Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2023 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 "analysis/AnalysisBase.h"
      23             : #include "reference/ReferenceAtoms.h"
      24             : #include "reference/ReferenceArguments.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "core/PlumedMain.h"
      27             : #include "core/ActionSet.h"
      28             : #include "core/Atoms.h"
      29             : #include "core/GenericMolInfo.h"
      30             : #include "tools/PDB.h"
      31             : #include "PCA.h"
      32             : 
      33             : namespace PLMD {
      34             : namespace dimred {
      35             : 
      36             : //+PLUMEDOC DIMRED OUTPUT_PCA_PROJECTION
      37             : /*
      38             : This is used to output the projection calculated by principle component analysis
      39             : 
      40             : \par Examples
      41             : 
      42             : */
      43             : //+ENDPLUMEDOC
      44             : 
      45             : class OutputPCAProjection : public analysis::AnalysisBase {
      46             : private:
      47             :   PDB mypdb;
      48             :   PCA* mypca;
      49             :   std::string fmt;
      50             :   std::string filename;
      51             : public:
      52             :   static void registerKeywords( Keywords& keys );
      53             :   explicit OutputPCAProjection( const ActionOptions& );
      54           0 :   void performTask( const unsigned&, const unsigned&, MultiValue& ) const {
      55           0 :     plumed_error();
      56             :   }
      57             :   void performAnalysis();
      58             : };
      59             : 
      60       13789 : PLUMED_REGISTER_ACTION(OutputPCAProjection,"OUTPUT_PCA_PROJECTION")
      61             : 
      62           6 : void OutputPCAProjection::registerKeywords( Keywords& keys ) {
      63           6 :   analysis::AnalysisBase::registerKeywords( keys );
      64          12 :   keys.add("compulsory","FILE","the name of the file to output to");
      65          12 :   keys.add("optional","FMT","the format to use in the output file");
      66          12 :   keys.add("compulsory","STRIDE","0","the frequency with which to perform the required analysis and to output the data.  The default value of 0 tells plumed to use all the data");
      67           6 : }
      68             : 
      69           2 : OutputPCAProjection::OutputPCAProjection( const ActionOptions& ao ):
      70             :   Action(ao),
      71             :   analysis::AnalysisBase(ao),
      72           2 :   fmt("%f") {
      73             :   // Setup the PCA object
      74           2 :   mypca = dynamic_cast<PCA*>( my_input_data );
      75           2 :   if( !mypca ) {
      76           0 :     error("input must be a PCA object");
      77             :   }
      78             : 
      79             :   // Get setup the pdb
      80           2 :   mypdb.setAtomNumbers( my_input_data->getAtomIndexes() );
      81           2 :   mypdb.setArgumentNames( (mypca->my_input_data)->getArgumentNames() );
      82             : 
      83             :   // Find a moldata object
      84           2 :   auto* moldat=plumed.getActionSet().selectLatest<GenericMolInfo*>(this);
      85           2 :   if( moldat ) {
      86           2 :     warning("PDB output files do not have atom types unless you use MOLDATA");
      87             :   }
      88             : 
      89           2 :   parse("FILE",filename);
      90           4 :   parse("FMT",fmt);
      91           2 :   if( !getRestart() ) {
      92           2 :     OFile ofile;
      93           2 :     ofile.link(*this);
      94           2 :     ofile.setBackupString("analysis");
      95           2 :     ofile.backupAllFiles(filename);
      96           2 :   }
      97           2 :   log.printf("  printing data to file named %s \n",filename.c_str() );
      98           2 : }
      99             : 
     100           2 : void OutputPCAProjection::performAnalysis() {
     101             :   // Find a moldata object
     102           2 :   auto* mymoldat=plumed.getActionSet().selectLatest<GenericMolInfo*>(this);
     103             :   // Output the embedding in plumed pdb format
     104           2 :   OFile afile;
     105           2 :   afile.link(*this);
     106           2 :   afile.setBackupString("analysis");
     107           2 :   mypdb.setAtomPositions( (mypca->myref)->getReferencePositions() );
     108           4 :   for(unsigned j=0; j<mypca->getArguments().size(); ++j) {
     109           2 :     mypdb.setArgumentValue( (mypca->getArguments()[j])->getName(), (mypca->myref)->getReferenceArgument(j) );
     110             :   }
     111             :   // And output the first frame
     112           2 :   afile.open( filename );
     113           2 :   afile.printf("REMARK TYPE=%s \n", mypca->mtype.c_str() );
     114           2 :   if( plumed.getAtoms().usingNaturalUnits() ) {
     115           0 :     mypdb.print( 1.0, mymoldat, afile, fmt );
     116             :   } else {
     117           2 :     mypdb.print( atoms.getUnits().getLength()/0.1, mymoldat, afile, fmt );
     118             :   }
     119             :   // And now output the eigenvectors
     120           6 :   for(unsigned dim=0; dim<mypca->nlow; ++dim) {
     121           4 :     afile.printf("REMARK TYPE=DIRECTION \n");
     122           4 :     mypdb.setAtomPositions( mypca->directions[dim].getReferencePositions() );
     123           8 :     for(unsigned j=0; j<mypca->getArguments().size(); ++j) {
     124           4 :       mypdb.setArgumentValue( (mypca->getArguments()[j])->getName(), mypca->directions[dim].getReferenceArgument(j) );
     125             :     }
     126           4 :     if( plumed.getAtoms().usingNaturalUnits() ) {
     127           0 :       mypdb.print( 1.0, mymoldat, afile, fmt );
     128             :     } else {
     129           4 :       mypdb.print( atoms.getUnits().getLength()/0.1, mymoldat, afile, fmt );
     130             :     }
     131             :   }
     132           2 :   afile.close();
     133           2 : }
     134             : 
     135             : }
     136             : }