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 "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "core/ActionWithArguments.h"
      25             : #include "core/PlumedMain.h"
      26             : #include "core/ActionSet.h"
      27             : 
      28             : //+PLUMEDOC ANALYSIS COLLECT_FRAMES
      29             : /*
      30             : This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object
      31             : 
      32             : \par Examples
      33             : 
      34             : */
      35             : //+ENDPLUMEDOC
      36             : 
      37             : namespace PLMD {
      38             : namespace landmarks {
      39             : 
      40             : class CollectFrames : public ActionShortcut {
      41             : private:
      42             :   std::string fixArgumentName( const std::string& argin );
      43             : public:
      44             :   static void registerKeywords( Keywords& keys );
      45             :   explicit CollectFrames( const ActionOptions& ao );
      46             : };
      47             : 
      48             : PLUMED_REGISTER_ACTION(CollectFrames,"COLLECT_FRAMES")
      49             : 
      50          31 : void CollectFrames::registerKeywords( Keywords& keys ) {
      51          31 :   ActionShortcut::registerKeywords( keys );
      52          62 :   keys.addInputKeyword("optional","ARG","scalar/vector","the labels of the values whose time series you would like to collect for later analysis");
      53          62 :   keys.add("compulsory","STRIDE","1","the frequency with which data should be stored for analysis.  By default data is collected on every step");
      54          62 :   keys.add("compulsory","CLEAR","0","the frequency with which data should all be deleted and restarted");
      55          62 :   keys.add("compulsory","ALIGN","OPTIMAL","if storing atoms how would you like the alignment to be done can be SIMPLE/OPTIMAL");
      56          62 :   keys.add("optional","ATOMS","list of atomic positions that you would like to collect and store for later analysis");
      57          62 :   keys.add("optional","LOGWEIGHTS","list of actions that calculates log weights that should be used to weight configurations when calculating averages");
      58          62 :   keys.addOutputComponent("data","default","matrix","the data that is being collected by this action");
      59          62 :   keys.addOutputComponent("logweights","default","vector","the logarithms of the weights of the data points");
      60         124 :   keys.needsAction("POSITION"); keys.needsAction("CONCATENATE"); keys.needsAction("MEAN"); keys.needsAction("CUSTOM");
      61         124 :   keys.needsAction("CONCATENATE"); keys.needsAction("COLLECT"); keys.needsAction("TRANSPOSE"); keys.needsAction("RMSD_VECTOR");
      62          93 :   keys.needsAction("COMBINE"); keys.needsAction("VSTACK"); keys.needsAction("CONSTANT");
      63          31 : }
      64             : 
      65          48 : std::string CollectFrames::fixArgumentName( const std::string& argin ) {
      66          48 :   std::string argout = argin; std::size_t dot=argin.find(".");
      67          52 :   if( dot!=std::string::npos ) argout = argin.substr(0,dot) + "_" + argin.substr(dot+1);
      68          48 :   return argout;
      69             : }
      70             : 
      71          19 : CollectFrames::CollectFrames( const ActionOptions& ao ):
      72             :   Action(ao),
      73          19 :   ActionShortcut(ao)
      74             : {
      75          57 :   std::string stride, clearstride; parse("STRIDE",stride); parse("CLEAR",clearstride);
      76          38 :   std::vector<std::string> argn; parseVector("ARG",argn); std::vector<Value*> theargs;
      77          19 :   ActionWithArguments::interpretArgumentList( argn, plumed.getActionSet(), this, theargs );
      78          38 :   std::string indices; parse("ATOMS",indices);
      79          19 :   if( theargs.size()==0 && indices.length()==0 ) error("no arguments or atoms were specified for collection");
      80             : 
      81             :   // Create the values to collect the atomic positions
      82          19 :   if( indices.length()>0 ) {
      83             :     // Collect reference position
      84          12 :     readInputLine( getShortcutLabel() + "_getposx: POSITION ATOMS=" + indices ); std::string align; parse("ALIGN",align);
      85          12 :     readInputLine( getShortcutLabel() + "_getpos: CONCATENATE ARG=" + getShortcutLabel() + "_getposx.x," + getShortcutLabel() + "_getposx.y," + getShortcutLabel() + "_getposx.z");
      86             :     // Find atomic center
      87          12 :     readInputLine( getShortcutLabel() + "_cposx: MEAN ARG=" + getShortcutLabel() + "_getposx.x PERIODIC=NO");
      88          12 :     readInputLine( getShortcutLabel() + "_cposy: MEAN ARG=" + getShortcutLabel() + "_getposx.y PERIODIC=NO");
      89          12 :     readInputLine( getShortcutLabel() + "_cposz: MEAN ARG=" + getShortcutLabel() + "_getposx.z PERIODIC=NO");
      90             :     // Subtract atomimc center
      91          12 :     readInputLine( getShortcutLabel() + "_refx: CUSTOM ARG=" + getShortcutLabel() + "_getposx.x," + getShortcutLabel() + "_cposx FUNC=x-y PERIODIC=NO");
      92          12 :     readInputLine( getShortcutLabel() + "_refy: CUSTOM ARG=" + getShortcutLabel() + "_getposx.y," + getShortcutLabel() + "_cposy FUNC=x-y PERIODIC=NO");
      93          12 :     readInputLine( getShortcutLabel() + "_refz: CUSTOM ARG=" + getShortcutLabel() + "_getposx.z," + getShortcutLabel() + "_cposz FUNC=x-y PERIODIC=NO");
      94          12 :     readInputLine( getShortcutLabel() + "_ref: CONCATENATE ARG=" + getShortcutLabel() + "_refx," + getShortcutLabel() + "_refy," + getShortcutLabel() + "_refz");
      95             :     // Store the reference position in a collect action
      96          12 :     readInputLine( getShortcutLabel() + "_refpos: COLLECT TYPE=matrix ARG=" + getShortcutLabel() + "_ref STRIDE=" + clearstride + " CLEAR=" + clearstride );
      97          12 :     readInputLine( getShortcutLabel() + "_refposT: TRANSPOSE ARG=" + getShortcutLabel() + "_refpos");
      98             :     // Calculate the RMSD between the instaneous position and the reference position
      99          12 :     readInputLine( getShortcutLabel() + "_rmsd: RMSD_VECTOR ARG=" + getShortcutLabel() + "_getpos," + getShortcutLabel() + "_refpos DISPLACEMENT SQUARED TYPE=" + align );
     100             :     // Add the reference position to the RMSD displacement
     101          12 :     readInputLine( getShortcutLabel() + "_fpos: COMBINE ARG=" + getShortcutLabel() + "_refposT," + getShortcutLabel() + "_rmsd.disp PERIODIC=NO");
     102             :     // Store the reference data
     103           6 :     std::string suffix = "_atomdata"; if( theargs.size()==0 ) suffix = "_data";
     104          12 :     readInputLine( getShortcutLabel() + suffix + ": COLLECT TYPE=matrix ARG=" + getShortcutLabel() + "_fpos STRIDE=" + stride + " CLEAR=" + clearstride );
     105             :   }
     106             : 
     107             :   // Create all the collect actions for arguments
     108          43 :   for(unsigned i=0; i<theargs.size(); ++i) {
     109          24 :     if( theargs[i]->getNumberOfValues()!=theargs[0]->getNumberOfValues() ) error("mismatch between number of arguments calculated by each collected argument");
     110          48 :     readInputLine( getShortcutLabel() + "_" + fixArgumentName( theargs[i]->getName() ) + ": COLLECT ARG=" + theargs[i]->getName() + " STRIDE=" + stride + " CLEAR=" + clearstride );
     111             :   }
     112             :   // Make a list of collect actions
     113          19 :   if( theargs.size()>0 ) {
     114          26 :     std::string allcol = getShortcutLabel() + "_" + fixArgumentName( theargs[0]->getName() );
     115          24 :     for(unsigned i=1; i<theargs.size(); ++i) allcol += "," + getShortcutLabel() + "_" + fixArgumentName( theargs[i]->getName() );
     116             :     // And transfer everything to a matrix
     117          13 :     std::string suffix = "_argdata"; if( indices.length()==0 ) suffix = "_data";
     118          26 :     readInputLine( getShortcutLabel() + suffix + ": VSTACK ARG=" + allcol );
     119             :   }
     120             :   // Merge all the collected data together into a single matrix
     121          19 :   if( theargs.size()>0 && indices.length()>0 ) readInputLine( getShortcutLabel() + "_data: CONCATENATE MATRIX11=" + getShortcutLabel() + "_atomdata MATRIX12=" + getShortcutLabel() + "_argdata");
     122             : 
     123             :   // Now get the logweights
     124          38 :   std::vector<std::string> logw; parseVector("LOGWEIGHTS",logw); std::vector<Value*> thew;
     125          19 :   if( logw.size()>0 ) ActionWithArguments::interpretArgumentList( logw, plumed.getActionSet(), this, thew );
     126          19 :   if( logw.size()>1 ) error("maximum of one argument should be specified for logweights");
     127             : 
     128          19 :   if( logw.size()==0 ) {
     129          19 :     std::string zeros="0"; if( theargs.size()>0 ) { for(unsigned i=1; i<theargs[0]->getNumberOfValues(); ++i) zeros += ",0"; }
     130          38 :     readInputLine( getShortcutLabel() + "_cweight: CONSTANT VALUE=" + zeros );
     131          38 :     readInputLine( getShortcutLabel() + "_logweights: COLLECT ARG=" + getShortcutLabel() + "_cweight STRIDE=" + stride + " CLEAR=" + clearstride );
     132             :   } else {
     133           0 :     if( theargs[0]->getNumberOfValues()!=thew[0]->getNumberOfValues() ) error("mismatch between number of weights and number of collected arguments");
     134           0 :     readInputLine( getShortcutLabel() + "_logweights: COLLECT ARG=" + thew[0]->getName() + " STRIDE=" + stride + " CLEAR=" + clearstride );
     135             :   }
     136             :   // And finally create a value that contains as many ones as there are data points (this is used if we want to do Classical MDS
     137          19 :   readInputLine( getShortcutLabel() + "_one: CONSTANT VALUE=1");
     138          38 :   readInputLine( getShortcutLabel() + "_ones: COLLECT ARG=" + getShortcutLabel() + "_one STRIDE=" + stride + " CLEAR=" + clearstride );
     139          57 : }
     140             : 
     141             : }
     142             : }