Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2019 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 "AtomValuePack.h"
      23             : #include "CatomPack.h"
      24             : #include "tools/LinkCells.h"
      25             : 
      26             : namespace PLMD {
      27             : namespace multicolvar {
      28             : 
      29      461915 : AtomValuePack::AtomValuePack( MultiValue& vals, MultiColvarBase const * mcolv ):
      30             :   myvals(vals),
      31             :   mycolv(mcolv),
      32             :   natoms(0),
      33      461915 :   indices( vals.getIndices() ),
      34      461936 :   sort_vector( vals.getSortIndices() ),
      35     1385830 :   myatoms( vals.getAtomVector() )
      36             : {
      37      461949 :   if( indices.size()!=mcolv->getNumberOfAtoms() ) {
      38       23782 :     indices.resize( mcolv->getNumberOfAtoms() );
      39       23777 :     sort_vector.resize( mcolv->getNumberOfAtoms() );
      40       23786 :     myatoms.resize( mcolv->getNumberOfAtoms() );
      41             :   }
      42      461934 : }
      43             : 
      44      234771 : unsigned AtomValuePack::setupAtomsFromLinkCells( const std::vector<unsigned>& cind, const Vector& cpos, const LinkCells& linkcells ) {
      45      234771 :   if( cells_required.size()!=linkcells.getNumberOfCells() ) cells_required.resize( linkcells.getNumberOfCells() );
      46             :   // Build the list of cells that we need
      47      234825 :   unsigned ncells_required=0; linkcells.addRequiredCells( linkcells.findMyCell( cpos ), ncells_required, cells_required );
      48             :   // Now build the list of atoms we need
      49      234812 :   natoms=cind.size(); for(unsigned i=0; i<natoms; ++i) indices[i]=cind[i];
      50      234803 :   linkcells.retrieveAtomsInCells( ncells_required, cells_required, natoms, indices );
      51             : //  linkcells.retrieveNeighboringAtoms( cpos, natoms, indices );
      52      362695 :   for(unsigned i=0; i<natoms; ++i) myatoms[i]=mycolv->getPositionOfAtomForLinkCells( indices[i] ) - cpos;
      53      234788 :   if( mycolv->usesPbc() ) mycolv->applyPbc( myatoms, natoms );
      54      234810 :   return natoms;
      55             : }
      56             : 
      57      530323 : void AtomValuePack::updateUsingIndices() {
      58     1060613 :   if( myvals.updateComplete() ) return;
      59             : 
      60      476809 :   unsigned jactive=0;
      61   399878309 :   for(unsigned i=0; i<natoms; ++i) {
      62   399549468 :     unsigned base=3*indices[i];
      63   399547302 :     if( myvals.isActive( base ) ) { sort_vector[jactive]=indices[i]; jactive++; }
      64             :   }
      65      328841 :   std::sort( sort_vector.begin(), sort_vector.begin()+jactive );
      66             : 
      67      328810 :   myvals.emptyActiveMembers();
      68     4744476 :   for(unsigned i=0; i<jactive; ++i) {
      69     4415860 :     unsigned base=3*sort_vector[i]; // indices[i];
      70     4418567 :     myvals.putIndexInActiveArray( base );
      71     4415271 :     myvals.putIndexInActiveArray( base + 1 );
      72     4415354 :     myvals.putIndexInActiveArray( base + 2 );
      73             :   }
      74      328616 :   unsigned nvir=3*mycolv->getNumberOfAtoms();
      75      328715 :   if( myvals.isActive( nvir ) ) {
      76      231013 :     for(unsigned i=0; i<9; ++i) myvals.putIndexInActiveArray( nvir + i );
      77             :   }
      78      324735 :   myvals.completeUpdate();
      79             : }
      80             : 
      81      905722 : void AtomValuePack::addComDerivatives( const int& ind, const Vector& der, CatomPack& catom_der ) {
      82      905722 :   if( ind<0 ) {
      83      104392 :     for(unsigned ider=0; ider<catom_der.getNumberOfAtomsWithDerivatives(); ++ider) {
      84       54660 :       unsigned jder=3*catom_der.getIndex(ider);
      85       54660 :       myvals.addTemporyDerivative( jder+0, catom_der.getDerivative(ider,0,der) );
      86       54660 :       myvals.addTemporyDerivative( jder+1, catom_der.getDerivative(ider,1,der) );
      87       54660 :       myvals.addTemporyDerivative( jder+2, catom_der.getDerivative(ider,2,der) );
      88             :     }
      89             :   } else {
      90     1716908 :     for(unsigned ider=0; ider<catom_der.getNumberOfAtomsWithDerivatives(); ++ider) {
      91      860918 :       unsigned jder=3*catom_der.getIndex(ider);
      92      860918 :       myvals.addDerivative( ind, jder+0, catom_der.getDerivative(ider,0,der) );
      93      860918 :       myvals.addDerivative( ind, jder+1, catom_der.getDerivative(ider,1,der) );
      94      860918 :       myvals.addDerivative( ind, jder+2, catom_der.getDerivative(ider,2,der) );
      95             :     }
      96             :   }
      97      905722 : }
      98             : 
      99             : }
     100        4821 : }