Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "ActionWithInputMatrix.h"
      23             : #include "AdjacencyMatrixVessel.h"
      24             : #include "AdjacencyMatrixBase.h"
      25             : #include "vesselbase/ActionWithVessel.h"
      26             : #include "core/PlumedMain.h"
      27             : #include "core/ActionSet.h"
      28             : 
      29             : namespace PLMD {
      30             : namespace adjmat {
      31             : 
      32          32 : void ActionWithInputMatrix::registerKeywords( Keywords& keys ) {
      33          32 :   MultiColvarBase::registerKeywords( keys );
      34          64 :   keys.add("compulsory","MATRIX","the action that calculates the adjacency matrix vessel we would like to analyze");
      35          32 : }
      36             : 
      37             : 
      38          27 : ActionWithInputMatrix::ActionWithInputMatrix(const ActionOptions& ao):
      39             :   Action(ao),
      40             :   MultiColvarBase(ao),
      41          27 :   mymatrix(NULL)
      42             : {
      43          27 :   matsums=true;
      44          54 :   if( keywords.exists("MATRIX") ) {
      45             :     std::vector<AtomNumber> fake_atoms;
      46          50 :     if( !parseMultiColvarAtomList("MATRIX",-1,fake_atoms ) ) error("unable to interpret input matrix");
      47          25 :     if( mybasemulticolvars.size()!=1 ) error("should be exactly one matrix input");
      48             : 
      49             :     // Retrieve the adjacency matrix of interest
      50          25 :     for(unsigned i=0; i<mybasemulticolvars[0]->getNumberOfVessels(); ++i) {
      51          25 :       mymatrix = dynamic_cast<AdjacencyMatrixVessel*>( mybasemulticolvars[0]->getPntrToVessel(i) );
      52          25 :       if( mymatrix ) break ;
      53             :     }
      54          25 :     if( !mymatrix ) error( mybasemulticolvars[0]->getLabel() + " does not calculate an adjacency matrix");
      55             : 
      56          25 :     atom_lab.resize(0); unsigned nnodes; // Delete all the atom labels that have been created
      57          25 :     if( mymatrix->undirectedGraph() ) nnodes = (mymatrix->function)->ablocks[0].size();
      58           2 :     else nnodes = (mymatrix->function)->ablocks[0].size() + (mymatrix->function)->ablocks[1].size();
      59        6816 :     for(unsigned i=0; i<nnodes; ++i) atom_lab.push_back( std::pair<unsigned,unsigned>( 1, i ) );
      60             :   }
      61          27 : }
      62             : 
      63       13250 : unsigned ActionWithInputMatrix::getNumberOfDerivatives() {
      64       13250 :   return (mymatrix->function)->getNumberOfDerivatives();
      65             : }
      66             : 
      67    16261547 : unsigned ActionWithInputMatrix::getNumberOfNodes() const {
      68    16261547 :   return (mymatrix->function)->ablocks[0].size();
      69             : }
      70             : 
      71       78058 : AdjacencyMatrixVessel* ActionWithInputMatrix::getAdjacencyVessel() const {
      72       78058 :   return mymatrix;
      73             : }
      74             : 
      75         504 : AtomNumber ActionWithInputMatrix::getAbsoluteIndexOfCentralAtom(const unsigned& i) const {
      76         504 :   return (mymatrix->function)->getAbsoluteIndexOfCentralAtom(i);
      77             : }
      78             : 
      79       46452 : double ActionWithInputMatrix::retrieveConnectionValue( const unsigned& i, const unsigned& j, std::vector<double>& vals ) const {
      80       46452 :   if( !mymatrix->matrixElementIsActive( i, j ) ) return 0;
      81       25360 :   unsigned myelem = mymatrix->getStoreIndexFromMatrixIndices( i, j );
      82             : 
      83             :   // unsigned vi; double df;
      84       25360 :   mymatrix->retrieveValueWithIndex( myelem, false, vals );
      85       25360 :   return vals[0]*vals[1];       // (mymatrix->function)->transformStoredValues( vals, vi, df );
      86             : }
      87             : 
      88        2004 : void ActionWithInputMatrix::getInputData( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms, std::vector<double>& orient0 ) const {
      89        2004 :   if( (mymatrix->function)->mybasemulticolvars.size()==0  ) {
      90         305 :     std::vector<double> tvals( mymatrix->getNumberOfComponents() ); orient0.assign(orient0.size(),0);
      91       38263 :     for(unsigned i=0; i<mymatrix->getNumberOfColumns(); ++i) {
      92       37958 :       if( mymatrix->undirectedGraph() && ind==i ) continue;
      93       37678 :       orient0[1]+=retrieveConnectionValue( ind, i, tvals );
      94             :     }
      95         305 :     orient0[0]=1.0; return;
      96             :   }
      97        1699 :   (mymatrix->function)->getInputData( ind, normed, myatoms, orient0 );
      98             : }
      99             : 
     100        1440 : void ActionWithInputMatrix::addConnectionDerivatives( const unsigned& i, const unsigned& j, MultiValue& myvals, MultiValue& myvout ) const {
     101        1440 :   if( !mymatrix->matrixElementIsActive( i, j ) ) return;
     102        1440 :   unsigned myelem = mymatrix->getStoreIndexFromMatrixIndices( i, j );
     103             :   // Get derivatives and add
     104        1440 :   mymatrix->retrieveDerivatives( myelem, false, myvals );
     105       31086 :   for(unsigned jd=0; jd<myvals.getNumberActive(); ++jd) {
     106       29646 :     unsigned ider=myvals.getActiveIndex(jd);
     107       29646 :     myvout.addDerivative( 1, ider, myvals.getDerivative( 1, ider ) );
     108             :   }
     109             : }
     110             : 
     111        1679 : MultiValue& ActionWithInputMatrix::getInputDerivatives( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const {
     112        1679 :   if( (mymatrix->function)->mybasemulticolvars.size()==0  ) {
     113          90 :     MultiValue& myder=mymatrix->getTemporyMultiValue(0);
     114          90 :     if( myder.getNumberOfValues()!=2 || myder.getNumberOfDerivatives()!=(mymatrix->function)->getNumberOfDerivatives() ) {
     115           3 :       myder.resize( 2, (mymatrix->function)->getNumberOfDerivatives() );
     116             :     }
     117          90 :     myder.clearAll();
     118          90 :     MultiValue myvals( (mymatrix->function)->getNumberOfQuantities(), (mymatrix->function)->getNumberOfDerivatives() );
     119         885 :     for(unsigned i=0; i<mymatrix->getNumberOfColumns(); ++i) {
     120         795 :       if( mymatrix->undirectedGraph() && ind==i ) continue;
     121         730 :       addConnectionDerivatives( ind, i, myvals, myder );
     122             :     }
     123             :     myder.updateDynamicList(); return myder;
     124          90 :   }
     125        1589 :   return (mymatrix->function)->getInputDerivatives( ind, normed, myatoms );
     126             : }
     127             : 
     128          66 : unsigned ActionWithInputMatrix::getNumberOfNodeTypes() const {
     129          66 :   unsigned size = (mymatrix->function)->mybasemulticolvars.size();
     130             :   if( size==0 ) return 1;
     131             :   return size;
     132             : }
     133             : 
     134        2181 : unsigned ActionWithInputMatrix::getNumberOfQuantities() const {
     135        2181 :   if( (mymatrix->function)->mybasemulticolvars.size()==0 ) return 2;
     136        2082 :   return (mymatrix->function)->mybasemulticolvars[0]->getNumberOfQuantities();
     137             : }
     138             : 
     139          34 : unsigned ActionWithInputMatrix::getNumberOfAtomsInGroup( const unsigned& igrp ) const {
     140             :   plumed_dbg_assert( igrp<(mymatrix->function)->mybasemulticolvars.size() );
     141          34 :   return (mymatrix->function)->mybasemulticolvars[igrp]->getFullNumberOfTasks();
     142             : }
     143             : 
     144           7 : multicolvar::MultiColvarBase* ActionWithInputMatrix::getBaseMultiColvar( const unsigned& igrp ) const {
     145             :   plumed_dbg_assert( igrp<(mymatrix->function)->mybasemulticolvars.size() );
     146           7 :   return (mymatrix->function)->mybasemulticolvars[igrp];
     147             : }
     148             : 
     149       54763 : Vector ActionWithInputMatrix::getPositionOfAtomForLinkCells( const unsigned& iatom ) const {
     150       54763 :   return (getAdjacencyVessel()->function)->getPositionOfAtomForLinkCells( iatom );
     151             : }
     152             : 
     153             : }
     154             : }