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       10421 : PLUMED_REGISTER_VESSEL(GradientVessel,"GRADIENT")
      48             : 
      49           2 : void GradientVessel::registerKeywords( Keywords& keys ) {
      50           2 :   vesselbase::FunctionVessel::registerKeywords(keys);
      51           2 : }
      52             : 
      53        3473 : void GradientVessel::reserveKeyword( Keywords& keys ) {
      54        6946 :   keys.reserve("vessel","GRADIENT","calculate the gradient");
      55        6946 :   keys.addOutputComponent("gradient","GRADIENT","the gradient");
      56        3473 : }
      57             : 
      58           2 : GradientVessel::GradientVessel( const vesselbase::VesselOptions& da ) :
      59           2 :   FunctionVessel(da)
      60             : {
      61           2 :   Gradient* vg=dynamic_cast<Gradient*>( getAction() );
      62           2 :   plumed_assert( vg ); 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 ) starts.push_back( nweights );
      76           2 :     } else if( vg->nbins[2]>0 ) {
      77           0 :       starts.push_back( nweights );
      78             :     }
      79           0 :   } else if( vg->nbins[1]>0 ) {
      80           0 :     starts.push_back( vg->nbins[1] );
      81           0 :     if( vg->nbins[2]>0 ) starts.push_back( nweights );
      82           0 :   } else if( vg->nbins[2]>0 ) {
      83           0 :     starts.push_back( nweights );
      84             :   }
      85           2 : }
      86             : 
      87           2 : std::string GradientVessel::value_descriptor() {
      88           2 :   return "the gradient";
      89             : }
      90             : 
      91           4 : void GradientVessel::resize() {
      92           4 :   if( getAction()->derivativesAreRequired() ) {
      93           2 :     unsigned nder=getAction()->getNumberOfDerivatives();
      94           2 :     resizeBuffer( (1+nder)*(ncomponents+1)*nweights );
      95           2 :     getFinalValue()->resizeDerivatives( nder );
      96             :   } else {
      97           2 :     resizeBuffer( (ncomponents+1)*nweights );
      98             :   }
      99           4 : }
     100             : 
     101       11600 : void GradientVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
     102             :   unsigned nder;
     103       11600 :   if( getAction()->derivativesAreRequired() ) nder=getAction()->getNumberOfDerivatives();
     104             :   else nder=0;
     105       11600 :   unsigned wstart, cstart; if( ncomponents==1 ) { cstart=1; wstart=2; } else { cstart=2; wstart=2+ncomponents; }
     106             : 
     107       58000 :   for(unsigned iw=0; iw<nweights; ++iw) {
     108       46400 :     unsigned xx = (ncomponents+1)*iw;
     109       46400 :     double weight=myvals.get(wstart+iw);
     110       46400 :     buffer[bufstart+xx*(nder+1)] += weight;
     111       46400 :     myvals.chainRule( wstart + iw, xx, 1, 0, 1.0, bufstart, buffer );
     112       92800 :     for(unsigned jc=0; jc<ncomponents; ++jc) {
     113       46400 :       double colvar=myvals.get( cstart + jc );
     114       46400 :       buffer[bufstart+(xx+1+jc)*(nder+1) ] += weight*colvar;
     115       46400 :       myvals.chainRule( cstart + jc, xx + 1 + jc, 1, 0, weight, bufstart, buffer );
     116       46400 :       myvals.chainRule( wstart + iw, xx + 1 + jc, 1, 0, colvar, bufstart, buffer );
     117             :     }
     118             :   }
     119       11600 : }
     120             : 
     121         232 : void GradientVessel::finish( const std::vector<double>& buffer ) {
     122         232 :   std::vector<double> val_interm( ncomponents*nweights );
     123             :   unsigned nder;
     124         232 :   if( getAction()->derivativesAreRequired() ) nder=getAction()->getNumberOfDerivatives();
     125             :   else nder=0;
     126         232 :   Matrix<double> der_interm( ncomponents*nweights, nder ); der_interm=0;
     127             : 
     128         232 :   if( isdens ) {
     129         580 :     for(unsigned iw=0; iw<nweights; ++iw) {
     130         464 :       val_interm[iw] = buffer[bufstart + 2*iw*(1+nder)];
     131         464 :       if( getAction()->derivativesAreRequired() ) {
     132         464 :         unsigned wstart = bufstart + 2*iw*(nder+1) + 1;
     133       75632 :         for(unsigned jder=0; jder<nder; ++jder) der_interm( iw, jder ) += buffer[ wstart + jder ];
     134             :       }
     135             :     }
     136             :   } else {
     137         580 :     for(unsigned iw=0; iw<nweights; ++iw) {
     138         464 :       unsigned xx = (ncomponents+1)*iw;
     139         464 :       double ww=buffer[bufstart + xx*(1+nder)];
     140         928 :       for(unsigned jc=0; jc<ncomponents; ++jc) val_interm[ iw*ncomponents + jc ] = buffer[bufstart + (xx+1+jc)*(1+nder)] / ww;
     141         464 :       if( getAction()->derivativesAreRequired() ) {
     142         464 :         unsigned wstart = bufstart + xx*(nder+1) + 1;
     143         928 :         for(unsigned jc=0; jc<ncomponents; ++jc) {
     144         464 :           unsigned bstart = bufstart + ( xx + 1 + jc )*(nder+1) + 1;
     145         464 :           double val = buffer[bufstart + (nder+1)*(xx+1+jc)];
     146       75632 :           for(unsigned jder=0; jder<nder; ++jder)
     147       75168 :             der_interm( iw*ncomponents + jc, jder ) = (1.0/ww)*buffer[bstart + jder] - (val/(ww*ww))*buffer[wstart + jder];
     148             :         }
     149             :       }
     150             :     }
     151             :   }
     152             : 
     153             :   double tmp, diff2=0.0;
     154             : 
     155         232 :   if( getAction()->derivativesAreRequired() ) {
     156             :     Value* fval=getFinalValue();
     157         464 :     for(unsigned j=0; j<starts.size()-1; ++j) {
     158        1160 :       for(unsigned bin=starts[j]; bin<starts[j+1]; ++bin) {
     159        1856 :         for(unsigned jc=0; jc<ncomponents; ++jc) {
     160         928 :           if( bin==starts[j] ) {
     161         232 :             tmp=val_interm[(starts[j+1]-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     162       37816 :             for(unsigned jder=0; jder<nder; ++jder) {
     163       37584 :               fval->addDerivative( jder, +2.0*tmp*der_interm( (starts[j+1]-1)*ncomponents + jc, jder) );
     164       37584 :               fval->addDerivative( jder, -2.0*tmp*der_interm( bin*ncomponents + jc, jder ) );
     165             :             }
     166             :           } else {
     167         696 :             tmp=val_interm[(bin-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     168      113448 :             for(unsigned jder=0; jder<nder; ++jder) {
     169      112752 :               fval->addDerivative( jder, +2.0*tmp*der_interm( (bin-1)*ncomponents + jc, jder) );
     170      112752 :               fval->addDerivative( jder, -2.0*tmp*der_interm( bin*ncomponents + jc, jder ) );
     171             :             }
     172             :           }
     173         928 :           diff2+=tmp*tmp;
     174             :         }
     175             :       }
     176             :     }
     177             :   } else {
     178           0 :     for(unsigned j=0; j<starts.size()-1; ++j) {
     179           0 :       for(unsigned bin=starts[j]; bin<starts[j+1]; ++bin) {
     180           0 :         for(unsigned jc=0; jc<ncomponents; ++jc) {
     181           0 :           if( bin==starts[j] ) tmp=val_interm[(starts[j+1]-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     182           0 :           else tmp=val_interm[(bin-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];
     183           0 :           diff2+=tmp*tmp;
     184             :         }
     185             :       }
     186             :     }
     187             :   }
     188             :   setOutputValue( diff2 );
     189         232 : }
     190             : 
     191             : }
     192             : }