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 analysis technique.
      35             : The following input illustrates how this is used in practise to analyze the output from a series of umbrella sampling calculations.
      36             : The trajectory from each of the simulations run with the different biases should be concatenated into a
      37             : single trajectory before running the following analysis script on the concatenated trajectory using PLUMED
      38             : driver.  The umbrella sampling simulations that will be analyzed using the script below applied a harmonic
      39             : restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values.  The script
      40             : below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm
      41             : to determine a weight for each configuration in the concatenated trajectory.  A histogram is then constructed from
      42             : the configurations visited and their weights.  This histogram is then converted into a free energy surface and output
      43             : to a file called fes.dat
      44             : 
      45             : ```plumed
      46             : #SETTINGS NREPLICAS=4
      47             : phi: TORSION ATOMS=5,7,9,15
      48             : psi: TORSION ATOMS=7,9,15,17
      49             : rp: RESTRAINT ARG=phi KAPPA=50.0 AT=@replicas:{-3.00,-1.45,0.10,1.65}
      50             : hh: WHAM_HISTOGRAM ARG=phi BIAS=rp.bias TEMP=300 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=50
      51             : fes: CONVERT_TO_FES ARG=hh TEMP=300
      52             : DUMPGRID ARG=fes FILE=fes.dat
      53             : ```
      54             : 
      55             : The script above must be run with multiple replicas using the following command:
      56             : 
      57             : ````
      58             : mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4
      59             : ````
      60             : 
      61             : For more details on how the weights for configurations are determined using the wham method see the documentation
      62             : for the [WHAM](WHAM.md) action.
      63             : 
      64             : */
      65             : //+ENDPLUMEDOC
      66             : 
      67             : class WhamHistogram : public ActionShortcut {
      68             : public:
      69             :   static void registerKeywords( Keywords& keys );
      70             :   explicit WhamHistogram( const ActionOptions& );
      71             : };
      72             : 
      73             : PLUMED_REGISTER_ACTION(WhamHistogram,"WHAM_HISTOGRAM")
      74             : 
      75          10 : void WhamHistogram::registerKeywords( Keywords& keys ) {
      76          10 :   ActionShortcut::registerKeywords( keys );
      77          10 :   keys.add("compulsory","ARG","the arguments that you would like to make the histogram for");
      78          10 :   keys.add("compulsory","BIAS","*.bias","the value of the biases to use when performing WHAM");
      79          10 :   keys.add("compulsory","TEMP","the temperature at which the simulation was run");
      80          10 :   keys.add("compulsory","STRIDE","1","the frequency with which the data should be stored to perform WHAM");
      81          10 :   keys.add("compulsory","GRID_MIN","the minimum to use for the grid");
      82          10 :   keys.add("compulsory","GRID_MAX","the maximum to use for the grid");
      83          10 :   keys.add("compulsory","GRID_BIN","the number of bins to use for the grid");
      84          10 :   keys.add("optional","BANDWIDTH","the bandwidth for kernel density estimation");
      85          20 :   keys.setValueDescription("grid","the histogram that was generated using the WHAM weights");
      86          10 :   keys.needsAction("GATHER_REPLICAS");
      87          10 :   keys.needsAction("CONCATENATE");
      88          10 :   keys.needsAction("COLLECT");
      89          10 :   keys.needsAction("WHAM");
      90          10 :   keys.needsAction("KDE");
      91          10 : }
      92             : 
      93             : 
      94           7 : WhamHistogram::WhamHistogram( const ActionOptions& ao ) :
      95             :   Action(ao),
      96           7 :   ActionShortcut(ao) {
      97             :   // Input for collection of weights for WHAM
      98             :   std::string bias;
      99          14 :   parse("BIAS",bias);
     100             :   std::string stride;
     101           7 :   parse("STRIDE",stride);
     102             :   // Input for GATHER_REPLICAS
     103          14 :   readInputLine( getShortcutLabel() + "_gather: GATHER_REPLICAS ARG=" + bias );
     104             :   // Put all the replicas in a single vector
     105          14 :   readInputLine( getShortcutLabel() + "_gatherv: CONCATENATE ARG=" + getShortcutLabel() + "_gather.*");
     106             :   // Input for COLLECT_FRAMES
     107          14 :   readInputLine( getShortcutLabel() + "_collect: COLLECT TYPE=vector ARG=" + getShortcutLabel() + "_gatherv STRIDE=" + stride);
     108             :   // Input for WHAM
     109           7 :   std::string temp, tempstr="";
     110          14 :   parse("TEMP",temp);
     111           7 :   if( temp.length()>0 ) {
     112          14 :     tempstr="TEMP=" + temp;
     113             :   }
     114          14 :   readInputLine( getShortcutLabel() + "_wham: WHAM ARG=" + getShortcutLabel() + "_collect " + tempstr );
     115             :   // Input for COLLECT_FRAMES
     116             :   std::vector<std::string> args;
     117          14 :   parseVector("ARG",args);
     118             :   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 ) {
     122             :       argstr = " ARG=";
     123             :     } else {
     124             :       argstr += ",";
     125             :     }
     126          14 :     argstr += getShortcutLabel() + "_data_" + args[i];
     127             :   }
     128             :   // Input for HISTOGRAM
     129           7 :   std::string histo_line, bw="";
     130          14 :   parse("BANDWIDTH",bw);
     131           7 :   if( bw!="" ) {
     132           0 :     histo_line += " BANDWIDTH=" + bw;
     133             :   } else {
     134             :     histo_line += " KERNEL=DISCRETE";
     135             :   }
     136             :   std::string min;
     137           7 :   parse("GRID_MIN",min);
     138          14 :   histo_line += " GRID_MIN=" + min;
     139             :   std::string max;
     140           7 :   parse("GRID_MAX",max);
     141          14 :   histo_line += " GRID_MAX=" + max;
     142             :   std::string bin;
     143           7 :   parse("GRID_BIN",bin);
     144           7 :   histo_line += " GRID_BIN=" + bin;
     145          14 :   readInputLine( getShortcutLabel() + ": KDE " + argstr + " HEIGHTS=" + getShortcutLabel() + "_wham" + histo_line );
     146          14 : }
     147             : 
     148             : }
     149             : }