Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2017 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 "RDF.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC ANALYSIS RDF
      26             : /*
      27             : Calculate the radial distribution function
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace gridtools {
      36             : 
      37             : PLUMED_REGISTER_ACTION(RDF,"RDF")
      38             : 
      39           3 : void RDF::createX2ReferenceObject( const std::string& lab, const std::string& grid_setup, const bool& calc_dens, ActionShortcut* action ) {
      40             :   // Create grid with normalizing function
      41           6 :   action->readInputLine( lab  + "_x2: REFERENCE_GRID PERIODIC=NO FUNC=x*x " + grid_setup );
      42             :   // Compute density if required
      43           3 :   if( calc_dens ) {
      44           6 :     action->readInputLine( lab + "_vol: VOLUME" );
      45             :   }
      46           3 : }
      47             : 
      48         267 : void RDF::registerKeywords( Keywords& keys ) {
      49         267 :   ActionShortcut::registerKeywords( keys );
      50         267 :   keys.add("atoms","GROUP","the atoms that are being used to calculate the RDF");
      51         267 :   keys.add("atoms","ATOMS","the atoms that are being used to calculate the RDF");
      52         267 :   keys.add("atoms-2","GROUPA","the atoms that you would like to compute the RDF about.  Must be used with GROUPB.");
      53         267 :   keys.add("atoms-2","GROUPB","the atoms that you would like to to use when computing the RDF around the atoms that were specified with GROUPA");
      54         267 :   keys.add("compulsory","GRID_BIN","the number of bins to use when computing the RDF");
      55         267 :   keys.add("compulsory","KERNEL","GAUSSIAN","the type of kernel to use for computing the histograms for the RDF");
      56         267 :   keys.add("compulsory","CUTOFF","6.25","the cutoff at which to stop evaluating the kernel functions is set equal to sqrt(2*x)*bandwidth in each direction where x is this number");
      57         267 :   keys.add("compulsory","MAXR","the maximum distance to use for the rdf");
      58         267 :   keys.add("compulsory","BANDWIDTH","the bandwidths for kernel density esimtation");
      59         267 :   keys.add("compulsory","CLEAR","1","the frequency with which to clear the estimate of the rdf.  Set equal to 0 if you want to compute an rdf over the whole trajectory");
      60         267 :   keys.add("compulsory","STRIDE","1","the frequency with which to compute the rdf and accumulate averages");
      61         267 :   keys.add("optional","DENSITY","the reference density to use when normalizing the RDF");
      62         267 :   keys.add("hidden","REFERENCE","this is the label of the reference objects");
      63         534 :   keys.setValueDescription("grid","the radial distribution function");
      64         267 :   keys.needsAction("REFERENCE_GRID");
      65         267 :   keys.needsAction("VOLUME");
      66         267 :   keys.needsAction("DISTANCE_MATRIX");
      67         267 :   keys.needsAction("CUSTOM");
      68         267 :   keys.needsAction("KDE");
      69         267 :   keys.needsAction("ACCUMULATE");
      70         267 :   keys.needsAction("CONSTANT");
      71         267 : }
      72             : 
      73          66 : RDF::RDF(const ActionOptions&ao):
      74             :   Action(ao),
      75          66 :   ActionShortcut(ao) {
      76             :   // Read in grid extent and number of bins
      77             :   std::string maxr, nbins, dens;
      78          66 :   parse("MAXR",maxr);
      79          66 :   parse("GRID_BIN",nbins);
      80          66 :   parse("DENSITY",dens);
      81         132 :   std::string grid_setup = "GRID_MIN=0 GRID_MAX=" + maxr + " GRID_BIN=" + nbins;
      82             :   // Create grid with normalizing function on it
      83             :   std::string refstr;
      84         132 :   parse("REFERENCE",refstr);
      85          66 :   if( refstr.length()==0 ) {
      86           2 :     createX2ReferenceObject( getShortcutLabel(), grid_setup, dens.length()==0, this );
      87           2 :     refstr = getShortcutLabel();
      88             :   }
      89             :   // Read input to histogram
      90             :   std::string cutoff, kernel, bandwidth, kernel_data;
      91         132 :   parse("KERNEL",kernel);
      92          66 :   if( kernel=="DISCRETE" ) {
      93             :     cutoff = maxr;
      94             :     kernel_data="KERNEL=DISCRETE";
      95           2 :     warning("rdf is normalised by dividing by the surface area at the grid value and not by the volume of the bin as it should be with discrete kernels");
      96             :   } else {
      97          65 :     parse("BANDWIDTH",bandwidth);
      98             :     double rcut;
      99          65 :     parse("CUTOFF",rcut);
     100         130 :     kernel_data="KERNEL=" + kernel + " IGNORE_IF_OUT_OF_RANGE BANDWIDTH=" + bandwidth;
     101             :     double bw;
     102          65 :     Tools::convert( bandwidth, bw );
     103             :     double fcut;
     104          65 :     Tools::convert( maxr, fcut );
     105          65 :     Tools::convert( fcut + sqrt(2.0*rcut)*bw, cutoff );
     106             :   }
     107             : 
     108             :   // Create contact matrix
     109             :   std::string natoms, str_norm_atoms, atom_str, group_str, groupa_str, groupb_str;
     110         132 :   parse("GROUP",group_str);
     111          66 :   if( group_str.size()==0 ) {
     112         128 :     parse("ATOMS",group_str);
     113             :   }
     114          66 :   if( group_str.length()>0 ) {
     115           2 :     atom_str="GROUP=" + group_str;
     116           2 :     std::vector<std::string> awords=Tools::getWords(group_str,"\t\n ,");
     117           2 :     Tools::interpretRanges( awords );
     118           2 :     Tools::convert( awords.size(), natoms );
     119             :     str_norm_atoms = natoms;
     120           2 :   } else {
     121          64 :     parse("GROUPA",groupa_str);
     122          64 :     parse("GROUPB",groupb_str);
     123          64 :     std::vector<std::string> awords=Tools::getWords(groupb_str,"\t\n ,");
     124          64 :     Tools::interpretRanges( awords );
     125          64 :     Tools::convert( awords.size(), natoms );
     126         128 :     atom_str="GROUPA=" + groupa_str + " GROUPB=" + groupb_str;
     127          64 :     std::vector<std::string> bwords=Tools::getWords(groupa_str,"\t\n ,");
     128          64 :     Tools::interpretRanges( bwords );
     129          64 :     Tools::convert( bwords.size()+1, str_norm_atoms );
     130          64 :   }
     131             :   // Retrieve the number of atoms
     132         132 :   readInputLine( getShortcutLabel() + "_mat: DISTANCE_MATRIX CUTOFF=" + cutoff + " " + atom_str);
     133             : 
     134             :   // Calculate weights of distances
     135         132 :   readInputLine( getShortcutLabel() + "_wmat: CUSTOM ARG=" + getShortcutLabel() + "_mat FUNC=step(" + cutoff + "-x) PERIODIC=NO");
     136             :   // Now create a histogram from the contact matrix
     137             :   unsigned clear, stride;
     138          66 :   parse("CLEAR",clear);
     139          66 :   parse("STRIDE",stride);
     140          66 :   if( clear==1 ) {
     141         130 :     readInputLine( getShortcutLabel() + "_kde: KDE ARG=" + getShortcutLabel() + "_mat VOLUMES=" + getShortcutLabel() + "_wmat " + grid_setup + " " + kernel_data);
     142             :   } else {
     143             :     std::string stridestr, clearstr;
     144           1 :     Tools::convert( stride, stridestr );
     145           1 :     Tools::convert( clear, clearstr );
     146           2 :     readInputLine( getShortcutLabel() + "_okde: KDE ARG=" + getShortcutLabel() + "_mat HEIGHTS=" + getShortcutLabel() + "_wmat " + grid_setup + " " + kernel_data);
     147           2 :     readInputLine( getShortcutLabel() + "_kde: ACCUMULATE ARG=" + getShortcutLabel() + "_okde STRIDE=" + stridestr + " CLEAR=" + clearstr );
     148           1 :     readInputLine( getShortcutLabel() + "_one: CONSTANT VALUE=1");
     149           2 :     readInputLine( getShortcutLabel() + "_norm: ACCUMULATE ARG=" + getShortcutLabel() + "_one STRIDE=" + stridestr + " CLEAR=" + clearstr );
     150             :   }
     151             :   // Transform the histogram by normalizing factor for rdf
     152         132 :   readInputLine( getShortcutLabel() + "_vrdf: CUSTOM ARG=" + getShortcutLabel() + "_kde," + refstr + "_x2 FUNC=x/(4*pi*y) PERIODIC=NO");
     153             :   // And normalize by density and number of atoms (separated from above to avoid nans)
     154         132 :   std::string func_str = "PERIODIC=NO ARG=" + getShortcutLabel() + "_vrdf";
     155          66 :   if( dens.length()>0 ) {
     156           0 :     if( clear==1 ) {
     157           0 :       func_str += " FUNC=x/(" + dens + "*" + str_norm_atoms + ")";
     158             :     } else {
     159           0 :       func_str += "," + getShortcutLabel() + "_norm FUNC=x/(y*" + dens + "*" + str_norm_atoms + ")";
     160             :     }
     161             :   } else {
     162          66 :     if( clear==1 ) {
     163         130 :       func_str += "," + refstr + "_vol FUNC=x*y/(" + natoms + "*" + str_norm_atoms + ")";
     164             :     } else {
     165           2 :       func_str += "," + refstr + "_vol," + getShortcutLabel() + "_norm FUNC=x*y/(z*" + natoms + "*" + str_norm_atoms + ")";
     166             :     }
     167             :   }
     168         132 :   readInputLine( getShortcutLabel() + ": CUSTOM " + func_str);
     169          66 : }
     170             : 
     171             : }
     172             : }