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.add("compulsory","STRIDE","1","the frequency with which data should be stored for analysis.  By default data is collected on every step");
      53          62 :   keys.add("compulsory","CLEAR","0","the frequency with which data should all be deleted and restarted");
      54          62 :   keys.add("compulsory","ALIGN","OPTIMAL","if storing atoms how would you like the alignment to be done can be SIMPLE/OPTIMAL");
      55          62 :   keys.add("optional","ARG","the arguments you would like to collect");
      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","the data that is being collected by this action");
      59          62 :   keys.addOutputComponent("logweights","default","the logarithms of the weights of the data points");
      60          31 :   keys.needsAction("POSITION");
      61          31 :   keys.needsAction("CONCATENATE");
      62          31 :   keys.needsAction("MEAN");
      63          31 :   keys.needsAction("CUSTOM");
      64          31 :   keys.needsAction("CONCATENATE");
      65          31 :   keys.needsAction("COLLECT");
      66          31 :   keys.needsAction("TRANSPOSE");
      67          31 :   keys.needsAction("RMSD_VECTOR");
      68          31 :   keys.needsAction("COMBINE");
      69          31 :   keys.needsAction("VSTACK");
      70          31 :   keys.needsAction("CONSTANT");
      71          31 : }
      72             : 
      73          48 : std::string CollectFrames::fixArgumentName( const std::string& argin ) {
      74          48 :   std::string argout = argin;
      75          48 :   std::size_t dot=argin.find(".");
      76          48 :   if( dot!=std::string::npos ) {
      77           8 :     argout = argin.substr(0,dot) + "_" + argin.substr(dot+1);
      78             :   }
      79          48 :   return argout;
      80             : }
      81             : 
      82          19 : CollectFrames::CollectFrames( const ActionOptions& ao ):
      83             :   Action(ao),
      84          19 :   ActionShortcut(ao) {
      85             :   std::string stride, clearstride;
      86          19 :   parse("STRIDE",stride);
      87          38 :   parse("CLEAR",clearstride);
      88             :   std::vector<std::string> argn;
      89          38 :   parseVector("ARG",argn);
      90             :   std::vector<Value*> theargs;
      91          19 :   ActionWithArguments::interpretArgumentList( argn, plumed.getActionSet(), this, theargs );
      92             :   std::string indices;
      93          38 :   parse("ATOMS",indices);
      94          19 :   if( theargs.size()==0 && indices.length()==0 ) {
      95           0 :     error("no arguments or atoms were specified for collection");
      96             :   }
      97             : 
      98             :   // Create the values to collect the atomic positions
      99          19 :   if( indices.length()>0 ) {
     100             :     // Collect reference position
     101          12 :     readInputLine( getShortcutLabel() + "_getposx: POSITION ATOMS=" + indices );
     102             :     std::string align;
     103           6 :     parse("ALIGN",align);
     104          12 :     readInputLine( getShortcutLabel() + "_getpos: CONCATENATE ARG=" + getShortcutLabel() + "_getposx.x," + getShortcutLabel() + "_getposx.y," + getShortcutLabel() + "_getposx.z");
     105             :     // Find atomic center
     106          12 :     readInputLine( getShortcutLabel() + "_cposx: MEAN ARG=" + getShortcutLabel() + "_getposx.x PERIODIC=NO");
     107          12 :     readInputLine( getShortcutLabel() + "_cposy: MEAN ARG=" + getShortcutLabel() + "_getposx.y PERIODIC=NO");
     108          12 :     readInputLine( getShortcutLabel() + "_cposz: MEAN ARG=" + getShortcutLabel() + "_getposx.z PERIODIC=NO");
     109             :     // Subtract atomimc center
     110          12 :     readInputLine( getShortcutLabel() + "_refx: CUSTOM ARG=" + getShortcutLabel() + "_getposx.x," + getShortcutLabel() + "_cposx FUNC=x-y PERIODIC=NO");
     111          12 :     readInputLine( getShortcutLabel() + "_refy: CUSTOM ARG=" + getShortcutLabel() + "_getposx.y," + getShortcutLabel() + "_cposy FUNC=x-y PERIODIC=NO");
     112          12 :     readInputLine( getShortcutLabel() + "_refz: CUSTOM ARG=" + getShortcutLabel() + "_getposx.z," + getShortcutLabel() + "_cposz FUNC=x-y PERIODIC=NO");
     113          12 :     readInputLine( getShortcutLabel() + "_ref: CONCATENATE ARG=" + getShortcutLabel() + "_refx," + getShortcutLabel() + "_refy," + getShortcutLabel() + "_refz");
     114             :     // Store the reference position in a collect action
     115          12 :     readInputLine( getShortcutLabel() + "_refpos: COLLECT TYPE=matrix ARG=" + getShortcutLabel() + "_ref STRIDE=" + clearstride + " CLEAR=" + clearstride );
     116          12 :     readInputLine( getShortcutLabel() + "_refposT: TRANSPOSE ARG=" + getShortcutLabel() + "_refpos");
     117             :     // Calculate the RMSD between the instaneous position and the reference position
     118          12 :     readInputLine( getShortcutLabel() + "_rmsd: RMSD_VECTOR ARG=" + getShortcutLabel() + "_getpos," + getShortcutLabel() + "_refpos DISPLACEMENT SQUARED TYPE=" + align );
     119             :     // Add the reference position to the RMSD displacement
     120          12 :     readInputLine( getShortcutLabel() + "_fpos: COMBINE ARG=" + getShortcutLabel() + "_refposT," + getShortcutLabel() + "_rmsd.disp PERIODIC=NO");
     121             :     // Store the reference data
     122           6 :     std::string suffix = "_atomdata";
     123           6 :     if( theargs.size()==0 ) {
     124             :       suffix = "_data";
     125             :     }
     126          12 :     readInputLine( getShortcutLabel() + suffix + ": COLLECT TYPE=matrix ARG=" + getShortcutLabel() + "_fpos STRIDE=" + stride + " CLEAR=" + clearstride );
     127             :   }
     128             : 
     129             :   // Create all the collect actions for arguments
     130          43 :   for(unsigned i=0; i<theargs.size(); ++i) {
     131          24 :     if( theargs[i]->getNumberOfValues()!=theargs[0]->getNumberOfValues() ) {
     132           0 :       error("mismatch between number of arguments calculated by each collected argument");
     133             :     }
     134          48 :     readInputLine( getShortcutLabel() + "_" + fixArgumentName( theargs[i]->getName() ) + ": COLLECT ARG=" + theargs[i]->getName() + " STRIDE=" + stride + " CLEAR=" + clearstride );
     135             :   }
     136             :   // Make a list of collect actions
     137          19 :   if( theargs.size()>0 ) {
     138          26 :     std::string allcol = getShortcutLabel() + "_" + fixArgumentName( theargs[0]->getName() );
     139          24 :     for(unsigned i=1; i<theargs.size(); ++i) {
     140          22 :       allcol += "," + getShortcutLabel() + "_" + fixArgumentName( theargs[i]->getName() );
     141             :     }
     142             :     // And transfer everything to a matrix
     143          13 :     std::string suffix = "_argdata";
     144          13 :     if( indices.length()==0 ) {
     145             :       suffix = "_data";
     146             :     }
     147          26 :     readInputLine( getShortcutLabel() + suffix + ": VSTACK ARG=" + allcol );
     148             :   }
     149             :   // Merge all the collected data together into a single matrix
     150          19 :   if( theargs.size()>0 && indices.length()>0 ) {
     151           0 :     readInputLine( getShortcutLabel() + "_data: CONCATENATE MATRIX11=" + getShortcutLabel() + "_atomdata MATRIX12=" + getShortcutLabel() + "_argdata");
     152             :   }
     153             : 
     154             :   // Now get the logweights
     155             :   std::vector<std::string> logw;
     156          38 :   parseVector("LOGWEIGHTS",logw);
     157             :   std::vector<Value*> thew;
     158          19 :   if( logw.size()>0 ) {
     159           0 :     ActionWithArguments::interpretArgumentList( logw, plumed.getActionSet(), this, thew );
     160             :   }
     161          19 :   if( logw.size()>1 ) {
     162           0 :     error("maximum of one argument should be specified for logweights");
     163             :   }
     164             : 
     165          19 :   if( logw.size()==0 ) {
     166          19 :     std::string zeros="0";
     167          19 :     if( theargs.size()>0 ) {
     168          13 :       for(unsigned i=1; i<theargs[0]->getNumberOfValues(); ++i) {
     169             :         zeros += ",0";
     170             :       }
     171             :     }
     172          38 :     readInputLine( getShortcutLabel() + "_cweight: CONSTANT VALUE=" + zeros );
     173          38 :     readInputLine( getShortcutLabel() + "_logweights: COLLECT ARG=" + getShortcutLabel() + "_cweight STRIDE=" + stride + " CLEAR=" + clearstride );
     174             :   } else {
     175           0 :     if( theargs[0]->getNumberOfValues()!=thew[0]->getNumberOfValues() ) {
     176           0 :       error("mismatch between number of weights and number of collected arguments");
     177             :     }
     178           0 :     readInputLine( getShortcutLabel() + "_logweights: COLLECT ARG=" + thew[0]->getName() + " STRIDE=" + stride + " CLEAR=" + clearstride );
     179             :   }
     180             :   // 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
     181          19 :   readInputLine( getShortcutLabel() + "_one: CONSTANT VALUE=1");
     182          38 :   readInputLine( getShortcutLabel() + "_ones: COLLECT ARG=" + getShortcutLabel() + "_one STRIDE=" + stride + " CLEAR=" + clearstride );
     183          57 : }
     184             : 
     185             : }
     186             : }