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             : #include <algorithm>
      25             : 
      26             : 
      27             : namespace PLMD {
      28             : namespace bias {
      29             : 
      30        2004 : Bias::Bias(const ActionOptions&ao):
      31             :   Action(ao),
      32             :   ActionPilot(ao),
      33             :   ActionWithValue(ao),
      34             :   ActionWithArguments(ao),
      35        2004 :   outputForces(getNumberOfArguments(),0.0) {
      36        4006 :   addComponentWithDerivatives("bias");
      37        2003 :   componentIsNotPeriodic("bias");
      38        2003 :   valueBias=getPntrToComponent("bias");
      39             : 
      40        2003 :   if(getStride()>1) {
      41          16 :     log<<"  multiple time step "<<getStride()<<" ";
      42          32 :     log<<cite("Ferrarotti, Bottaro, Perez-Villa, and Bussi, J. Chem. Theory Comput. 11, 139 (2015)")<<"\n";
      43             :   }
      44        7893 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
      45             :     // only the first element of a vector or matrix argument would be read and biased
      46        5891 :     if(getPntrToArgument(i)->getRank()!=0 && getPntrToArgument(i)->getNumberOfValues()!=1) {
      47           3 :       error("argument " + getPntrToArgument(i)->getName() + " is not a scalar: biases act on scalars (use e.g. SUM to make a scalar)");
      48             :     }
      49        5890 :     (getPntrToArgument(i)->getPntrToAction())->turnOnDerivatives();
      50             :   }
      51             : 
      52        2002 :   ActionWithValue::turnOnDerivatives();
      53        2005 : }
      54             : 
      55        2571 : void Bias::registerKeywords( Keywords& keys ) {
      56        2571 :   Action::registerKeywords(keys);
      57        2571 :   ActionPilot::registerKeywords(keys);
      58        2571 :   ActionWithValue::registerKeywords(keys);
      59        2571 :   ActionWithArguments::registerKeywords(keys);
      60        5142 :   keys.addInputKeyword("compulsory","ARG","scalar","the labels of the scalars on which the bias will act");
      61        2571 :   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");
      62        5142 :   keys.addOutputComponent("bias","default","scalar","the instantaneous value of the bias potential");
      63        2571 : }
      64             : 
      65      225047 : void Bias::clearDerivatives(const bool& force) {
      66      225047 :   ActionWithValue::clearDerivatives(force);
      67             :   std::fill(outputForces.begin(),outputForces.end(),0.0);
      68      225047 : }
      69             : 
      70      224929 : void Bias::apply() {
      71      224929 :   const unsigned noa=getNumberOfArguments();
      72      224929 :   const unsigned ncp=getNumberOfComponents();
      73             : 
      74      224929 :   if(onStep()) {
      75      224929 :     double gstr = static_cast<double>(getStride());
      76      635303 :     for(unsigned i=0; i<noa; ++i) {
      77      410374 :       getPntrToArgument(i)->addForce(gstr*outputForces[i]);
      78             :     }
      79             :   }
      80             : 
      81      224929 :   accumForces.assign(noa,0.0);
      82      224929 :   forces.resize(noa);
      83             : 
      84             :   bool at_least_one_forced=false;
      85     1043302 :   for(unsigned i=0; i<ncp; ++i) {
      86      818373 :     if(getPntrToComponent(i)->applyForce(forces)) {
      87             :       at_least_one_forced=true;
      88        1313 :       for(unsigned j=0; j<noa; j++) {
      89         807 :         accumForces[j]+=forces[j];
      90             :       }
      91             :       //it may be faster like this(needs some measurements):
      92             :       //(it produces ~20 less asm instructions)
      93             :       /*
      94             :       auto aF = accumForces.begin();
      95             :       auto f = forces.begin();
      96             :       //accumForces and forces have the same size:
      97             :       while (aF!=accumForces.end()) {
      98             :         *aF+=*f;
      99             :         ++aF;
     100             :         ++f;
     101             :       }
     102             :       */
     103             :     }
     104             :   }
     105             : 
     106      224929 :   if(at_least_one_forced && !onStep()) {
     107           0 :     error("you are biasing a bias with an inconsistent STRIDE");
     108             :   }
     109             : 
     110      224929 :   if(at_least_one_forced)
     111        1241 :     for(unsigned i=0; i<noa; ++i) {
     112         759 :       getPntrToArgument(i)->addForce(accumForces[i]);
     113             :     }
     114             : 
     115      224929 : }
     116             : 
     117             : }
     118             : }
     119             : 
     120             :