Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016,2017 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 "PathProjectionCalculator.h"
      23             : #include "core/ActionWithValue.h"
      24             : #include "core/ActionWithArguments.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "core/ActionSet.h"
      27             : #include "core/PlumedMain.h"
      28             : 
      29             : namespace PLMD {
      30             : namespace mapping {
      31             : 
      32          24 : void PathProjectionCalculator::registerKeywords(Keywords& keys) {
      33          48 :   keys.addInputKeyword("compulsory","ARG","matrix","the labels of the matrix that contains the vectors of displacements from each frame in the path");
      34          48 :   keys.add("compulsory","METRIC","the method to use for computing the displacement vectors between the reference frames");
      35          48 :   keys.add("compulsory","METRIC_COMPONENT","if the final action in your metric contains multiple components this keyword is used to specify the component that should be used");
      36          48 :   keys.addInputKeyword("compulsory","REFERENCE","vector","labels for actions that contain reference coordinates for each point on the path");
      37          24 : }
      38             : 
      39          10 : PathProjectionCalculator::PathProjectionCalculator( Action* act ):
      40          10 :   mypath_obj(NULL)
      41             : {
      42          10 :   ActionWithArguments* aarg=dynamic_cast<ActionWithArguments*>( act );
      43          10 :   if( aarg ) {
      44           6 :     mypath_obj = aarg->getPntrToArgument(0);
      45             :     // Check that we have only one argument as input
      46           6 :     if( aarg->getNumberOfArguments()!=1 ) act->error("should only have one argument to this function");
      47             :   }
      48             :   // Ensure that values are stored in base calculation and that PLUMED doesn't try to calculate this in the stream
      49          10 :   if( mypath_obj ) mypath_obj->buildDataStore();
      50             :   // Check that the input is a matrix
      51          10 :   if( mypath_obj ) if( mypath_obj->getRank()!=2 ) act->error("the input to this action should be a matrix");
      52             :   // Get the labels for the reference points
      53          10 :   std::vector<std::string> reference_data; act->parseVector("REFERENCE", reference_data);
      54          10 :   std::vector<colvar::RMSDVector*> allrmsd = act->plumed.getActionSet().select<colvar::RMSDVector*>();
      55          10 :   ActionWithArguments::interpretArgumentList( reference_data, act->plumed.getActionSet(), act, refargs );
      56          26 :   for(unsigned i=0; i<refargs.size(); ++i ) {
      57          16 :     Action* thisact = refargs[i]->getPntrToAction();
      58          16 :     for(unsigned j=0; j<allrmsd.size(); ++j) {
      59           4 :       if( allrmsd[j]->checkForDependency(thisact) ) { rmsd_objects.push_back( allrmsd[j] ); break; }
      60             :     }
      61          16 :     if( !refargs[i]->isConstant() ) act->error("input" + refargs[i]->getName() + " is not constant");
      62          16 :     if( refargs[i]->getRank()==2 && reference_data.size()!=1 ) act->error("should only be one matrix in input to path projection object");
      63          16 :     if( refargs[i]->getRank()>0 && refargs[i]->getShape()[0]!=refargs[0]->getShape()[0] ) act->error("mismatch in number of reference frames in input to reference_data");
      64             :   }
      65             :   // Create a plumed main object to compute distances between reference configurations
      66          10 :   int s=sizeof(double);
      67          10 :   metric.cmd("setRealPrecision",&s);
      68          10 :   metric.cmd("setMDEngine","plumed");
      69          10 :   int nat=0; metric.cmd("setNatoms",&nat); metric.cmd("setNoVirial");
      70          10 :   unsigned nargs=refargs.size(); if( refargs[0]->getRank()==2 ) nargs = refargs[0]->getShape()[1];
      71          10 :   std::string str_nargs; Tools::convert( nargs, str_nargs ); std::string period_str=" PERIODIC=NO";
      72          11 :   if( mypath_obj && mypath_obj->isPeriodic() ) { std::string min, max; mypath_obj->getDomain( min, max ); period_str=" PERIODIC=" + min + "," + max; }
      73          20 :   metric.readInputLine("arg1: PUT UNIT=number SHAPE=" + str_nargs + period_str, true);
      74          20 :   metric.readInputLine("arg2: PUT UNIT=number SHAPE=" + str_nargs + period_str, true);
      75          10 :   double tstep=1.0; metric.cmd("setTimestep",&tstep);
      76          20 :   std::string inp; act->parse("METRIC",inp); inp += " ARG=arg2,arg1"; const char* cinp=inp.c_str();
      77          10 :   std::vector<std::string> input=Tools::getWords(inp);
      78          10 :   if( input.size()==1 && !actionRegister().check(input[0]) ) {
      79           0 :     metric.cmd("setPlumedDat",cinp); metric.cmd("init");
      80             :   } else {
      81          10 :     metric.cmd("init"); metric.cmd("readInputLine",cinp);
      82             :   }
      83             :   // Now setup stuff to retrieve the final displacement
      84          10 :   unsigned aind = metric.getActionSet().size()-1;
      85             :   while( true ) {
      86          15 :     const ActionShortcut* as=dynamic_cast<const ActionShortcut*>( metric.getActionSet()[aind].get() );
      87          15 :     if( !as ) break ; aind = aind - 1; plumed_assert( aind>=0 );
      88           5 :   }
      89          10 :   ActionWithValue* fav = dynamic_cast<ActionWithValue*>( metric.getActionSet()[aind].get() );
      90          10 :   if( !fav ) act->error("final value should calculate relevant value that you want as reference");
      91          10 :   std::string name = (fav->copyOutput(0))->getName();
      92          10 :   if( fav->getNumberOfComponents()>1 ) {
      93          15 :     std::string comp; act->parse("METRIC_COMPONENT",comp); name = fav->getLabel() + "." + comp;
      94             :   }
      95          20 :   long rank; metric.cmd("getDataRank " + name, &rank );
      96          10 :   if( rank==0 ) rank=1;
      97          20 :   std::vector<long> ishape( rank ); metric.cmd("getDataShape " + name, &ishape[0] );
      98          20 :   unsigned nvals=1; for(unsigned i=0; i<ishape.size(); ++i) nvals *= ishape[i];
      99          30 :   data.resize( nvals ); metric.cmd("setMemoryForData " + name, &data[0] );
     100          20 : }
     101             : 
     102        1114 : unsigned PathProjectionCalculator::getNumberOfFrames() const {
     103        1114 :   return refargs[0]->getShape()[0];
     104             : }
     105             : 
     106       11728 : void PathProjectionCalculator::computeVectorBetweenFrames( const unsigned& ifrom, const unsigned& ito ) {
     107       11728 :   int step = 1; metric.cmd("setStep",&step);
     108       11728 :   std::vector<double> valdata1( data.size() ), valdata2( data.size() );
     109       11728 :   getReferenceConfiguration( ito, valdata2 ); getReferenceConfiguration( ifrom, valdata1 );
     110       11728 :   metric.cmd("setValue arg1", &valdata1[0] );
     111       11728 :   metric.cmd("setValue arg2", &valdata2[0] );
     112       11728 :   metric.cmd("calc");
     113       11728 : }
     114             : 
     115       11728 : void PathProjectionCalculator::getDisplaceVector( const unsigned& ifrom, const unsigned& ito, std::vector<double>& displace ) {
     116       11728 :   if( displace.size()!=data.size() ) displace.resize( data.size() );
     117      404063 :   computeVectorBetweenFrames( ifrom, ito ); for(unsigned i=0; i<data.size(); ++i) displace[i] = data[i];
     118       11728 : }
     119             : 
     120       27778 : void PathProjectionCalculator::getReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos ) const {
     121       27778 :   if( refpos.size()!=data.size() ) refpos.resize( data.size() );
     122       27778 :   if( refargs[0]->getRank()==2 ) {
     123      962880 :     for(unsigned i=0; i<refpos.size(); ++i) refpos[i] = refargs[0]->get( iframe*refpos.size() + i );
     124             :   } else {
     125       11178 :     for(unsigned i=0; i<refpos.size(); ++i) refpos[i] = refargs[i]->get(iframe);
     126             :   }
     127       27778 : }
     128             : 
     129        4322 : void PathProjectionCalculator::setReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos ) {
     130             :   plumed_dbg_assert( refpos.size()==data.size() );
     131        4322 :   if( refargs[0]->getRank()==2 ) {
     132      165360 :     for(unsigned i=0; i<refpos.size(); ++i) refargs[0]->set( iframe*refpos.size() + i, refpos[i] );
     133             :   } else {
     134         572 :     for(unsigned i=0; i<refpos.size(); ++i) refargs[i]->set( iframe, refpos[i] );
     135             :   }
     136        4322 : }
     137             : 
     138          27 : void PathProjectionCalculator::updateDepedentRMSDObjects() {
     139          50 :   for(unsigned i=0; i<rmsd_objects.size(); ++i) rmsd_objects[i]->setReferenceConfigurations();
     140          27 : }
     141             : 
     142             : }
     143             : }
     144             :