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 "AtomValuePack.h"
      23             : #include "CatomPack.h"
      24             : #include "tools/LinkCells.h"
      25             : 
      26             : namespace PLMD {
      27             : namespace multicolvar {
      28             : 
      29      449463 : AtomValuePack::AtomValuePack( MultiValue& vals, MultiColvarBase const * mcolv ):
      30      449463 :   myvals(vals),
      31      449463 :   mycolv(mcolv),
      32      449463 :   natoms(0),
      33      449463 :   indices( vals.getIndices() ),
      34      449463 :   sort_vector( vals.getSortIndices() ),
      35      449463 :   myatoms( vals.getAtomVector() ) {
      36      449463 :   if( indices.size()!=mcolv->getNumberOfAtoms() ) {
      37       23864 :     indices.resize( mcolv->getNumberOfAtoms() );
      38       23864 :     sort_vector.resize( mcolv->getNumberOfAtoms() );
      39       23864 :     myatoms.resize( mcolv->getNumberOfAtoms() );
      40             :   }
      41      449463 : }
      42             : 
      43      222049 : unsigned AtomValuePack::setupAtomsFromLinkCells( const std::vector<unsigned>& cind, const Vector& cpos, const LinkCells& linkcells ) {
      44      222049 :   if( cells_required.size()!=linkcells.getNumberOfCells() ) {
      45      218659 :     cells_required.resize( linkcells.getNumberOfCells() );
      46             :   }
      47             :   // Build the list of cells that we need
      48      222049 :   unsigned ncells_required=0;
      49      222049 :   linkcells.addRequiredCells( linkcells.findMyCell( cpos ), ncells_required, cells_required );
      50             :   // Now build the list of atoms we need
      51      222049 :   natoms=cind.size();
      52      483914 :   for(unsigned i=0; i<natoms; ++i) {
      53      261865 :     indices[i]=cind[i];
      54             :   }
      55      222049 :   linkcells.retrieveAtomsInCells( ncells_required, cells_required, natoms, indices );
      56             : //  linkcells.retrieveNeighboringAtoms( cpos, natoms, indices );
      57   401982235 :   for(unsigned i=0; i<natoms; ++i) {
      58   401760186 :     myatoms[i]=mycolv->getPositionOfAtomForLinkCells( indices[i] ) - cpos;
      59             :   }
      60      222049 :   if( mycolv->usesPbc() ) {
      61      222049 :     mycolv->applyPbc( myatoms, natoms );
      62             :   }
      63      222049 :   return natoms;
      64             : }
      65             : 
      66      520523 : void AtomValuePack::updateUsingIndices() {
      67      520523 :   if( myvals.updateComplete() ) {
      68      204368 :     return;
      69             :   }
      70             : 
      71             :   unsigned jactive=0;
      72   400639874 :   for(unsigned i=0; i<natoms; ++i) {
      73   400323719 :     unsigned base=3*indices[i];
      74   400323719 :     if( myvals.isActive( base ) ) {
      75     4130161 :       sort_vector[jactive]=indices[i];
      76     4130161 :       jactive++;
      77             :     }
      78             :   }
      79      316155 :   std::sort( sort_vector.begin(), sort_vector.begin()+jactive );
      80             : 
      81      316155 :   myvals.emptyActiveMembers();
      82     4446316 :   for(unsigned i=0; i<jactive; ++i) {
      83     4130161 :     unsigned base=3*sort_vector[i]; // indices[i];
      84     4130161 :     myvals.putIndexInActiveArray( base );
      85     4130161 :     myvals.putIndexInActiveArray( base + 1 );
      86     4130161 :     myvals.putIndexInActiveArray( base + 2 );
      87             :   }
      88      316155 :   unsigned nvir=3*mycolv->getNumberOfAtoms();
      89      316155 :   if( myvals.isActive( nvir ) ) {
      90     2074510 :     for(unsigned i=0; i<9; ++i) {
      91     1867059 :       myvals.putIndexInActiveArray( nvir + i );
      92             :     }
      93             :   }
      94      316155 :   myvals.completeUpdate();
      95             : }
      96             : 
      97      980606 : void AtomValuePack::addComDerivatives( const int& ind, const Vector& der, const CatomPack& catom_der ) {
      98      980606 :   if( ind<0 ) {
      99      109936 :     for(unsigned ider=0; ider<catom_der.getNumberOfAtomsWithDerivatives(); ++ider) {
     100       57432 :       unsigned jder=3*catom_der.getIndex(ider);
     101       57432 :       myvals.addTemporyDerivative( jder+0, catom_der.getDerivative(ider,0,der) );
     102       57432 :       myvals.addTemporyDerivative( jder+1, catom_der.getDerivative(ider,1,der) );
     103       57432 :       myvals.addTemporyDerivative( jder+2, catom_der.getDerivative(ider,2,der) );
     104             :     }
     105             :   } else {
     106     1861132 :     for(unsigned ider=0; ider<catom_der.getNumberOfAtomsWithDerivatives(); ++ider) {
     107      933030 :       unsigned jder=3*catom_der.getIndex(ider);
     108      933030 :       myvals.addDerivative( ind, jder+0, catom_der.getDerivative(ider,0,der) );
     109      933030 :       myvals.addDerivative( ind, jder+1, catom_der.getDerivative(ider,1,der) );
     110      933030 :       myvals.addDerivative( ind, jder+2, catom_der.getDerivative(ider,2,der) );
     111             :     }
     112             :   }
     113      980606 : }
     114             : 
     115             : }
     116             : }