Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2018-2023 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/PlumedMain.h"
      24             : #include "core/ActionSet.h"
      25             : #include "core/ActionRegister.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace wham {
      29             : 
      30             : //+PLUMEDOC REWEIGHTING WHAM_HISTOGRAM
      31             : /*
      32             : This can be used to output the a histogram using the weighted histogram technique
      33             : 
      34             : This shortcut action allows you to calculate a histogram using the weighted histogram
      35             : analysis technique.  For more detail on how this the weights for configurations are
      36             : computed see \ref REWEIGHT_WHAM
      37             : 
      38             : \par Examples
      39             : 
      40             : The following input can be used to analyze the output from a series of umbrella sampling calculations.
      41             : The trajectory from each of the simulations run with the different biases should be concatenated into a
      42             : single trajectory before running the following analysis script on the concatenated trajectory using PLUMED
      43             : driver.  The umbrella sampling simulations that will be analyzed using the script below applied a harmonic
      44             : restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values.  The script
      45             : below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm
      46             : to determine a weight for each configuration in the concatenated trajectory.  A histogram is then constructed from
      47             : the configurations visited and their weights.  This histogram is then converted into a free energy surface and output
      48             : to a file called fes.dat
      49             : 
      50             : \plumedfile
      51             : #SETTINGS NREPLICAS=4
      52             : phi: TORSION ATOMS=5,7,9,15
      53             : psi: TORSION ATOMS=7,9,15,17
      54             : rp: RESTRAINT ARG=phi KAPPA=50.0 ...
      55             :   AT=@replicas:{
      56             :         -3.00000000000000000000
      57             :         -1.45161290322580645168
      58             :         .09677419354838709664
      59             :         1.64516129032258064496
      60             :      }
      61             : ...
      62             : 
      63             : hh: WHAM_HISTOGRAM ARG=phi BIAS=rp.bias TEMP=300 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=50
      64             : fes: CONVERT_TO_FES GRID=hh TEMP=300
      65             : DUMPGRID GRID=fes FILE=fes.dat
      66             : \endplumedfile
      67             : 
      68             : The script above must be run with multiple replicas using the following command:
      69             : 
      70             : \verbatim
      71             : mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4
      72             : \endverbatim
      73             : 
      74             : */
      75             : //+ENDPLUMEDOC
      76             : 
      77             : class WhamHistogram : public ActionShortcut {
      78             : public:
      79             :   static void registerKeywords( Keywords& keys );
      80             :   explicit WhamHistogram( const ActionOptions& );
      81             : };
      82             : 
      83             : PLUMED_REGISTER_ACTION(WhamHistogram,"WHAM_HISTOGRAM")
      84             : 
      85          10 : void WhamHistogram::registerKeywords( Keywords& keys ) {
      86          10 :   ActionShortcut::registerKeywords( keys );
      87          20 :   keys.add("compulsory","ARG","the arguments that you would like to make the histogram for");
      88          20 :   keys.add("compulsory","BIAS","*.bias","the value of the biases to use when performing WHAM");
      89          20 :   keys.add("compulsory","TEMP","the temperature at which the simulation was run");
      90          20 :   keys.add("compulsory","STRIDE","1","the frequency with which the data should be stored to perform WHAM");
      91          20 :   keys.add("compulsory","GRID_MIN","the minimum to use for the grid");
      92          20 :   keys.add("compulsory","GRID_MAX","the maximum to use for the grid");
      93          20 :   keys.add("compulsory","GRID_BIN","the number of bins to use for the grid");
      94          20 :   keys.add("optional","BANDWIDTH","the bandwidth for kernel density estimation");
      95          10 :   keys.setValueDescription("the histogram that was generated using the WHAM weights");
      96          20 :   keys.needsAction("GATHER_REPLICAS"); keys.needsAction("CONCATENATE");
      97          30 :   keys.needsAction("COLLECT"); keys.needsAction("WHAM"); keys.needsAction("KDE");
      98          10 : }
      99             : 
     100             : 
     101           7 : WhamHistogram::WhamHistogram( const ActionOptions& ao ) :
     102             :   Action(ao),
     103           7 :   ActionShortcut(ao)
     104             : {
     105             :   // Input for collection of weights for WHAM
     106          14 :   std::string bias; parse("BIAS",bias);
     107           7 :   std::string stride; parse("STRIDE",stride);
     108             :   // Input for GATHER_REPLICAS
     109          14 :   readInputLine( getShortcutLabel() + "_gather: GATHER_REPLICAS ARG=" + bias );
     110             :   // Put all the replicas in a single vector
     111          14 :   readInputLine( getShortcutLabel() + "_gatherv: CONCATENATE ARG=" + getShortcutLabel() + "_gather.*");
     112             :   // Input for COLLECT_FRAMES
     113          14 :   readInputLine( getShortcutLabel() + "_collect: COLLECT TYPE=vector ARG=" + getShortcutLabel() + "_gatherv STRIDE=" + stride);
     114             :   // Input for WHAM
     115          21 :   std::string temp, tempstr=""; parse("TEMP",temp); if( temp.length()>0 ) tempstr="TEMP=" + temp;
     116          14 :   readInputLine( getShortcutLabel() + "_wham: WHAM ARG=" + getShortcutLabel() + "_collect " + tempstr );
     117             :   // Input for COLLECT_FRAMES
     118          14 :   std::vector<std::string> args; parseVector("ARG",args); std::string argstr;
     119          14 :   for(unsigned i=0; i<args.size(); ++i) {
     120          14 :     readInputLine( getShortcutLabel() + "_data_" + args[i] + ": COLLECT ARG=" + args[i] );
     121           7 :     if( i==0 ) argstr = " ARG="; else argstr += ",";
     122          14 :     argstr += getShortcutLabel() + "_data_" + args[i];
     123             :   }
     124             :   // Input for HISTOGRAM
     125          14 :   std::string histo_line, bw=""; parse("BANDWIDTH",bw);
     126           7 :   if( bw!="" ) histo_line += " BANDWIDTH=" + bw;
     127             :   else histo_line += " KERNEL=DISCRETE";
     128          21 :   std::string min; parse("GRID_MIN",min); histo_line += " GRID_MIN=" + min;
     129          21 :   std::string max; parse("GRID_MAX",max); histo_line += " GRID_MAX=" + max;
     130          14 :   std::string bin; parse("GRID_BIN",bin); histo_line += " GRID_BIN=" + bin;
     131          14 :   readInputLine( getShortcutLabel() + ": KDE " + argstr + " HEIGHTS=" + getShortcutLabel() + "_wham" + histo_line );
     132          14 : }
     133             : 
     134             : }
     135             : }