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.  For more detail on how this technique works see \ref REWEIGHT_WHAM
      34             : 
      35             : \par Examples
      36             : 
      37             : The following input can be used to analyze the output from a series of umbrella sampling calculations.
      38             : The trajectory from each of the simulations run with the different biases should be concatenated into a
      39             : single trajectory before running the following analysis script on the concatenated trajectory using PLUMED
      40             : driver.  The umbrella sampling simulations that will be analyzed using the script below applied a harmonic
      41             : restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values.  The script
      42             : below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm
      43             : to determine a weight for each configuration in the concatenated trajectory.
      44             : 
      45             : \plumedfile
      46             : #SETTINGS NREPLICAS=4
      47             : phi: TORSION ATOMS=5,7,9,15
      48             : rp: RESTRAINT ARG=phi KAPPA=50.0 ...
      49             :   AT=@replicas:{
      50             :         -3.00000000000000000000
      51             :         -1.45161290322580645168
      52             :         .09677419354838709664
      53             :         1.64516129032258064496
      54             :      }
      55             : ...
      56             : 
      57             : WHAM_WEIGHTS BIAS=rp.bias TEMP=300 FILE=wham-weights
      58             : \endplumedfile
      59             : 
      60             : The script above must be run with multiple replicas using the following command:
      61             : 
      62             : \verbatim
      63             : mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4
      64             : \endverbatim
      65             : 
      66             : */
      67             : //+ENDPLUMEDOC
      68             : 
      69             : class WhamWeights : public ActionShortcut {
      70             : public:
      71             :   static void registerKeywords( Keywords& keys );
      72             :   explicit WhamWeights( const ActionOptions& );
      73             : };
      74             : 
      75             : PLUMED_REGISTER_ACTION(WhamWeights,"WHAM_WEIGHTS")
      76             : 
      77           8 : void WhamWeights::registerKeywords( Keywords& keys ) {
      78           8 :   ActionShortcut::registerKeywords( keys ); keys.remove("LABEL");
      79          16 :   keys.add("compulsory","BIAS","*.bias","the value of the biases to use when performing WHAM");
      80          16 :   keys.add("optional","TEMP","the temperature at which the simulation was run");
      81          16 :   keys.add("compulsory","STRIDE","1","the frequency with which the bias should be stored to perform WHAM");
      82          16 :   keys.add("compulsory","FILE","the file on which to output the WHAM weights");
      83          16 :   keys.add("optional","FMT","the format to use for the real numbers in the output file");
      84           8 :   keys.setValueDescription("the weights that were calculated using WHAM");
      85          16 :   keys.needsAction("GATHER_REPLICAS"); keys.needsAction("CONCATENATE");
      86          24 :   keys.needsAction("COLLECT"); keys.needsAction("WHAM"); keys.needsAction("DUMPVECTOR");
      87           8 : }
      88             : 
      89           6 : WhamWeights::WhamWeights( const ActionOptions& ao ) :
      90             :   Action(ao),
      91           6 :   ActionShortcut(ao)
      92             : {
      93             :   // Input for collection of weights for WHAM
      94          12 :   std::string bias; parse("BIAS",bias);
      95           6 :   std::string stride; parse("STRIDE",stride);
      96             :   // Input for GATHER_REPLICAS
      97          12 :   readInputLine( getShortcutLabel() + "_gather: GATHER_REPLICAS ARG=" + bias );
      98             :   // Put all the replicas in a single vector
      99          12 :   readInputLine( getShortcutLabel() + "_gatherv: CONCATENATE ARG=" + getShortcutLabel() + "_gather.*");
     100             :   // Input for COLLECT_FRAMES
     101          12 :   readInputLine( getShortcutLabel() + "_collect: COLLECT TYPE=vector ARG=" + getShortcutLabel() + "_gatherv STRIDE=" + stride);
     102             :   // Input for WHAM
     103          18 :   std::string temp, tempstr=""; parse("TEMP",temp); if( temp.length()>0 ) tempstr="TEMP=" + temp;
     104          12 :   readInputLine( getShortcutLabel() + ": WHAM ARG=" + getShortcutLabel() + "_collect " + tempstr );
     105             :   // Input for PRINT (will just output at end of calc
     106          12 :   std::string filename, fmt; parse("FILE",filename); parse("FMT",fmt);
     107          12 :   readInputLine( "DUMPVECTOR STRIDE=0 ARG=" + getShortcutLabel() + " FILE=" + filename + " FMT=" + fmt );
     108           6 : }
     109             : 
     110             : }
     111             : }