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          26 : void PathProjectionCalculator::registerKeywords(Keywords& keys) {
      33          52 :   keys.addInputKeyword("compulsory","ARG","matrix","the labels of the matrix that contains the vectors of displacements from each frame in the path");
      34          26 :   keys.add("compulsory","METRIC","the method to use for computing the displacement vectors between the reference frames");
      35          26 :   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          52 :   keys.addInputKeyword("compulsory","REFERENCE","vector","labels for actions that contain reference coordinates for each point on the path");
      37          26 : }
      38             : 
      39          11 : PathProjectionCalculator::PathProjectionCalculator( Action* act ):
      40          11 :   mypath_obj(NULL) {
      41          11 :   ActionWithArguments* aarg=dynamic_cast<ActionWithArguments*>( act );
      42          11 :   if( aarg ) {
      43           7 :     mypath_obj = aarg->getPntrToArgument(0);
      44             :     // Check that we have only one argument as input
      45           7 :     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          11 :   if( mypath_obj )
      52           7 :     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             :   std::vector<std::string> reference_data;
      57          11 :   act->parseVector("REFERENCE", reference_data);
      58          11 :   std::vector<colvar::RMSDVector*> allrmsd = act->plumed.getActionSet().select<colvar::RMSDVector*>();
      59          11 :   ActionWithArguments::interpretArgumentList( reference_data, act->plumed.getActionSet(), act, refargs );
      60          28 :   for(unsigned i=0; i<refargs.size(); ++i ) {
      61          17 :     Action* thisact = refargs[i]->getPntrToAction();
      62          17 :     for(unsigned j=0; j<allrmsd.size(); ++j) {
      63           5 :       if( allrmsd[j]->checkForDependency(thisact) ) {
      64           5 :         rmsd_objects.push_back( allrmsd[j] );
      65             :         break;
      66             :       }
      67             :     }
      68          17 :     if( !refargs[i]->isConstant() ) {
      69           0 :       act->error("input" + refargs[i]->getName() + " is not constant");
      70             :     }
      71          17 :     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          17 :     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          11 :   int s=sizeof(double);
      80          11 :   metric.cmd("setRealPrecision",&s);
      81          11 :   metric.cmd("setMDEngine","plumed");
      82          11 :   int nat=0;
      83          11 :   metric.cmd("setNatoms",&nat);
      84          11 :   metric.cmd("setNoVirial");
      85          11 :   unsigned nargs=refargs.size();
      86          11 :   if( refargs[0]->getRank()==2 ) {
      87           6 :     nargs = refargs[0]->getShape()[1];
      88             :   }
      89             :   std::string str_nargs;
      90          11 :   Tools::convert( nargs, str_nargs );
      91          11 :   std::string period_str=" PERIODIC=NO";
      92          11 :   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          22 :   metric.readInputLine("arg1: PUT UNIT=number SHAPE=" + str_nargs + period_str, true);
      98          22 :   metric.readInputLine("arg2: PUT UNIT=number SHAPE=" + str_nargs + period_str, true);
      99          11 :   double tstep=1.0;
     100          11 :   metric.cmd("setTimestep",&tstep);
     101             :   std::string inp;
     102          22 :   act->parse("METRIC",inp);
     103             :   inp += " ARG=arg2,arg1";
     104             :   const char* cinp=inp.c_str();
     105          11 :   std::vector<std::string> input=Tools::getWords(inp);
     106          11 :   if( input.size()==1 && !actionRegister().check(input[0]) ) {
     107           0 :     metric.cmd("setPlumedDat",cinp);
     108           0 :     metric.cmd("init");
     109             :   } else {
     110          11 :     metric.cmd("init");
     111          11 :     metric.cmd("readInputLine",cinp);
     112             :   }
     113             :   // Now setup stuff to retrieve the final displacement
     114          11 :   unsigned aind = metric.getActionSet().size()-1;
     115             :   while( true ) {
     116          22 :     const ActionShortcut* as=dynamic_cast<const ActionShortcut*>( metric.getActionSet()[aind].get() );
     117          22 :     if( !as ) {
     118             :       break ;
     119             :     }
     120          11 :     aind = aind - 1;
     121             :     plumed_assert( aind>=0 );
     122          11 :   }
     123          11 :   ActionWithValue* fav = dynamic_cast<ActionWithValue*>( metric.getActionSet()[aind].get() );
     124          11 :   if( !fav ) {
     125           0 :     act->error("final value should calculate relevant value that you want as reference");
     126             :   }
     127          11 :   std::string name = (fav->copyOutput(0))->getName();
     128          11 :   if( fav->getNumberOfComponents()>1 ) {
     129             :     std::string comp;
     130           6 :     act->parse("METRIC_COMPONENT",comp);
     131          12 :     name = fav->getLabel() + "." + comp;
     132             :   }
     133             :   long rank;
     134          22 :   metric.cmd("getDataRank " + name, &rank );
     135          11 :   if( rank==0 ) {
     136           0 :     rank=1;
     137             :   }
     138          11 :   std::vector<long> ishape( rank );
     139          22 :   metric.cmd("getDataShape " + name, &ishape[0] );
     140             :   unsigned nvals=1;
     141          22 :   for(unsigned i=0; i<ishape.size(); ++i) {
     142          11 :     nvals *= ishape[i];
     143             :   }
     144          11 :   data.resize( nvals );
     145          22 :   metric.cmd("setMemoryForData " + name, &data[0] );
     146          22 : }
     147             : 
     148        1114 : unsigned PathProjectionCalculator::getNumberOfFrames() const {
     149        1114 :   return refargs[0]->getShape()[0];
     150             : }
     151             : 
     152       12820 : void PathProjectionCalculator::computeVectorBetweenFrames( const unsigned& ifrom, const unsigned& ito ) {
     153       12820 :   int step = 1;
     154       12820 :   metric.cmd("setStep",&step);
     155       12820 :   std::vector<double> valdata1( data.size() ), valdata2( data.size() );
     156       12820 :   getReferenceConfiguration( ito, valdata2 );
     157       12820 :   getReferenceConfiguration( ifrom, valdata1 );
     158       12820 :   metric.cmd("setValue arg1", &valdata1[0] );
     159       12820 :   metric.cmd("setValue arg2", &valdata2[0] );
     160       12820 :   metric.cmd("calc");
     161       12820 : }
     162             : 
     163       12820 : void PathProjectionCalculator::getDisplaceVector( const unsigned& ifrom, const unsigned& ito, std::vector<double>& displace ) {
     164       12820 :   if( displace.size()!=data.size() ) {
     165        2215 :     displace.resize( data.size() );
     166             :   }
     167       12820 :   computeVectorBetweenFrames( ifrom, ito );
     168      447743 :   for(unsigned i=0; i<data.size(); ++i) {
     169      434923 :     displace[i] = data[i];
     170             :   }
     171       12820 : }
     172             : 
     173       29962 : void PathProjectionCalculator::getReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos ) const {
     174       29962 :   if( refpos.size()!=data.size() ) {
     175           2 :     refpos.resize( data.size() );
     176             :   }
     177       29962 :   if( refargs[0]->getRank()==2 ) {
     178     1050240 :     for(unsigned i=0; i<refpos.size(); ++i) {
     179     1023984 :       refpos[i] = refargs[0]->get( iframe*refpos.size() + i );
     180             :     }
     181             :   } else {
     182       11178 :     for(unsigned i=0; i<refpos.size(); ++i) {
     183        7472 :       refpos[i] = refargs[i]->get(iframe);
     184             :     }
     185             :   }
     186       29962 : }
     187             : 
     188        4322 : void PathProjectionCalculator::setReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos ) {
     189             :   plumed_dbg_assert( refpos.size()==data.size() );
     190        4322 :   if( refargs[0]->getRank()==2 ) {
     191      165360 :     for(unsigned i=0; i<refpos.size(); ++i) {
     192      161226 :       refargs[0]->set( iframe*refpos.size() + i, refpos[i] );
     193             :     }
     194             :   } else {
     195         572 :     for(unsigned i=0; i<refpos.size(); ++i) {
     196         384 :       refargs[i]->set( iframe, refpos[i] );
     197             :     }
     198             :   }
     199        4322 : }
     200             : 
     201          27 : void PathProjectionCalculator::updateDepedentRMSDObjects() {
     202          50 :   for(unsigned i=0; i<rmsd_objects.size(); ++i) {
     203          23 :     rmsd_objects[i]->setReferenceConfigurations();
     204             :   }
     205          27 : }
     206             : 
     207             : }
     208             : }
     209             :