Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2017 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 "core/ActionWithMatrix.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC MCOLVAR VSTACK
      26             : /*
      27             : Create a matrix by stacking vectors together
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace valtools {
      36             : 
      37             : class VStack : public ActionWithMatrix {
      38             : private:
      39             :   std::vector<bool> stored;
      40             : public:
      41             :   static void registerKeywords( Keywords& keys );
      42             : /// Constructor
      43             :   explicit VStack(const ActionOptions&);
      44             : /// Get the number of derivatives
      45         294 :   unsigned getNumberOfDerivatives() override { return 0; }
      46             : ///
      47             :   void prepare() override ;
      48             : ///
      49     1270505 :   unsigned getNumberOfColumns() const override { return getNumberOfArguments(); }
      50             : ///
      51             :   void setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const override ;
      52             : ///
      53             :   void performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const override ;
      54             : ///
      55             :   void runEndOfRowJobs( const unsigned& ival, const std::vector<unsigned> & indices, MultiValue& myvals ) const override ;
      56             : ///
      57             :   void getMatrixColumnTitles( std::vector<std::string>& argnames ) const override ;
      58             : };
      59             : 
      60             : PLUMED_REGISTER_ACTION(VStack,"VSTACK")
      61             : 
      62         254 : void VStack::registerKeywords( Keywords& keys ) {
      63         254 :   ActionWithMatrix::registerKeywords( keys ); keys.use("ARG");
      64         254 :   keys.setValueDescription("a matrix that contains the input vectors in its columns");
      65         254 : }
      66             : 
      67         139 : VStack::VStack(const ActionOptions& ao):
      68             :   Action(ao),
      69         139 :   ActionWithMatrix(ao)
      70             : {
      71         139 :   if( getNumberOfArguments()==0 ) error("no arguments were specificed");
      72         139 :   if( getPntrToArgument(0)->getRank()>1 ) error("all arguments should be vectors");
      73             :   unsigned nvals=1; bool periodic=false; std::string smin, smax;
      74         139 :   if( getPntrToArgument(0)->getRank()==1 ) nvals = getPntrToArgument(0)->getShape()[0];
      75         139 :   if( getPntrToArgument(0)->isPeriodic() ) { periodic=true; getPntrToArgument(0)->getDomain( smin, smax ); }
      76             : 
      77        1228 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
      78        1089 :     if( getPntrToArgument(i)->getRank()>1 || (getPntrToArgument(i)->getRank()==1 && getPntrToArgument(i)->hasDerivatives()) ) error("all arguments should be vectors");
      79        1089 :     if( getPntrToArgument(i)->getRank()==0 ) {
      80          41 :       if( nvals!=1 ) error("all input vector should have same number of elements");
      81        1048 :     } else if( getPntrToArgument(i)->getShape()[0]!=nvals ) error("all input vector should have same number of elements");
      82        1089 :     if( periodic ) {
      83          51 :       if( !getPntrToArgument(i)->isPeriodic() ) error("one argument is periodic but " + getPntrToArgument(i)->getName() + " is not periodic");
      84          51 :       std::string tmin, tmax; getPntrToArgument(i)->getDomain( tmin, tmax );
      85          51 :       if( tmin!=smin || tmax!=smax ) error("domain of argument " + getPntrToArgument(i)->getName() + " is different from domain for all other arguments");
      86        1038 :     } else if( getPntrToArgument(i)->isPeriodic() ) error("one argument is not periodic but " + getPntrToArgument(i)->getName() + " is periodic");
      87             :   }
      88             :   // And create a value to hold the matrix
      89         139 :   std::vector<unsigned> shape(2); shape[0]=nvals; shape[1]=getNumberOfArguments(); addValue( shape );
      90         139 :   if( periodic ) setPeriodic( smin, smax ); else setNotPeriodic();
      91             :   // And store this value
      92         139 :   getPntrToComponent(0)->buildDataStore(); getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
      93             :   // Setup everything so we can build the store
      94         139 :   done_in_chain=true; ActionWithVector* av=dynamic_cast<ActionWithVector*>( getPntrToArgument(0)->getPntrToAction() );
      95         139 :   if( av ) {
      96          99 :     const ActionWithVector* head0 = av->getFirstActionInChain();
      97         996 :     for(unsigned i=0; i<getNumberOfArguments(); ++i) {
      98         928 :       ActionWithVector* avv=dynamic_cast<ActionWithVector*>( getPntrToArgument(i)->getPntrToAction() );
      99         928 :       if( !avv ) continue;
     100         924 :       if( head0!=avv->getFirstActionInChain() ) { done_in_chain=false; break; }
     101             :     }
     102          40 :   } else done_in_chain=false;
     103         139 :   unsigned nder = buildArgumentStore(0);
     104             :   // This checks which values have been stored
     105         139 :   stored.resize( getNumberOfArguments() ); std::string headstr=getFirstActionInChain()->getLabel();
     106        1228 :   for(unsigned i=0; i<stored.size(); ++i) stored[i] = getPntrToArgument(i)->ignoreStoredValue( headstr );
     107         139 : }
     108             : 
     109          23 : void VStack::getMatrixColumnTitles( std::vector<std::string>& argnames ) const {
     110          60 :   for(unsigned j=0; j<getNumberOfArguments(); ++j) {
     111          37 :     if( (getPntrToArgument(j)->getPntrToAction())->getName()=="COLLECT" ) {
     112          17 :       ActionWithArguments* aa = dynamic_cast<ActionWithArguments*>( getPntrToArgument(j)->getPntrToAction() );
     113          17 :       plumed_assert( aa && aa->getNumberOfArguments()==1 ); argnames.push_back( (aa->getPntrToArgument(0))->getName() );
     114          20 :     } else argnames.push_back( getPntrToArgument(j)->getName() );
     115             :   }
     116          23 : }
     117             : 
     118        3100 : void VStack::prepare() {
     119        3100 :   ActionWithVector::prepare();
     120        3100 :   if( getPntrToArgument(0)->getRank()==0 || getPntrToArgument(0)->getShape()[0]==getPntrToComponent(0)->getShape()[0] ) return ;
     121          18 :   std::vector<unsigned> shape(2); shape[0] = getPntrToArgument(0)->getShape()[0]; shape[1] = getNumberOfArguments();
     122          18 :   getPntrToComponent(0)->setShape(shape); getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
     123             : }
     124             : 
     125      214418 : void VStack::setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const {
     126      214418 :   unsigned nargs = getNumberOfArguments(); unsigned nvals = getConstPntrToComponent(0)->getShape()[0];
     127      214418 :   if( indices.size()!=nargs+1 ) indices.resize( nargs+1 );
     128     4287565 :   for(unsigned i=0; i<nargs; ++i) indices[i+1] = nvals + i;
     129             :   myvals.setSplitIndex( nargs + 1 );
     130      214418 : }
     131             : 
     132     4073147 : void VStack::performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const {
     133     4073147 :   unsigned ind2 = index2; if( index2>=getConstPntrToComponent(0)->getShape()[0] ) ind2 = index2 - getConstPntrToComponent(0)->getShape()[0];
     134     4073147 :   myvals.addValue( getConstPntrToComponent(0)->getPositionInStream(), getArgumentElement( ind2, index1, myvals ) );
     135             : 
     136     4073147 :   if( doNotCalculateDerivatives() ) return;
     137     3692599 :   addDerivativeOnVectorArgument( stored[ind2], 0, ind2, index1, 1.0, myvals );
     138             : }
     139             : 
     140      214418 : void VStack::runEndOfRowJobs( const unsigned& ival, const std::vector<unsigned> & indices, MultiValue& myvals ) const {
     141      214418 :   if( doNotCalculateDerivatives() || !matrixChainContinues() ) return ;
     142             : 
     143           3 :   unsigned nmat = getConstPntrToComponent(0)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
     144             :   std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices( nmat ) );
     145           3 :   plumed_assert( nmat_ind<matrix_indices.size() );
     146          12 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     147           9 :     bool found=false; ActionWithValue* iav = getPntrToArgument(i)->getPntrToAction();
     148           9 :     for(unsigned j=0; j<i; ++j) {
     149           6 :       if( iav==getPntrToArgument(j)->getPntrToAction() ) { found=true; break; }
     150             :     }
     151           9 :     if( found ) continue ;
     152             : 
     153             :     unsigned istrn = getPntrToArgument(i)->getPositionInStream();
     154          48 :     for(unsigned k=0; k<myvals.getNumberActive(istrn); ++k) {
     155          45 :       matrix_indices[nmat_ind] = myvals.getActiveIndex(istrn,k); nmat_ind++;
     156             :     }
     157             :   }
     158             :   myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind );
     159             : }
     160             : 
     161             : }
     162             : }