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 "Bias.h"
      23             : 
      24             : 
      25             : namespace PLMD {
      26             : namespace bias {
      27             : 
      28         722 : Bias::Bias(const ActionOptions&ao):
      29             :   Action(ao),
      30             :   ActionPilot(ao),
      31             :   ActionWithValue(ao),
      32             :   ActionWithArguments(ao),
      33         722 :   outputForces(getNumberOfArguments(),0.0) {
      34         719 :   addComponentWithDerivatives("bias");
      35         719 :   componentIsNotPeriodic("bias");
      36         719 :   valueBias=getPntrToComponent("bias");
      37             : 
      38         719 :   if(getStride()>1) {
      39           3 :     log<<"  multiple time step "<<getStride()<<" ";
      40           6 :     log<<cite("Ferrarotti, Bottaro, Perez-Villa, and Bussi, J. Chem. Theory Comput. 11, 139 (2015)")<<"\n";
      41             :   }
      42        4666 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
      43        3947 :     (getPntrToArgument(i)->getPntrToAction())->turnOnDerivatives();
      44             :   }
      45             : 
      46         719 :   ActionWithValue::turnOnDerivatives();
      47         722 : }
      48             : 
      49         823 : void Bias::registerKeywords( Keywords& keys ) {
      50         823 :   Action::registerKeywords(keys);
      51         823 :   ActionPilot::registerKeywords(keys);
      52         823 :   ActionWithValue::registerKeywords(keys);
      53         823 :   ActionWithArguments::registerKeywords(keys);
      54        1646 :   keys.add("hidden","STRIDE","the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms");
      55         823 :   componentsAreNotOptional(keys);
      56        1646 :   keys.addOutputComponent("bias","default","the instantaneous value of the bias potential");
      57         823 : }
      58             : 
      59       81061 : void Bias::apply() {
      60       81061 :   const unsigned noa=getNumberOfArguments();
      61       81061 :   const unsigned ncp=getNumberOfComponents();
      62             : 
      63       81061 :   if(onStep()) {
      64       81061 :     double gstr = static_cast<double>(getStride());
      65      231175 :     for(unsigned i=0; i<noa; ++i) {
      66      150114 :       getPntrToArgument(i)->addForce(gstr*outputForces[i]);
      67             :     }
      68             :   }
      69             : 
      70             :   // additional forces on the bias component
      71       81061 :   std::vector<double> f(noa,0.0);
      72       81061 :   std::vector<double> forces(noa);
      73             : 
      74             :   bool at_least_one_forced=false;
      75      416703 :   for(unsigned i=0; i<ncp; ++i) {
      76      335642 :     if(getPntrToComponent(i)->applyForce(forces)) {
      77             :       at_least_one_forced=true;
      78         913 :       for(unsigned j=0; j<noa; j++) {
      79         607 :         f[j]+=forces[j];
      80             :       }
      81             :     }
      82             :   }
      83             : 
      84       81061 :   if(at_least_one_forced && !onStep()) {
      85           0 :     error("you are biasing a bias with an inconsistent STRIDE");
      86             :   }
      87             : 
      88       81061 :   if(at_least_one_forced)
      89         841 :     for(unsigned i=0; i<noa; ++i) {
      90         559 :       getPntrToArgument(i)->addForce(f[i]);
      91             :     }
      92             : 
      93       81061 : }
      94             : 
      95             : }
      96             : }
      97             : 
      98             :