Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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 "PathBase.h"
      23             : #include "tools/SwitchingFunction.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace mapping {
      27             : 
      28          11 : void PathBase::registerKeywords( Keywords& keys ) {
      29          11 :   Mapping::registerKeywords( keys );
      30          22 :   keys.add("compulsory","LAMBDA","0","the value of the lambda parameter for paths");
      31          22 :   keys.addFlag("NOZPATH",false,"do not calculate the zpath position");
      32          11 : }
      33             : 
      34           9 : PathBase::PathBase(const ActionOptions& ao):
      35             :   Action(ao),
      36           9 :   Mapping(ao)
      37             : {
      38             :   setLowMemOption( true );
      39           9 :   weightHasDerivatives=true;
      40           9 :   bool noz; parseFlag("NOZPATH",noz);
      41           9 :   parse("LAMBDA",lambda);
      42             : 
      43             :   // Create the list of tasks
      44         405 :   for(unsigned i=0; i<getNumberOfReferencePoints(); ++i) addTaskToList( i );
      45             :   // And activate them all
      46           9 :   deactivateAllTasks();
      47         405 :   for(unsigned i=0; i<getFullNumberOfTasks(); ++i) taskFlags[i]=1;
      48           9 :   lockContributors();
      49             : 
      50           9 :   std::string empty="LABEL=zpath";
      51           9 :   if(!noz) {
      52           7 :     if( lambda==0 ) error("you must set LAMDBA value in order to calculate ZPATH coordinate.  Use LAMBDA/NOZPATH keyword");
      53          14 :     addVessel("ZPATH",empty,0);
      54             :   }
      55           9 : }
      56             : 
      57        1103 : double PathBase::getLambda() {
      58        1103 :   return lambda;
      59             : }
      60             : 
      61        4914 : void PathBase::calculate() {
      62             :   // Loop over all frames is now performed by ActionWithVessel
      63        4914 :   runAllTasks();
      64        4914 : }
      65             : 
      66      170352 : void PathBase::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
      67             :   // This builds a pack to hold the derivatives
      68      170352 :   ReferenceValuePack mypack( getNumberOfArguments(), getNumberOfAtoms(), myvals );
      69      170352 :   finishPackSetup( current, mypack );
      70             :   // Calculate the distance from the frame
      71      170352 :   double val=calculateDistanceFunction( current, mypack, true );
      72             :   // Put the element value in element zero
      73             :   myvals.setValue( 0, val ); myvals.setValue( 1, 1.0 );
      74      170352 :   return;
      75      170352 : }
      76             : 
      77      170352 : double PathBase::transformHD( const double& dist, double& df ) const {
      78      170352 :   if( lambda==0 ) { df=1; return dist; }
      79      114660 :   double val = exp( -dist*lambda );
      80      114660 :   df = -lambda*val;
      81      114660 :   return val;
      82             : }
      83             : 
      84             : }
      85             : }