Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2023 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "vesselbase/VesselRegister.h"
      23             : #include "vesselbase/FunctionVessel.h"
      24             : #include "vesselbase/ActionWithVessel.h"
      25             : #include "multicolvar/ActionVolume.h"
      26             : #include "VectorMultiColvar.h"
      27             : #include "Gradient.h"
      28             : 
      29             : namespace PLMD {
      30             : namespace crystallization {
      31             : 
      32             : class GradientVessel : public vesselbase::FunctionVessel {
      33             : private:
      34             :   bool isdens;
      35             :   size_t nweights, ncomponents;
      36             :   std::vector<unsigned> starts;
      37             : public:
      38             :   static void registerKeywords( Keywords& keys );
      39             :   static void reserveKeyword( Keywords& keys );
      40             :   explicit GradientVessel( const vesselbase::VesselOptions& da );
      41             :   std::string value_descriptor();
      42             :   void resize();
      43             :   void calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
      44             :   void finish( const std::vector<double>& buffer );
      45             : };
      46             : 
      47       13787 : PLUMED_REGISTER_VESSEL(GradientVessel,"GRADIENT")
      48             : 
      49           2 : void GradientVessel::registerKeywords( Keywords& keys ) {
      50           2 :   vesselbase::FunctionVessel::registerKeywords(keys);
      51           2 : }
      52             : 
      53        4595 : void GradientVessel::reserveKeyword( Keywords& keys ) {
      54        9190 :   keys.reserve("vessel","GRADIENT","calculate the gradient");
      55        9190 :   keys.addOutputComponent("gradient","GRADIENT","the gradient");
      56        4595 : }
      57             : 
      58           2 : GradientVessel::GradientVessel( const vesselbase::VesselOptions& da ) :
      59           2 :   FunctionVessel(da) {
      60           2 :   Gradient* vg=dynamic_cast<Gradient*>( getAction() );
      61           2 :   plumed_assert( vg );
      62           2 :   isdens=(vg->getPntrToMultiColvar())->isDensity();
      63           2 :   nweights = vg->nbins[0] + vg->nbins[1] + vg->nbins[2];
      64           2 :   if( (vg->getPntrToMultiColvar())->getNumberOfQuantities()>2 ) {
      65           0 :     ncomponents = (vg->getPntrToMultiColvar())->getNumberOfQuantities() - 2;
      66             :   } else {
      67           2 :     ncomponents = 1;
      68             :   }
      69             : 
      70           2 :   starts.push_back(0);
      71           2 :   if( vg->nbins[0]>0 ) {
      72           2 :     starts.push_back( vg->nbins[0] );
      73           2 :     if( vg->nbins[1]>0 ) {
      74           0 :       starts.push_back( vg->nbins[0] + vg->nbins[1] );
      75           0 :       if( vg->nbins[2]>0 ) {
      76           0 :         starts.push_back( nweights );
      77             :       }
      78           2 :     } else if( vg->nbins[2]>0 ) {
      79           0 :       starts.push_back( nweights );
      80             :     }
      81           0 :   } else if( vg->nbins[1]>0 ) {
      82           0 :     starts.push_back( vg->nbins[1] );
      83           0 :     if( vg->nbins[2]>0 ) {
      84           0 :       starts.push_back( nweights );
      85             :     }
      86           0 :   } else if( vg->nbins[2]>0 ) {
      87           0 :     starts.push_back( nweights );
      88             :   }
      89           2 : }
      90             : 
      91           2 : std::string GradientVessel::value_descriptor() {
      92           2 :   return "the gradient";
      93             : }
      94             : 
      95           4 : void GradientVessel::resize() {
      96           4 :   if( getAction()->derivativesAreRequired() ) {
      97           2 :     unsigned nder=getAction()->getNumberOfDerivatives();
      98           2 :     resizeBuffer( (1+nder)*(ncomponents+1)*nweights );
      99           2 :     getFinalValue()->resizeDerivatives( nder );
     100             :   } else {
     101           2 :     resizeBuffer( (ncomponents+1)*nweights );
     102             :   }
     103           4 : }
     104             : 
     105       11600 : void GradientVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
     106             :   unsigned nder;
     107       11600 :   if( getAction()->derivativesAreRequired() ) {
     108       11600 :     nder=getAction()->getNumberOfDerivatives();
     109             :   } else {
     110             :     nder=0;
     111             :   }
     112             :   unsigned wstart, cstart;
     113       11600 :   if( ncomponents==1 ) {
     114             :     cstart=1;
     115             :     wstart=2;
     116             :   } else {
     117             :     cstart=2;
     118           0 :     wstart=2+ncomponents;
     119             :   }
     120             : 
     121       58000 :   for(unsigned iw=0; iw<nweights; ++iw) {
     122       46400 :     unsigned xx = (ncomponents+1)*iw;
     123       46400 :     double weight=myvals.get(wstart+iw);
     124       46400 :     buffer[bufstart+xx*(nder+1)] += weight;
     125       46400 :     myvals.chainRule( wstart + iw, xx, 1, 0, 1.0, bufstart, buffer );
     126       92800 :     for(unsigned jc=0; jc<ncomponents; ++jc) {
     127       46400 :       double colvar=myvals.get( cstart + jc );
     128       46400 :       buffer[bufstart+(xx+1+jc)*(nder+1) ] += weight*colvar;
     129       46400 :       myvals.chainRule( cstart + jc, xx + 1 + jc, 1, 0, weight, bufstart, buffer );
     130       46400 :       myvals.chainRule( wstart + iw, xx + 1 + jc, 1, 0, colvar, bufstart, buffer );
     131             :     }
     132             :   }
     133       11600 : }
     134             : 
     135         232 : void GradientVessel::finish( const std::vector<double>& buffer ) {
     136         232 :   std::vector<double> val_interm( ncomponents*nweights );
     137             :   unsigned nder;
     138         232 :   if( getAction()->derivativesAreRequired() ) {
     139         232 :     nder=getAction()->getNumberOfDerivatives();
     140             :   } else {
     141             :     nder=0;
     142             :   }
     143         232 :   Matrix<double> der_interm( ncomponents*nweights, nder );
     144             :   der_interm=0;
     145             : 
     146         232 :   if( isdens ) {
     147         580 :     for(unsigned iw=0; iw<nweights; ++iw) {
     148         464 :       val_interm[iw] = buffer[bufstart + 2*iw*(1+nder)];
     149         464 :       if( getAction()->derivativesAreRequired() ) {
     150         464 :         unsigned wstart = bufstart + 2*iw*(nder+1) + 1;
     151       75632 :         for(unsigned jder=0; jder<nder; ++jder) {
     152       75168 :           der_interm( iw, jder ) += buffer[ wstart + jder ];
     153             :         }
     154             :       }
     155             :     }
     156             :   } else {
     157         580 :     for(unsigned iw=0; iw<nweights; ++iw) {
     158         464 :       unsigned xx = (ncomponents+1)*iw;
     159         464 :       double ww=buffer[bufstart + xx*(1+nder)];
     160         928 :       for(unsigned jc=0; jc<ncomponents; ++jc) {
     161         464 :         val_interm[ iw*ncomponents + jc ] = buffer[bufstart + (xx+1+jc)*(1+nder)] / ww;
     162             :       }
     163         464 :       if( getAction()->derivativesAreRequired() ) {
     164         464 :         unsigned wstart = bufstart + xx*(nder+1) + 1;
     165         928 :         for(unsigned jc=0; jc<ncomponents; ++jc) {
     166         464 :           unsigned bstart = bufstart + ( xx + 1 + jc )*(nder+1) + 1;
     167         464 :           double val = buffer[bufstart + (nder+1)*(xx+1+jc)];
     168       75632 :           for(unsigned jder=0; jder<nder; ++jder) {
     169       75168 :             der_interm( iw*ncomponents + jc, jder ) = (1.0/ww)*buffer[bstart + jder] - (val/(ww*ww))*buffer[wstart + jder];
     170             :           }
     171             :         }
     172             :       }
     173             :     }
     174             :   }
     175             : 
     176             :   double tmp, diff2=0.0;
     177             : 
     178         232 :   if( getAction()->derivativesAreRequired() ) {
     179             :     Value* fval=getFinalValue();
     180         464 :     for(unsigned j=0; j<starts.size()-1; ++j) {
     181        1160 :       for(unsigned bin=starts[j]; bin<starts[j+1]; ++bin) {
     182        1856 :         for(unsigned jc=0; jc<ncomponents; ++jc) {
     183         928 :           if( bin==starts[j] ) {
     184         232 :             tmp=val_interm[(starts[j+1]-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     185       37816 :             for(unsigned jder=0; jder<nder; ++jder) {
     186       37584 :               fval->addDerivative( jder, +2.0*tmp*der_interm( (starts[j+1]-1)*ncomponents + jc, jder) );
     187       37584 :               fval->addDerivative( jder, -2.0*tmp*der_interm( bin*ncomponents + jc, jder ) );
     188             :             }
     189             :           } else {
     190         696 :             tmp=val_interm[(bin-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     191      113448 :             for(unsigned jder=0; jder<nder; ++jder) {
     192      112752 :               fval->addDerivative( jder, +2.0*tmp*der_interm( (bin-1)*ncomponents + jc, jder) );
     193      112752 :               fval->addDerivative( jder, -2.0*tmp*der_interm( bin*ncomponents + jc, jder ) );
     194             :             }
     195             :           }
     196         928 :           diff2+=tmp*tmp;
     197             :         }
     198             :       }
     199             :     }
     200             :   } else {
     201           0 :     for(unsigned j=0; j<starts.size()-1; ++j) {
     202           0 :       for(unsigned bin=starts[j]; bin<starts[j+1]; ++bin) {
     203           0 :         for(unsigned jc=0; jc<ncomponents; ++jc) {
     204           0 :           if( bin==starts[j] ) {
     205           0 :             tmp=val_interm[(starts[j+1]-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     206             :           } else {
     207           0 :             tmp=val_interm[(bin-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     208             :           }
     209           0 :           diff2+=tmp*tmp;
     210             :         }
     211             :       }
     212             :     }
     213             :   }
     214             :   setOutputValue( diff2 );
     215         232 : }
     216             : 
     217             : }
     218             : }