Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2018 The VES code team
       3             :    (see the PEOPLE-VES file at the root of this folder for a list of names)
       4             : 
       5             :    See http://www.ves-code.org for more information.
       6             : 
       7             :    This file is part of VES code module.
       8             : 
       9             :    The VES code module 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             :    The VES code module 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 the VES code module.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : 
      23             : #include "CoeffsVector.h"
      24             : #include "VesTools.h"
      25             : #include "VesBias.h"
      26             : 
      27             : 
      28             : #include "tools/File.h"
      29             : #include "core/ActionRegister.h"
      30             : #include "core/PlumedMain.h"
      31             : 
      32             : 
      33             : namespace PLMD {
      34             : namespace ves {
      35             : 
      36             : //+PLUMEDOC VES_UTILS VES_OUTPUT_FES
      37             : /*
      38             : Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients.
      39             : 
      40             : This action can be used to output to file biases and free energy surfaces for VES biases from
      41             : previously obtained coefficients. It should be used through the \ref driver and
      42             : can only be used in post processing. The VES bias needs to be defined in the
      43             : exact same way as during the simulation. At the current moment this action does
      44             : not support dynamic target distributions (e.g. well-tempered).
      45             : 
      46             : \par Examples
      47             : 
      48             : In the following input we define a VES bias and then read in the coefficient
      49             : file coeffs.input.data and output the FES and bias every 500 iterations.
      50             : 
      51             : \plumedfile
      52             : phi:   TORSION ATOMS=5,7,9,15
      53             : psi:   TORSION ATOMS=7,9,15,17
      54             : 
      55             : bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
      56             : bf2: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
      57             : 
      58             : VES_LINEAR_EXPANSION ...
      59             :  ARG=phi,psi
      60             :  BASIS_FUNCTIONS=bf1,bf2
      61             :  LABEL=ves1
      62             :  GRID_BINS=100,100
      63             :  PROJ_ARG1=phi
      64             :  PROJ_ARG2=psi
      65             : ... VES_LINEAR_EXPANSION
      66             : 
      67             : VES_OUTPUT_FES ...
      68             :   BIAS=ves1
      69             :   FES_OUTPUT=500
      70             :   FES_PROJ_OUTPUT=500
      71             :   BIAS_OUTPUT=500
      72             :   COEFFS_INPUT=coeffs.input.data
      73             : ... VES_OUTPUT_FES
      74             : \endplumedfile
      75             : 
      76             : This input should be run through the driver by using a command similar to the
      77             : following one where the trajectory/configuration file configuration.gro is needed to
      78             : correctly define the CVs
      79             : \verbatim
      80             : plumed driver --plumed plumed.dat --igro configuration.gro
      81             : \endverbatim
      82             : 
      83             : */
      84             : //+ENDPLUMEDOC
      85             : 
      86           3 : class OutputFesBias : public Action {
      87             : 
      88             : public:
      89             :   static void registerKeywords(Keywords&);
      90             :   explicit OutputFesBias(const ActionOptions&);
      91           0 :   void update() {}
      92           0 :   void calculate() {}
      93           0 :   void apply() {}
      94             : };
      95             : 
      96             : 
      97        7362 : PLUMED_REGISTER_ACTION(OutputFesBias,"VES_OUTPUT_FES")
      98             : 
      99             : 
     100           4 : void OutputFesBias::registerKeywords(Keywords& keys) {
     101          16 :   keys.add("compulsory","BIAS","the label of the VES bias for to output the free energy surfaces and the bias files");
     102          16 :   keys.add("compulsory","COEFFS_INPUT","the name of input coefficient file");
     103          16 :   keys.add("optional","BIAS_OUTPUT","how often the bias(es) should be written out to file. Note that the value is given in terms of coefficient iterations.");
     104          16 :   keys.add("optional","FES_OUTPUT","how often the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.");
     105          16 :   keys.add("optional","FES_PROJ_OUTPUT","how often the projections of the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.");
     106             :   //
     107           4 : }
     108             : 
     109             : 
     110           3 : OutputFesBias::OutputFesBias(const ActionOptions&ao):
     111           3 :   Action(ao)
     112             : {
     113             : 
     114           3 :   std::vector<std::string> bias_labels;
     115           6 :   parseVector("BIAS",bias_labels);
     116           3 :   if(bias_labels.size()>1) {
     117           0 :     plumed_merror(getName()+" only support one VES bias");
     118             :   }
     119             : 
     120           3 :   std::string error_msg = "";
     121           6 :   std::vector<VesBias*> bias_pntrs = VesTools::getPointersFromLabels<VesBias*>(bias_labels,plumed.getActionSet(),error_msg);
     122           3 :   if(error_msg.size()>0) {plumed_merror("Error in keyword BIAS of "+getName()+": "+error_msg);}
     123             : 
     124          15 :   for(unsigned int i=0; i<bias_pntrs.size(); i++) {
     125           6 :     if(bias_pntrs[i]->numberOfCoeffsSets()>1) {
     126           0 :       plumed_merror(getName()+" at the moment supports only VES biases with a single coefficient set");
     127             :     }
     128             :   }
     129             : 
     130           3 :   std::vector<std::string> coeffs_fnames;
     131           6 :   parseVector("COEFFS_INPUT",coeffs_fnames);
     132           3 :   if(coeffs_fnames.size()!=bias_pntrs.size()) {
     133           0 :     plumed_merror(getName()+": there have to be as many coefficient file given in COEFFS_INPUT as VES biases given in BIAS");
     134             :   }
     135             : 
     136           3 :   unsigned int bias_output_stride = 0;
     137           6 :   parse("BIAS_OUTPUT",bias_output_stride);
     138             : 
     139           3 :   unsigned int fes_output_stride = 0;
     140           6 :   parse("FES_OUTPUT",fes_output_stride);
     141             : 
     142           3 :   unsigned int fesproj_output_stride = 0;
     143           6 :   parse("FES_PROJ_OUTPUT",fesproj_output_stride);
     144             : 
     145           3 :   if(bias_output_stride == 0 && fes_output_stride == 0 && fesproj_output_stride == 0) {
     146           0 :     plumed_merror(getName()+": you are not telling the action to do anything, you need to use one of the keywords BIAS_OUTPUT, FES_OUTPUT, or FES_PROJ_OUTPUT");
     147             :   }
     148             : 
     149           3 :   checkRead();
     150             : 
     151          15 :   for(unsigned int i=0; i<bias_pntrs.size(); i++) {
     152             : 
     153           6 :     if(bias_pntrs[i]->dynamicTargetDistribution()) {
     154           0 :       plumed_merror(getName()+" does not support dynamic target distributions at the moment");
     155             :     }
     156             : 
     157           3 :     if(bias_pntrs[i]->isStaticTargetDistFileOutputActive()) {
     158           2 :       bias_pntrs[i]->setupTargetDistFileOutput();
     159           2 :       bias_pntrs[i]->writeTargetDistToFile();
     160           2 :       bias_pntrs[i]->setupTargetDistProjFileOutput();
     161           2 :       bias_pntrs[i]->writeTargetDistProjToFile();
     162             :     }
     163             : 
     164             : 
     165           3 :     if(bias_output_stride>0) {
     166           3 :       bias_pntrs[i]->enableBiasFileOutput();
     167           3 :       bias_pntrs[i]->setupBiasFileOutput();
     168             :     }
     169             : 
     170           3 :     if(fes_output_stride>0) {
     171           3 :       bias_pntrs[i]->enableFesFileOutput();
     172           3 :       bias_pntrs[i]->setupFesFileOutput();
     173             :     }
     174             : 
     175           3 :     if(fesproj_output_stride>0) {
     176           1 :       bias_pntrs[i]->enableFesProjFileOutput();
     177           1 :       bias_pntrs[i]->setupFesProjFileOutput();
     178             :     }
     179             : 
     180           3 :     bias_pntrs[i]->enableIterationNumberInFilenames();
     181             : 
     182           6 :     IFile ifile;
     183           3 :     ifile.open(coeffs_fnames[i]);
     184             : 
     185          39 :     while(ifile) {
     186             : 
     187          36 :       bias_pntrs[i]->resetBiasFileOutput();
     188          36 :       bias_pntrs[i]->resetFesFileOutput();
     189             : 
     190         108 :       if(bias_pntrs[i]->getCoeffsPntrs()[0]->readOneSetFromFile(ifile)>0) {
     191          99 :         unsigned int iteration = bias_pntrs[i]->getCoeffsPntrs()[0]->getIterationCounter();
     192             : 
     193          33 :         if(bias_output_stride>0 && iteration%bias_output_stride==0) {
     194           8 :           bias_pntrs[i]->writeBiasToFile();
     195             :         }
     196             : 
     197          33 :         if(fes_output_stride>0 && iteration%fes_output_stride==0) {
     198           8 :           bias_pntrs[i]->writeFesToFile();
     199             :         }
     200             : 
     201          33 :         if(fesproj_output_stride>0 && iteration%fesproj_output_stride==0) {
     202           3 :           bias_pntrs[i]->writeFesProjToFile();
     203             :         }
     204             : 
     205             :       }
     206             : 
     207             :     }
     208             : 
     209             :   }
     210             : 
     211           3 :   log.printf("Stopping");
     212           3 :   plumed.stop();
     213           3 : }
     214             : 
     215             : 
     216             : }
     217        5517 : }