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	Adding some documentation for HMC
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		@@ -72,6 +72,10 @@ namespace QCD {
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typedef WilsonGaugeAction<PeriodicGimplR>          WilsonGaugeActionR;
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typedef WilsonGaugeAction<PeriodicGimplF>          WilsonGaugeActionF;
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typedef WilsonGaugeAction<PeriodicGimplD>          WilsonGaugeActionD;
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typedef VariableWilsonGaugeAction<PeriodicGimplR>          VariableWilsonGaugeActionR;
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typedef VariableWilsonGaugeAction<PeriodicGimplF>          VariableWilsonGaugeActionF;
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typedef VariableWilsonGaugeAction<PeriodicGimplD>          VariableWilsonGaugeActionD;
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typedef PlaqPlusRectangleAction<PeriodicGimplR>    PlaqPlusRectangleActionR;
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typedef PlaqPlusRectangleAction<PeriodicGimplF>    PlaqPlusRectangleActionF;
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typedef PlaqPlusRectangleAction<PeriodicGimplD>    PlaqPlusRectangleActionD;
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@@ -1,86 +1,260 @@
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    /*************************************************************************************
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/*************************************************************************************
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    Grid physics library, www.github.com/paboyle/Grid 
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Grid physics library, www.github.com/paboyle/Grid
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    Source file: ./lib/qcd/action/gauge/WilsonGaugeAction.h
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Source file: ./lib/qcd/action/gauge/WilsonGaugeAction.h
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    Copyright (C) 2015
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Copyright (C) 2015
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Author: Azusa Yamaguchi <ayamaguc@staffmail.ed.ac.uk>
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Author: Peter Boyle <paboyle@ph.ed.ac.uk>
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Author: neo <cossu@post.kek.jp>
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Author: paboyle <paboyle@ph.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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    the Free Software Foundation; either version 2 of the License, or
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    (at your option) any later version.
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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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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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    This program is distributed in the hope that it will be useful,
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    but WITHOUT ANY WARRANTY; without even the implied warranty of
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    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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    GNU General Public License for more details.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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GNU General Public License for more details.
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    You should have received a copy of the GNU General Public License along
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    with this program; if not, write to the Free Software Foundation, Inc.,
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    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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You should have received a copy of the GNU General Public License along
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with this program; if not, write to the Free Software Foundation, Inc.,
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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    See the full license in the file "LICENSE" in the top level distribution directory
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    *************************************************************************************/
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    /*  END LEGAL */
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See the full license in the file "LICENSE" in the top level distribution
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directory
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*************************************************************************************/
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/*  END LEGAL */
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#ifndef QCD_WILSON_GAUGE_ACTION_H
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#define QCD_WILSON_GAUGE_ACTION_H
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namespace Grid{
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  namespace QCD{
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    ////////////////////////////////////////////////////////////////////////
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    // Wilson Gauge Action .. should I template the Nc etc..
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    ////////////////////////////////////////////////////////////////////////
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    template<class Gimpl>
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    class WilsonGaugeAction : public Action<typename Gimpl::GaugeField> {
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    public:
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namespace Grid {
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namespace QCD {
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      INHERIT_GIMPL_TYPES(Gimpl);
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////////////////////////////////////////////////////////////////////////
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// Wilson Gauge Action .. should I template the Nc etc..
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////////////////////////////////////////////////////////////////////////
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template <class Gimpl>
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class WilsonGaugeAction : public Action<typename Gimpl::GaugeField> {
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 public:
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  INHERIT_GIMPL_TYPES(Gimpl);
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      //      typedef LorentzScalar<GaugeField> GaugeLinkField;
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  //      typedef LorentzScalar<GaugeField> GaugeLinkField;
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    private:
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      RealD beta;
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    public:
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    WilsonGaugeAction(RealD b):beta(b){};
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 private:
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  RealD beta;
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 public:
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  WilsonGaugeAction(RealD b) : beta(b){};
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  virtual void refresh(const GaugeField &U,
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                       GridParallelRNG &pRNG){};  // noop as no pseudoferms
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  virtual RealD S(const GaugeField &U) {
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    RealD plaq = WilsonLoops<Gimpl>::avgPlaquette(U);
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    RealD vol = U._grid->gSites();
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    RealD action = beta * (1.0 - plaq) * (Nd * (Nd - 1.0)) * vol * 0.5;
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    return action;
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  };
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  virtual void deriv(const GaugeField &U, GaugeField &dSdU) {
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    // not optimal implementation FIXME
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    // extend Ta to include Lorentz indexes
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    // RealD factor = 0.5*beta/RealD(Nc);
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    RealD factor = 0.5 * beta / RealD(Nc);
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    GaugeLinkField Umu(U._grid);
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    GaugeLinkField dSdU_mu(U._grid);
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    for (int mu = 0; mu < Nd; mu++) {
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      Umu = PeekIndex<LorentzIndex>(U, mu);
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      // Staple in direction mu
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      WilsonLoops<Gimpl>::Staple(dSdU_mu, U, mu);
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      dSdU_mu = Ta(Umu * dSdU_mu) * factor;
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      virtual void refresh(const GaugeField &U, GridParallelRNG& pRNG) {}; // noop as no pseudoferms
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      virtual RealD S(const GaugeField &U) {
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	RealD plaq = WilsonLoops<Gimpl>::avgPlaquette(U);
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	RealD vol = U._grid->gSites();
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	RealD action=beta*(1.0 -plaq)*(Nd*(Nd-1.0))*vol*0.5;
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	return action;
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      };
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      PokeIndex<LorentzIndex>(dSdU, dSdU_mu, mu);
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    }
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  };
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};
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      virtual void deriv(const GaugeField &U,GaugeField & dSdU) {
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	//not optimal implementation FIXME
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	//extend Ta to include Lorentz indexes
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template <class Gimpl>
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class VariableWilsonGaugeAction : public Action<typename Gimpl::GaugeField> {
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 public:
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  INHERIT_GIMPL_TYPES(Gimpl);
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	//RealD factor = 0.5*beta/RealD(Nc);
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	RealD factor = 0.5*beta/RealD(Nc);
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 private:
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  std::vector<RealD> b_bulk;// bulk couplings
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  std::vector<RealD> b_xdim;//extra dimension couplings
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  GridBase *grid;
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  LatticeComplex beta_xdim;
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  LatticeComplex beta_xdim_shifted;
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  LatticeComplex beta_bulk;
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	GaugeLinkField Umu(U._grid);
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	GaugeLinkField dSdU_mu(U._grid);
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	for (int mu=0; mu < Nd; mu++){
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 public:
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  VariableWilsonGaugeAction(std::vector<RealD> bulk, std::vector<RealD> xdim,
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                            GridBase *_grid)
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      : b_bulk(bulk),
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        b_xdim(xdim),
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        grid(_grid),
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        beta_xdim(grid),
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        beta_xdim_shifted(grid),
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        beta_bulk(grid)
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        {
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          //check that the grid is ok
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          //todo
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          int Ndim = Nd;//change later
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	  Umu = PeekIndex<LorentzIndex>(U,mu);
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          LatticeComplex temp(grid);
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	  // Staple in direction mu
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	  WilsonLoops<Gimpl>::Staple(dSdU_mu,U,mu);
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	  dSdU_mu = Ta(Umu*dSdU_mu)*factor;
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	  PokeIndex<LorentzIndex>(dSdU, dSdU_mu, mu);
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	}
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      };
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    };
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          Lattice<iScalar<vInteger> > coor(grid);
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          LatticeCoordinate(coor, Ndim - 1);
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          int Nex = grid->_fdimensions[Ndim - 1];
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          assert(b_bulk.size() == Nex);
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          assert(b_xdim.size() == Nex);
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          beta_xdim = zero;
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          for (int tau = 0; tau < Nex; tau++) {
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            temp = b_xdim[tau];
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            beta_xdim = where(coor == tau, temp, beta_xdim);
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          }
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          beta_xdim_shifted = Cshift(beta_xdim, Ndim - 1, -1);
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          beta_bulk = zero;
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          for (int tau = 0; tau < Nex; tau++) {
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            temp = b_bulk[tau];
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            beta_bulk = where(coor == tau, temp, beta_bulk);
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          }
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        };
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  virtual void refresh(const GaugeField &U,
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                       GridParallelRNG &pRNG){};  // noop as no pseudoferms
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  virtual RealD S(const GaugeField &Umu) {
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    int Ndim = Nd; // change later for generality
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    conformable(grid, Umu._grid);
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    std::vector<GaugeLinkField> U(Ndim, grid);
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    for (int mu = 0; mu < Ndim; mu++) {
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      U[mu] = PeekIndex<LorentzIndex>(Umu, mu);
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    }
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    LatticeComplex dirPlaq(grid);
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    LatticeComplex Plaq(grid);
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    RealD OneOnNc = 1.0 / Real(Nc);
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    /////////////
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    // Lower dim plaquettes
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    /////////////
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    Plaq = zero;
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    for (int mu = 1; mu < Ndim - 1; mu++) {
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      for (int nu = 0; nu < mu; nu++) {
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        WilsonLoops<Gimpl>::traceDirPlaquette(dirPlaq, U, mu, nu);
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        Plaq = Plaq + (1.0 - dirPlaq * OneOnNc) * beta_bulk;
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      }
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    }
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    /////////////
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    // Extra dimension
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    /////////////
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    {
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      int mu = Ndim - 1;
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      for (int nu = 0; nu < mu; nu++) {
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        WilsonLoops<Gimpl>::traceDirPlaquette(dirPlaq, U, mu, nu);
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        Plaq = Plaq + (1.0 - dirPlaq * OneOnNc) * beta_xdim;
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      }
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    }
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    TComplex Tp = sum(Plaq);
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    Complex p = TensorRemove(Tp);
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    RealD action = p.real();
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    return action;
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  };
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  virtual void deriv(const GaugeField &U, GaugeField &dSdU) {
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    // not optimal implementation FIXME
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    // extend Ta to include Lorentz indexes
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    // for the higher dimension plaquettes take the upper plaq of the
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    // 4d slice and multiply by beta[s] and the lower and multiply by beta[s-1]
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    // todo
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    // derivative of links mu = 0, ... Nd-1 inside plaq (mu,5)
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    // for these I need upper and lower staples separated
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    // each multiplied with their own beta
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    // derivative of links mu = 5
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    // living on the same slice, share the same beta
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conformable(grid,U._grid);
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int Ndim = Nd;  // change later
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RealD factor = 0.5 / RealD(Nc);
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GaugeLinkField Umu(grid);
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GaugeLinkField dSdU_mu(grid);
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GaugeLinkField staple(grid);
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for (int mu = 0; mu < Ndim; mu++) {
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  Umu = PeekIndex<LorentzIndex>(U, mu);
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  dSdU_mu = zero;
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  for (int nu = 0; nu < Ndim; nu++) {
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    if (nu != mu) {
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      if ((mu < (Ndim - 1)) && (nu < (Ndim - 1))) {
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        // Spacelike case apply beta space
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        WilsonLoops<Gimpl>::Staple(staple, U, mu, nu);
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        staple = staple * beta_bulk;
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        dSdU_mu += staple;
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      } else if (mu == (Ndim - 1)) {
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        // nu space; mu time link
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        assert(nu < (Ndim - 1));
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        assert(mu == (Ndim - 1));
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        // mu==tau dir link deriv, nu spatial
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        WilsonLoops<Gimpl>::Staple(staple, U, mu, nu);
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        staple = staple * beta_xdim;
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        dSdU_mu += staple;
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      } else {
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        assert(mu < (Ndim - 1));
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        assert(nu == (Ndim - 1));
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        // nu time; mu space link
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        // staple forwards in tau
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        WilsonLoops<Gimpl>::StapleUpper(staple, U, mu, nu);
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        staple = staple * beta_xdim;
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        dSdU_mu += staple;
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        // staple backwards in tau
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        WilsonLoops<Gimpl>::StapleLower(staple, U, mu, nu);
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        staple = staple * beta_xdim_shifted;
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        dSdU_mu += staple;
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      }
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    }
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  }
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  dSdU_mu = Ta(Umu * dSdU_mu) * factor;
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  PokeIndex<LorentzIndex>(dSdU, dSdU_mu, mu);
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  }
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  };
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};
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}
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}
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#endif
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