = epsilon[ie_snk][0]; //a'
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         int b_snk = epsilon[ie_snk][1]; //b'
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         int c_snk = epsilon[ie_snk][2]; //c'
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         auto Daa = peekColour(q2,a_snk,a_src); //D_{alpha' alpha}
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         auto Dbb = peekColour(q3,b_snk,b_src); //D_{beta' beta}
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         auto Dcc = peekColour(q1,c_snk,c_src); //D_{gamma' gamma}
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         auto Dab = peekColour(q2,a_snk,b_src); //D_{alpha' beta}
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         auto Dac = peekColour(q2,a_snk,c_src); //D_{alpha' gamma}
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         auto Dba = peekColour(q3,b_snk,a_src); //D_{beta' alpha}
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         auto Dbc = peekColour(q3,b_snk,c_src); //D_{beta' gamma}
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         auto Dca = peekColour(q1,c_snk,a_src); //D_{gamma' alpha}
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         auto Dcb = peekColour(q1,c_snk,b_src); //D_{gamma' beta}
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         // This needs lees peekColours for some baryons, but does not compile - worth the effort?
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         /*if (wick_contraction[0] || wick_contraction[4]) 
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           auto Daa = peekColour(q2,a_snk,a_src); //D_{alpha' alpha}
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         if (wick_contraction[0] || wick_contraction[5]) 
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           auto Dbb = peekColour(q3,b_snk,b_src); //D_{beta' beta}
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         if (wick_contraction[0] || wick_contraction[3]) 
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           auto Dcc = peekColour(q1,c_snk,c_src); //D_{gamma' gamma}
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         if (wick_contraction[1] || wick_contraction[3]) 
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           auto Dab = peekColour(q2,a_snk,b_src); //D_{alpha' beta}
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         if (wick_contraction[2] || wick_contraction[5]) 
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           auto Dac = peekColour(q2,a_snk,c_src); //D_{alpha' gamma}
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         if (wick_contraction[2] || wick_contraction[3]) 
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           auto Dba = peekColour(q3,b_snk,a_src); //D_{beta' alpha}
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         if (wick_contraction[1] || wick_contraction[4]) 
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           auto Dbc = peekColour(q3,b_snk,c_src); //D_{beta' gamma}
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         if (wick_contraction[1] || wick_contraction[5]) 
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           auto Dca = peekColour(q1,c_snk,a_src); //D_{gamma' alpha}
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         if (wick_contraction[2] || wick_contraction[4]) 
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           auto Dcb = peekColour(q1,c_snk,b_src); //D_{gamma' beta}*/
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         // This is the \delta_{123}^{123} part
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         if (wick_contraction[0]){
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           diquark = trace(GammaB * Daa * GammaB * Dbb); //1st GammaB and Daa transposed????
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           auto temp = GammaA * Dcc * diquark;
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           auto g4_temp = GammaA * g4 * temp; 
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           c += epsilon_sgn[ie_src] * epsilon_sgn[ie_snk] * 0.5 * trace(GammaA * temp + (double)parity * g4_temp);
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         }
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         // This is the \delta_{123}^{231} part
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         if (wick_contraction[1]){
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           auto temp = GammaA * Dca * GammaB * Dab * GammaB * Dbc; //Dab transposed???
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           auto g4_temp = GammaA * g4 * temp; 
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           c += epsilon_sgn[ie_src] * epsilon_sgn[ie_snk] * 0.5 * trace(GammaA * temp + (double)parity * g4_temp);
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         }
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         // This is the \delta_{123}^{312} part
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         if (wick_contraction[2]){
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           auto temp = GammaA * Dcb * GammaB * Dba * GammaB * Dac; //both GammaB and Dba transposed???
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           auto g4_temp = GammaA * g4 * temp; 
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           c += epsilon_sgn[ie_src] * epsilon_sgn[ie_snk] * 0.5 * trace(GammaA * temp + (double)parity * g4_temp);
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         }
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         // This is the \delta_{123}^{132} part
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         if (wick_contraction[3]){
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           diquark = trace(GammaB * Dba * GammaB * Dab); //2nd GammaB and Dab transposed????
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           auto temp = GammaA * Dcc * diquark;
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           auto g4_temp = GammaA * g4 * temp; 
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           c -= epsilon_sgn[ie_src] * epsilon_sgn[ie_snk] * 0.5 * trace(GammaA * temp + (double)parity * g4_temp);
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         }
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         // This is the \delta_{123}^{321} part
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         if (wick_contraction[4]){
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           auto temp = GammaA * Dcb * GammaB * Daa * GammaB * Dbc; //1st GammaB and Daa transposed???
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           auto g4_temp = GammaA * g4 * temp; 
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           c -= epsilon_sgn[ie_src] * epsilon_sgn[ie_snk] * 0.5 * trace(GammaA * temp + (double)parity * g4_temp);
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         }
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         // This is the \delta_{123}^{213} part
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         if (wick_contraction[5]){
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           auto temp = GammaA * Dca * GammaB * Dbb * GammaB * Dac; //(Dbb*GammaB) transposed???
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           auto g4_temp = GammaA * g4 * temp; 
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           c -= epsilon_sgn[ie_src] * epsilon_sgn[ie_snk] * 0.5 * trace(GammaA * temp + (double)parity * g4_temp);
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         }
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      }
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    }
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    sliceSum(c,buf,Tp);
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    for (unsigned int t = 0; t < buf.size(); ++t)
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    {
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        result.corr[t] = TensorRemove(buf[t]);
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    }
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    saveResult(par().output, "baryon", result);
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}
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END_MODULE_NAMESPACE
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