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/ActionRegister.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace wham {
      27             : 
      28             : //+PLUMEDOC REWEIGHTING WHAM_WEIGHTS
      29             : /*
      30             : Calculate and output weights for configurations using the weighted histogram analysis method.
      31             : 
      32             : This shortcut action allows you to calculate and output weights computed using the weighted histogram
      33             : analysis technique.  The following input demonstrates how this works in practise by showing you how this
      34             : action can be used to analyze the output from a series of umbrella sampling calculations.
      35             : The trajectory from each of the simulations run with the different biases should be concatenated into a
      36             : single trajectory before running the following analysis script on the concatenated trajectory using PLUMED
      37             : driver.  The umbrella sampling simulations that will be analyzed using the script below applied a harmonic
      38             : restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values.  The script
      39             : below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm
      40             : to determine a weight for each configuration in the concatenated trajectory.
      41             : 
      42             : ```plumed
      43             : #SETTINGS NREPLICAS=4
      44             : phi: TORSION ATOMS=5,7,9,15
      45             : rp: RESTRAINT ARG=phi KAPPA=50.0 AT=@replicas:{-3.00,-1.45,0.10,1.65}
      46             : WHAM_WEIGHTS BIAS=rp.bias TEMP=300 FILE=wham-weights
      47             : ```
      48             : 
      49             : The script above must be run with multiple replicas using the following command:
      50             : 
      51             : ````
      52             : mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4
      53             : ````
      54             : 
      55             : For more details on how the weights for configurations are determined using the wham method see the documentation
      56             : for the [WHAM](WHAM.md) action.
      57             : 
      58             : */
      59             : //+ENDPLUMEDOC
      60             : 
      61             : class WhamWeights : public ActionShortcut {
      62             : public:
      63             :   static void registerKeywords( Keywords& keys );
      64             :   explicit WhamWeights( const ActionOptions& );
      65             : };
      66             : 
      67             : PLUMED_REGISTER_ACTION(WhamWeights,"WHAM_WEIGHTS")
      68             : 
      69           8 : void WhamWeights::registerKeywords( Keywords& keys ) {
      70           8 :   ActionShortcut::registerKeywords( keys );
      71          16 :   keys.remove("LABEL");
      72           8 :   keys.add("compulsory","BIAS","*.bias","the value of the biases to use when performing WHAM");
      73           8 :   keys.add("optional","TEMP","the temperature at which the simulation was run");
      74           8 :   keys.add("compulsory","STRIDE","1","the frequency with which the bias should be stored to perform WHAM");
      75           8 :   keys.add("compulsory","FILE","the file on which to output the WHAM weights");
      76           8 :   keys.add("optional","FMT","the format to use for the real numbers in the output file");
      77          16 :   keys.setValueDescription("vector","the weights that were calculated using WHAM");
      78           8 :   keys.needsAction("GATHER_REPLICAS");
      79           8 :   keys.needsAction("CONCATENATE");
      80           8 :   keys.needsAction("COLLECT");
      81           8 :   keys.needsAction("WHAM");
      82           8 :   keys.needsAction("DUMPVECTOR");
      83           8 : }
      84             : 
      85           6 : WhamWeights::WhamWeights( const ActionOptions& ao ) :
      86             :   Action(ao),
      87           6 :   ActionShortcut(ao) {
      88             :   // Input for collection of weights for WHAM
      89             :   std::string bias;
      90          12 :   parse("BIAS",bias);
      91             :   std::string stride;
      92           6 :   parse("STRIDE",stride);
      93             :   // Input for GATHER_REPLICAS
      94          12 :   readInputLine( getShortcutLabel() + "_gather: GATHER_REPLICAS ARG=" + bias );
      95             :   // Put all the replicas in a single vector
      96          12 :   readInputLine( getShortcutLabel() + "_gatherv: CONCATENATE ARG=" + getShortcutLabel() + "_gather.*");
      97             :   // Input for COLLECT_FRAMES
      98          12 :   readInputLine( getShortcutLabel() + "_collect: COLLECT TYPE=vector ARG=" + getShortcutLabel() + "_gatherv STRIDE=" + stride);
      99             :   // Input for WHAM
     100           6 :   std::string temp, tempstr="";
     101          12 :   parse("TEMP",temp);
     102           6 :   if( temp.length()>0 ) {
     103          12 :     tempstr="TEMP=" + temp;
     104             :   }
     105          12 :   readInputLine( getShortcutLabel() + ": WHAM ARG=" + getShortcutLabel() + "_collect " + tempstr );
     106             :   // Input for PRINT (will just output at end of calc
     107             :   std::string filename, fmt;
     108           6 :   parse("FILE",filename);
     109          12 :   parse("FMT",fmt);
     110           6 :   if(fmt.length()>0) {
     111          12 :     fmt=" FMT=" + fmt;
     112             :   }
     113          12 :   readInputLine( "DUMPVECTOR STRIDE=0 ARG=" + getShortcutLabel() + " FILE=" + filename + fmt );
     114           6 : }
     115             : 
     116             : }
     117             : }