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          48 : void PathProjectionCalculator::registerKeywords(Keywords& keys) {
      33          96 :   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          96 :   keys.addInputKeyword("compulsory","REFERENCE","vector/matrix","labels for actions that contain reference coordinates for each point on the path (one matrix, or vectors)");
      37          48 : }
      38             : 
      39          19 : PathProjectionCalculator::PathProjectionCalculator( Action* act ):
      40          19 :   mypath_obj(NULL) {
      41          19 :   ActionWithArguments* aarg=dynamic_cast<ActionWithArguments*>( act );
      42          19 :   if( aarg ) {
      43          13 :     mypath_obj = aarg->getPntrToArgument(0);
      44             :     // Check that we have only one argument as input
      45          13 :     if( aarg->getNumberOfArguments()!=1 ) {
      46           0 :       act->error("should only have one argument to this function");
      47             :     }
      48             :   }
      49             :   // Ensure that values are stored in base calculation and that PLUMED doesn't try to calculate this in the stream
      50             :   // Check that the input is a matrix
      51          19 :   if( mypath_obj )
      52          13 :     if( mypath_obj->getRank()!=2 ) {
      53           0 :       act->error("the input to this action should be a matrix");
      54             :     }
      55             :   // Get the labels for the reference points
      56          19 :   std::vector<std::string> reference_data;
      57          19 :   act->parseVector("REFERENCE", reference_data);
      58          19 :   std::vector<colvar::RMSDVector*> allrmsd = act->plumed.getActionSet().select<colvar::RMSDVector*>();
      59          19 :   ActionWithArguments::interpretArgumentList( reference_data, act->plumed.getActionSet(), act, refargs );
      60          44 :   for(unsigned i=0; i<refargs.size(); ++i ) {
      61          25 :     Action* thisact = refargs[i]->getPntrToAction();
      62          29 :     for(unsigned j=0; j<allrmsd.size(); ++j) {
      63          17 :       if( allrmsd[j]->checkForDependency(thisact) ) {
      64          13 :         rmsd_objects.push_back( allrmsd[j] );
      65             :         break;
      66             :       }
      67             :     }
      68          25 :     if( !refargs[i]->isConstant() ) {
      69           0 :       act->error("input" + refargs[i]->getName() + " is not constant");
      70             :     }
      71          25 :     if( refargs[i]->getRank()==2 && reference_data.size()!=1 ) {
      72           0 :       act->error("should only be one matrix in input to path projection object");
      73             :     }
      74          25 :     if( refargs[i]->getRank()>0 && refargs[i]->getShape()[0]!=refargs[0]->getShape()[0] ) {
      75           0 :       act->error("mismatch in number of reference frames in input to reference_data");
      76             :     }
      77             :   }
      78             :   // Create a plumed main object to compute distances between reference configurations
      79          19 :   int s=sizeof(double);
      80          19 :   metric.cmd("setRealPrecision",&s);
      81          19 :   metric.cmd("setMDEngine","plumed");
      82          19 :   int nat=0;
      83          19 :   metric.cmd("setNatoms",&nat);
      84          19 :   metric.cmd("setNoVirial");
      85          19 :   unsigned nargs=refargs.size();
      86          19 :   if( refargs[0]->getRank()==2 ) {
      87          14 :     nargs = refargs[0]->getShape()[1];
      88             :   }
      89             :   std::string str_nargs;
      90          19 :   Tools::convert( nargs, str_nargs );
      91          19 :   std::string period_str=" PERIODIC=NO";
      92          19 :   if( mypath_obj && mypath_obj->isPeriodic() ) {
      93             :     std::string min, max;
      94           0 :     mypath_obj->getDomain( min, max );
      95           0 :     period_str=" PERIODIC=" + min + "," + max;
      96             :   }
      97          19 :   metric.readInputLine("arg1: PUT UNIT=number SHAPE=" + str_nargs + period_str, true);
      98          19 :   metric.readInputLine("arg2: PUT UNIT=number SHAPE=" + str_nargs + period_str, true);
      99          19 :   double tstep=1.0;
     100          19 :   metric.cmd("setTimestep",&tstep);
     101             :   std::string inp;
     102          38 :   act->parse("METRIC",inp);
     103             :   inp += " ARG=arg2,arg1";
     104             :   const char* cinp=inp.c_str();
     105          19 :   std::vector<std::string> input=Tools::getWords(inp);
     106          19 :   if( input.size()==1 && !actionRegister().check(input[0]) ) {
     107           0 :     metric.cmd("setPlumedDat",cinp);
     108           0 :     metric.cmd("init");
     109             :   } else {
     110          19 :     metric.cmd("init");
     111          19 :     metric.cmd("readInputLine",cinp);
     112             :   }
     113             :   // Now setup stuff to retrieve the final displacement
     114          19 :   unsigned aind = metric.getActionSet().size()-1;
     115             :   while( true ) {
     116          38 :     const ActionShortcut* as=dynamic_cast<const ActionShortcut*>( metric.getActionSet()[aind].get() );
     117          38 :     if( !as ) {
     118             :       break ;
     119             :     }
     120             :     // aind is unsigned: check before decrementing, otherwise it wraps around
     121          19 :     plumed_assert( aind>0 );
     122          19 :     --aind;
     123          19 :   }
     124          19 :   ActionWithValue* fav = dynamic_cast<ActionWithValue*>( metric.getActionSet()[aind].get() );
     125          19 :   if( !fav ) {
     126           0 :     act->error("final value should calculate relevant value that you want as reference");
     127             :   }
     128          19 :   std::string name = (fav->copyOutput(0))->getName();
     129          19 :   if( fav->getNumberOfComponents()>1 ) {
     130             :     std::string comp;
     131          14 :     act->parse("METRIC_COMPONENT",comp);
     132          28 :     name = fav->getLabel() + "." + comp;
     133             :   }
     134             :   long rank;
     135          38 :   metric.cmd("getDataRank " + name, &rank );
     136          19 :   if( rank==0 ) {
     137           0 :     rank=1;
     138             :   }
     139          19 :   std::vector<long> ishape( rank );
     140          38 :   metric.cmd("getDataShape " + name, &ishape[0] );
     141             :   unsigned nvals=1;
     142          38 :   for(unsigned i=0; i<ishape.size(); ++i) {
     143          19 :     nvals *= ishape[i];
     144             :   }
     145          19 :   data.resize( nvals );
     146          38 :   metric.cmd("setMemoryForData " + name, &data[0] );
     147          38 : }
     148             : 
     149        2258 : unsigned PathProjectionCalculator::getNumberOfFrames() const {
     150        2258 :   return refargs[0]->getShape()[0];
     151             : }
     152             : 
     153       26471 : void PathProjectionCalculator::computeVectorBetweenFrames( const unsigned& ifrom, const unsigned& ito ) {
     154       26471 :   int step = 1;
     155       26471 :   metric.cmd("setStep",&step);
     156       26471 :   std::vector<double> valdata1( data.size() ), valdata2( data.size() );
     157       26471 :   getReferenceConfiguration( ito, valdata2 );
     158       26471 :   getReferenceConfiguration( ifrom, valdata1 );
     159       26471 :   metric.cmd("setValue arg1", &valdata1[0] );
     160       26471 :   metric.cmd("setValue arg2", &valdata2[0] );
     161       26471 :   metric.cmd("calc");
     162       26471 : }
     163             : 
     164       26471 : void PathProjectionCalculator::getDisplaceVector( const unsigned& ifrom, const unsigned& ito, std::vector<double>& displace ) {
     165       26471 :   if( displace.size()!=data.size() ) {
     166        4401 :     displace.resize( data.size() );
     167             :   }
     168       26471 :   computeVectorBetweenFrames( ifrom, ito );
     169      993783 :   for(unsigned i=0; i<data.size(); ++i) {
     170      967312 :     displace[i] = data[i];
     171             :   }
     172       26471 : }
     173             : 
     174       61342 : void PathProjectionCalculator::getReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos ) const {
     175       61342 :   if( refpos.size()!=data.size() ) {
     176           4 :     refpos.resize( data.size() );
     177             :   }
     178       61342 :   if( refargs[0]->getRank()==2 ) {
     179     2305440 :     for(unsigned i=0; i<refpos.size(); ++i) {
     180     2247804 :       refpos[i] = refargs[0]->get( iframe*refpos.size() + i );
     181             :     }
     182             :   } else {
     183       11178 :     for(unsigned i=0; i<refpos.size(); ++i) {
     184        7472 :       refpos[i] = refargs[i]->get(iframe);
     185             :     }
     186             :   }
     187       61342 : }
     188             : 
     189        8400 : void PathProjectionCalculator::setReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos ) {
     190             :   plumed_dbg_assert( refpos.size()==data.size() );
     191        8400 :   if( refargs[0]->getRank()==2 ) {
     192      328480 :     for(unsigned i=0; i<refpos.size(); ++i) {
     193      320268 :       refargs[0]->set( iframe*refpos.size() + i, refpos[i] );
     194             :     }
     195             :   } else {
     196         572 :     for(unsigned i=0; i<refpos.size(); ++i) {
     197         384 :       refargs[i]->set( iframe, refpos[i] );
     198             :     }
     199             :   }
     200        8400 : }
     201             : 
     202         108 : void PathProjectionCalculator::updateDepedentRMSDObjects() {
     203         212 :   for(unsigned i=0; i<rmsd_objects.size(); ++i) {
     204         104 :     rmsd_objects[i]->setReferenceConfigurations();
     205             :   }
     206         108 : }
     207             : 
     208             : }
     209             : }
     210             :