Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "AnalysisBase.h"
      23             : #include "reference/ReferenceAtoms.h"
      24             : #include "reference/ReferenceArguments.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "core/PlumedMain.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace analysis {
      30             : 
      31             : //+PLUMEDOC ANALYSIS OUTPUT_ANALYSIS_DATA_TO_COLVAR
      32             : /*
      33             : This can be used to output the data that has been stored in an Analysis object.
      34             : 
      35             : The most useful application of this method is to output all projections of all the
      36             : points that were stored in an analysis object that performs some form of dimensionality
      37             : reduction.  If you use the USE_DIMRED_DATA_FROM option below projections of all the
      38             : stored points will be output to a file.  The positions of these projections will be calculated
      39             : using that dimensionality reduction algorithms out-of-sample extension algorithm.
      40             : 
      41             : \par Examples
      42             : 
      43             : */
      44             : //+ENDPLUMEDOC
      45             : 
      46             : class OutputColvarFile : public AnalysisBase {
      47             : private:
      48             :   std::string fmt;
      49             :   std::string filename;
      50             :   bool output_for_all_replicas;
      51             :   std::vector<unsigned> preps;
      52             :   std::vector<std::string> req_vals;
      53             : public:
      54             :   static void registerKeywords( Keywords& keys );
      55             :   explicit OutputColvarFile( const ActionOptions& );
      56           0 :   void performTask( const unsigned&, const unsigned&, MultiValue& ) const override {
      57           0 :     plumed_error();
      58             :   }
      59             :   void performAnalysis() override;
      60             : };
      61             : 
      62       13825 : PLUMED_REGISTER_ACTION(OutputColvarFile,"OUTPUT_ANALYSIS_DATA_TO_COLVAR")
      63             : 
      64          24 : void OutputColvarFile::registerKeywords( Keywords& keys ) {
      65          24 :   AnalysisBase::registerKeywords( keys );
      66          24 :   keys.use("ARG");
      67          48 :   keys.add("compulsory","FILE","the name of the file to output to");
      68          48 :   keys.add("compulsory","REPLICA","0","the replicas for which you would like to output this information");
      69          48 :   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");
      70          48 :   keys.add("optional","FMT","the format to output the data using");
      71          24 : }
      72             : 
      73          20 : OutputColvarFile::OutputColvarFile( const ActionOptions& ao ):
      74             :   Action(ao),
      75             :   AnalysisBase(ao),
      76          40 :   fmt("%f"),
      77          20 :   output_for_all_replicas(false) {
      78          20 :   parse("FILE",filename);
      79          40 :   parse("FMT",fmt);
      80          20 :   if( !getRestart() ) {
      81          20 :     OFile ofile;
      82          20 :     ofile.link(*this);
      83          20 :     ofile.setBackupString("analysis");
      84          20 :     ofile.backupAllFiles(filename);
      85          20 :   }
      86          20 :   log.printf("  printing data to file named %s \n",filename.c_str() );
      87          20 :   if( getArguments().size()==0 ) {
      88          12 :     std::vector<std::string> tmp_vals( my_input_data->getArgumentNames() );
      89          12 :     req_vals.resize( tmp_vals.size() );
      90          18 :     for(unsigned i=0; i<tmp_vals.size(); ++i) {
      91             :       req_vals[i]=tmp_vals[i];
      92             :     }
      93          12 :   } else {
      94           8 :     req_vals.resize( getArguments().size() );
      95          24 :     for(unsigned i=0; i<req_vals.size(); ++i) {
      96             :       req_vals[i]=getPntrToArgument(i)->getName();
      97             :     }
      98             :   }
      99          20 :   if( req_vals.size()==0 ) {
     100           6 :     log.printf("  outputting weights from input action \n");
     101             :   } else {
     102          14 :     log.printf("  outputting %s", req_vals[0].c_str() );
     103          22 :     for(unsigned i=1; i<req_vals.size(); ++i) {
     104           8 :       log.printf(",", req_vals[i].c_str() );
     105             :     }
     106          14 :     log.printf("\n");
     107             :   }
     108             :   std::string rep_data;
     109          40 :   parse("REPLICA",rep_data);
     110          20 :   if( rep_data=="all" ) {
     111           0 :     output_for_all_replicas=true;
     112             :   } else {
     113          20 :     preps.resize(1);
     114          20 :     Tools::convert( rep_data, preps[0] );
     115             :   }
     116          20 :   if( output_for_all_replicas ) {
     117           0 :     log.printf("  outputting files for all replicas \n");
     118             :   } else {
     119          20 :     log.printf("  outputting data for replicas ");
     120          40 :     for(unsigned i=0; i<preps.size(); ++i) {
     121          20 :       log.printf("%d ", preps[i] );
     122             :     }
     123             :   }
     124          20 : }
     125             : 
     126          24 : void OutputColvarFile::performAnalysis() {
     127          24 :   if( !output_for_all_replicas ) {
     128             :     bool found=false;
     129          24 :     unsigned myrep=plumed.multi_sim_comm.Get_rank();
     130          29 :     for(unsigned i=0; i<preps.size(); ++i) {
     131          24 :       if( myrep==preps[i] ) {
     132             :         found=true;
     133             :         break;
     134             :       }
     135             :     }
     136          24 :     if( !found ) {
     137           5 :       return;
     138             :     }
     139             :   }
     140             :   // Output the embedding as long lists of data
     141          19 :   OFile gfile;
     142          19 :   gfile.link(*this);
     143          19 :   gfile.setBackupString("analysis");
     144          19 :   gfile.fmtField(fmt+" ");
     145          19 :   gfile.open( filename );
     146             : 
     147             :   // Print embedding coordinates
     148        2599 :   for(unsigned i=0; i<getNumberOfDataPoints(); ++i) {
     149        2580 :     const DataCollectionObject& mydata=getStoredData(i, false);
     150        6989 :     for(unsigned j=0; j<req_vals.size(); ++j) {
     151        4409 :       gfile.printField( req_vals[j], mydata.getArgumentValue(req_vals[j]) );
     152             :     }
     153        2580 :     gfile.printField( "weight", getWeight(i) );
     154        2580 :     gfile.printField();
     155             :   }
     156          19 :   gfile.close();
     157          19 : }
     158             : 
     159             : }
     160             : }