Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "ActionVolume.h"
      23             : 
      24             : namespace PLMD {
      25             : namespace multicolvar {
      26             : 
      27          52 : void ActionVolume::registerKeywords( Keywords& keys ) {
      28          52 :   VolumeGradientBase::registerKeywords( keys );
      29         104 :   if( keys.reserved("VMEAN") ) {
      30         104 :     keys.use("VMEAN");
      31             :   }
      32          52 :   keys.use("MEAN");
      33          52 :   keys.use("LESS_THAN");
      34          52 :   keys.use("MORE_THAN");
      35          52 :   keys.use("BETWEEN");
      36          52 :   keys.use("HISTOGRAM");
      37          52 :   keys.use("SUM");
      38         104 :   keys.add("compulsory","SIGMA","the width of the function to be used for kernel density estimation");
      39         104 :   keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used");
      40         104 :   keys.addFlag("OUTSIDE",false,"calculate quantities for colvars that are on atoms outside the region of interest");
      41          52 : }
      42             : 
      43          28 : ActionVolume::ActionVolume(const ActionOptions&ao):
      44             :   Action(ao),
      45          28 :   VolumeGradientBase(ao) {
      46             :   // Find number of quantities
      47          28 :   if( getPntrToMultiColvar()->isDensity() ) {
      48          11 :     nquantities=2;  // Value + weight
      49          17 :   } else if( getPntrToMultiColvar()->getNumberOfQuantities()==2 ) {
      50          15 :     nquantities=2;  // Value + weight
      51             :   } else {
      52           2 :     nquantities = 1 + getPntrToMultiColvar()->getNumberOfQuantities()-2 + 1;  // Norm  + vector + weight
      53             :   }
      54             : 
      55             :   // Output some nice information
      56          28 :   std::string functype=getPntrToMultiColvar()->getName();
      57          28 :   std::transform( functype.begin(), functype.end(), functype.begin(), [](unsigned char c) {
      58         251 :     return std::tolower(c);
      59             :   } );
      60          28 :   log.printf("  calculating %s inside region of insterest\n",functype.c_str() );
      61             : 
      62          28 :   parseFlag("OUTSIDE",not_in);
      63          28 :   sigma=0.0;
      64          56 :   if( keywords.exists("SIGMA") ) {
      65          50 :     parse("SIGMA",sigma);
      66             :   }
      67          56 :   if( keywords.exists("KERNEL") ) {
      68          56 :     parse("KERNEL",kerneltype);
      69             :   }
      70             : 
      71          28 :   if( getPntrToMultiColvar()->isDensity() ) {
      72             :     std::string input;
      73          22 :     addVessel( "SUM", input, -1 );  // -1 here means that this value will be named getLabel()
      74             :   }
      75          28 :   readVesselKeywords();
      76          28 : }
      77             : 
      78       69358 : void ActionVolume::calculateAllVolumes( const unsigned& curr, MultiValue& outvals ) const {
      79       69358 :   Vector catom_pos=getPntrToMultiColvar()->getCentralAtomPos( curr );
      80             : 
      81             :   double weight;
      82       69358 :   Vector wdf;
      83       69358 :   Tensor vir;
      84       69358 :   std::vector<Vector> refders( getNumberOfAtoms() );
      85       69358 :   weight=calculateNumberInside( catom_pos, wdf, vir, refders );
      86       69358 :   if( not_in ) {
      87        4000 :     weight = 1.0 - weight;
      88        4000 :     wdf *= -1.;
      89        4000 :     vir *=-1;
      90        8000 :     for(unsigned i=0; i<refders.size(); ++i) {
      91        4000 :       refders[i]*=-1;
      92             :     }
      93             :   }
      94       69358 :   setNumberInVolume( 0, curr, weight, wdf, vir, refders, outvals );
      95       69358 : }
      96             : 
      97      148129 : bool ActionVolume::inVolumeOfInterest( const unsigned& curr ) const {
      98      148129 :   Vector catom_pos=getPntrToMultiColvar()->getCentralAtomPos( curr );
      99      148129 :   Vector wdf;
     100      148129 :   Tensor vir;
     101      148129 :   std::vector<Vector> refders( getNumberOfAtoms() );
     102      148129 :   double weight=calculateNumberInside( catom_pos, wdf, vir, refders );
     103      148129 :   if( not_in ) {
     104           0 :     weight = 1.0 - weight;
     105             :   }
     106      148129 :   if( weight<getTolerance() ) {
     107      144691 :     return false;
     108             :   }
     109             :   return true;
     110             : }
     111             : 
     112             : }
     113             : }