Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2018,2019 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 analysis {
      27             : 
      28             : //+PLUMEDOC REWEIGHTING WHAM_HISTOGRAM
      29             : /*
      30             : This can be used to output the a histogram using the weighted histogram technique
      31             : 
      32             : \par Examples
      33             : 
      34             : */
      35             : //+ENDPLUMEDOC
      36             : 
      37          18 : class WhamHistogram : public ActionShortcut {
      38             : public:
      39             :   static void registerKeywords( Keywords& keys );
      40             :   explicit WhamHistogram( const ActionOptions& );
      41             : };
      42             : 
      43        7844 : PLUMED_REGISTER_ACTION(WhamHistogram,"WHAM_HISTOGRAM")
      44             : 
      45           7 : void WhamHistogram::registerKeywords( Keywords& keys ) {
      46           7 :   ActionShortcut::registerKeywords( keys );
      47          28 :   keys.add("compulsory","ARG","the arguments that you would like to make the histogram for");
      48          35 :   keys.add("compulsory","BIAS","*.bias","the value of the biases to use when performing WHAM");
      49          28 :   keys.add("compulsory","TEMP","the temperature at which the simulation was run");
      50          35 :   keys.add("compulsory","STRIDE","1","the frequency with which the data should be stored to perform WHAM");
      51          28 :   keys.add("compulsory","GRID_MIN","the minimum to use for the grid");
      52          28 :   keys.add("compulsory","GRID_MAX","the maximum to use for the grid");
      53          28 :   keys.add("compulsory","GRID_BIN","the number of bins to use for the grid");
      54          28 :   keys.add("optional","BANDWIDTH","the bandwidth for kernel density estimation");
      55           7 : }
      56             : 
      57             : 
      58           6 : WhamHistogram::WhamHistogram( const ActionOptions& ao ) :
      59             :   Action(ao),
      60           6 :   ActionShortcut(ao)
      61             : {
      62             :   // Input for REWEIGHT_WHAM
      63           6 :   std::string rew_line = getShortcutLabel() + "_weights: REWEIGHT_WHAM";
      64          18 :   std::string bias; parse("BIAS",bias); rew_line += " ARG=" + bias;
      65          18 :   std::string temp; parse("TEMP",temp); rew_line += " TEMP=" + temp;
      66           6 :   readInputLine( rew_line );
      67             :   // Input for COLLECT_FRAMES
      68          18 :   std::string col_line = getShortcutLabel() + "_collect: COLLECT_FRAMES LOGWEIGHTS=" + getShortcutLabel() + "_weights";
      69          18 :   std::string stride; parse("STRIDE",stride); col_line += " STRIDE=" + stride;
      70          18 :   std::string arg; parse("ARG",arg); col_line += " ARG=" + arg;
      71           6 :   readInputLine( col_line );
      72             :   // Input for HISTOGRAM
      73          18 :   std::string histo_line = getShortcutLabel() + ": HISTOGRAM ARG=" + getShortcutLabel() + "_collect.*";
      74          18 :   std::string min; parse("GRID_MIN",min); histo_line += " GRID_MIN=" + min;
      75          18 :   std::string max; parse("GRID_MAX",max); histo_line += " GRID_MAX=" + max;
      76          18 :   std::string bin; parse("GRID_BIN",bin); histo_line += " GRID_BIN=" + bin;
      77          12 :   std::string bw=""; parse("BANDWIDTH",bw);
      78           6 :   if( bw!="" ) histo_line += " BANDWIDTH=" + bw;
      79             :   else histo_line += " KERNEL=DISCRETE";
      80           6 :   readInputLine( histo_line );
      81           6 : }
      82             : 
      83             : }
      84        5874 : }