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             : #include "ActionRegister.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace bias {
      27             : 
      28             : //+PLUMEDOC BIAS RESTRAINT
      29             : /*
      30             : Adds harmonic and/or linear restraints on one or more variables.
      31             : 
      32             : Either or both
      33             : of SLOPE and KAPPA must be present to specify the linear and harmonic force constants
      34             : respectively.  The resulting potential is given by:
      35             : \f[
      36             :   \sum_i \frac{k_i}{2} (x_i-a_i)^2 + m_i*(x_i-a_i)
      37             : \f].
      38             : 
      39             : The number of components for any vector of force constants must be equal to the number
      40             : of arguments to the action.
      41             : 
      42             : Additional material and examples can be also found in the tutorial \ref lugano-2
      43             : 
      44             : \par Examples
      45             : 
      46             : The following input tells plumed to restrain the distance between atoms 3 and 5
      47             : and the distance between atoms 2 and 4, at different equilibrium
      48             : values, and to print the energy of the restraint
      49             : \plumedfile
      50             : DISTANCE ATOMS=3,5 LABEL=d1
      51             : DISTANCE ATOMS=2,4 LABEL=d2
      52             : RESTRAINT ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 LABEL=restraint
      53             : PRINT ARG=restraint.bias
      54             : \endplumedfile
      55             : 
      56             : */
      57             : //+ENDPLUMEDOC
      58             : 
      59             : class Restraint : public Bias {
      60             :   std::vector<double> at;
      61             :   std::vector<double> kappa;
      62             :   std::vector<double> slope;
      63             :   Value* valueForce2;
      64             : public:
      65             :   explicit Restraint(const ActionOptions&);
      66             :   void calculate() override;
      67             :   static void registerKeywords(Keywords& keys);
      68             : };
      69             : 
      70       14144 : PLUMED_REGISTER_ACTION(Restraint,"RESTRAINT")
      71             : 
      72         185 : void Restraint::registerKeywords(Keywords& keys) {
      73         185 :   Bias::registerKeywords(keys);
      74         185 :   keys.use("ARG");
      75         370 :   keys.add("compulsory","SLOPE","0.0","specifies that the restraint is linear and what the values of the force constants on each of the variables are");
      76         370 :   keys.add("compulsory","KAPPA","0.0","specifies that the restraint is harmonic and what the values of the force constants on each of the variables are");
      77         370 :   keys.add("compulsory","AT","the position of the restraint");
      78         370 :   keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
      79         185 : }
      80             : 
      81         181 : Restraint::Restraint(const ActionOptions&ao):
      82             :   PLUMED_BIAS_INIT(ao),
      83         356 :   at(getNumberOfArguments()),
      84         178 :   kappa(getNumberOfArguments(),0.0),
      85         359 :   slope(getNumberOfArguments(),0.0) {
      86         178 :   parseVector("SLOPE",slope);
      87         178 :   parseVector("KAPPA",kappa);
      88         178 :   parseVector("AT",at);
      89         178 :   checkRead();
      90             : 
      91         178 :   log.printf("  at");
      92         409 :   for(unsigned i=0; i<at.size(); i++) {
      93         231 :     log.printf(" %f",at[i]);
      94             :   }
      95         178 :   log.printf("\n");
      96         178 :   log.printf("  with harmonic force constant");
      97         409 :   for(unsigned i=0; i<kappa.size(); i++) {
      98         231 :     log.printf(" %f",kappa[i]);
      99             :   }
     100         178 :   log.printf("\n");
     101         178 :   log.printf("  and linear force constant");
     102         409 :   for(unsigned i=0; i<slope.size(); i++) {
     103         231 :     log.printf(" %f",slope[i]);
     104             :   }
     105         178 :   log.printf("\n");
     106             : 
     107         178 :   addComponent("force2");
     108         178 :   componentIsNotPeriodic("force2");
     109         178 :   valueForce2=getPntrToComponent("force2");
     110         181 : }
     111             : 
     112             : 
     113        4688 : void Restraint::calculate() {
     114             :   double ene=0.0;
     115             :   double totf2=0.0;
     116        9751 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     117        5063 :     const double cv=difference(i,at[i],getArgument(i));
     118        5063 :     const double k=kappa[i];
     119        5063 :     const double m=slope[i];
     120        5063 :     const double f=-(k*cv+m);
     121        5063 :     ene+=0.5*k*cv*cv+m*cv;
     122             :     setOutputForce(i,f);
     123        5063 :     totf2+=f*f;
     124             :   }
     125             :   setBias(ene);
     126        4688 :   valueForce2->set(totf2);
     127        4688 : }
     128             : 
     129             : }
     130             : 
     131             : 
     132             : }