Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2018 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             : 
      28             : namespace PLMD {
      29             : namespace crystallization {
      30             : 
      31           0 : class VectorSum : public vesselbase::FunctionVessel {
      32             : private:
      33             :   unsigned nder;
      34             : public:
      35             :   static void registerKeywords( Keywords& keys );
      36             :   static void reserveKeyword( Keywords& keys );
      37             :   explicit VectorSum( const vesselbase::VesselOptions& da );
      38             :   std::string value_descriptor();
      39             :   void resize();
      40             :   void calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
      41             :   void finish( const std::vector<double>& buffer );
      42             : };
      43             : 
      44        2523 : PLUMED_REGISTER_VESSEL(VectorSum,"VSUM")
      45             : 
      46           0 : void VectorSum::registerKeywords( Keywords& keys ) {
      47           0 :   vesselbase::FunctionVessel::registerKeywords(keys);
      48           0 : }
      49             : 
      50         841 : void VectorSum::reserveKeyword( Keywords& keys ) {
      51         841 :   keys.reserve("vessel","VSUM","calculate the norm of the sum of vectors.");
      52             :   keys.addOutputComponent("vsum","VSUM","the norm of sum of vectors. The output component can be refererred to elsewhere in the input "
      53         841 :                           "file by using the label.vsum");
      54         841 : }
      55             : 
      56           0 : VectorSum::VectorSum( const vesselbase::VesselOptions& da ) :
      57             :   FunctionVessel(da),
      58           0 :   nder(0)
      59             : {
      60           0 : }
      61             : 
      62           0 : std::string VectorSum::value_descriptor() {
      63           0 :   return "the norm of the mean vector";
      64             : }
      65             : 
      66           0 : void VectorSum::resize() {
      67           0 :   unsigned ncomp=getAction()->getNumberOfQuantities() - 2;
      68             : 
      69           0 :   if( getAction()->derivativesAreRequired() ) {
      70           0 :     nder=getAction()->getNumberOfDerivatives();
      71           0 :     resizeBuffer( (1+nder)*ncomp ); getFinalValue()->resizeDerivatives( nder );
      72             :   } else {
      73           0 :     nder=0; resizeBuffer(ncomp);
      74             :   }
      75           0 : }
      76             : 
      77           0 : void VectorSum::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
      78           0 :   unsigned ncomp=getAction()->getNumberOfQuantities()-2;
      79             : 
      80           0 :   double weight=myvals.get(0);
      81             :   plumed_dbg_assert( weight>=getTolerance() );
      82           0 :   buffer[bufstart] += weight;
      83           0 :   for(unsigned i=0; i<ncomp; ++i) buffer[bufstart + i*(1+nder)] += weight*myvals.get(2+i);
      84           0 :   if( !getAction()->derivativesAreRequired() ) return;
      85             : 
      86           0 :   for(unsigned i=0; i<ncomp; ++i) {
      87           0 :     double colvar=myvals.get(2+i);
      88           0 :     myvals.chainRule( 2+i, i, 1, 0, weight, bufstart, buffer );
      89           0 :     if( diffweight ) myvals.chainRule( 0, i, 1, 0, colvar, bufstart, buffer );
      90             :   }
      91           0 :   return;
      92             : }
      93             : 
      94           0 : void VectorSum::finish( const std::vector<double>& buffer ) {
      95           0 :   unsigned ncomp=getAction()->getNumberOfQuantities()-2;
      96             : 
      97           0 :   double sum=0;
      98           0 :   for(unsigned i=0; i<ncomp; ++i) {
      99           0 :     double tmp = buffer[bufstart+(nder+1)*i];
     100           0 :     sum+=tmp*tmp;
     101             :   }
     102           0 :   double tw = 1.0 / sqrt(sum);
     103           0 :   setOutputValue( sqrt(sum) );
     104           0 :   if( !getAction()->derivativesAreRequired() ) return;
     105             : 
     106           0 :   Value* fval=getFinalValue();
     107           0 :   for(unsigned icomp=0; icomp<ncomp; ++icomp) {
     108           0 :     double tmp = buffer[icomp*(1+nder)];
     109           0 :     unsigned bstart = bufstart + icomp*(nder+1) + 1;
     110           0 :     for(unsigned jder=0; jder<nder; ++jder) fval->addDerivative( jder, tw*tmp*buffer[bstart + jder] );
     111             :   }
     112             : }
     113             : 
     114             : }
     115        2523 : }