Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2020 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             : 
      26             : using namespace std;
      27             : 
      28             : 
      29             : namespace PLMD {
      30             : namespace bias {
      31             : 
      32             : //+PLUMEDOC BIAS RESTRAINT
      33             : /*
      34             : Adds harmonic and/or linear restraints on one or more variables.
      35             : 
      36             : Either or both
      37             : of SLOPE and KAPPA must be present to specify the linear and harmonic force constants
      38             : respectively.  The resulting potential is given by:
      39             : \f[
      40             :   \sum_i \frac{k_i}{2} (x_i-a_i)^2 + m_i*(x_i-a_i)
      41             : \f].
      42             : 
      43             : The number of components for any vector of force constants must be equal to the number
      44             : of arguments to the action.
      45             : 
      46             : Additional material and examples can be also found in the tutorial \ref lugano-2
      47             : 
      48             : \par Examples
      49             : 
      50             : The following input tells plumed to restrain the distance between atoms 3 and 5
      51             : and the distance between atoms 2 and 4, at different equilibrium
      52             : values, and to print the energy of the restraint
      53             : \plumedfile
      54             : DISTANCE ATOMS=3,5 LABEL=d1
      55             : DISTANCE ATOMS=2,4 LABEL=d2
      56             : RESTRAINT ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 LABEL=restraint
      57             : PRINT ARG=restraint.bias
      58             : \endplumedfile
      59             : 
      60             : */
      61             : //+ENDPLUMEDOC
      62             : 
      63         492 : class Restraint : public Bias {
      64             :   std::vector<double> at;
      65             :   std::vector<double> kappa;
      66             :   std::vector<double> slope;
      67             :   Value* valueForce2;
      68             : public:
      69             :   explicit Restraint(const ActionOptions&);
      70             :   void calculate();
      71             :   static void registerKeywords(Keywords& keys);
      72             : };
      73             : 
      74        7687 : PLUMED_REGISTER_ACTION(Restraint,"RESTRAINT")
      75             : 
      76         168 : void Restraint::registerKeywords(Keywords& keys) {
      77         168 :   Bias::registerKeywords(keys);
      78         336 :   keys.use("ARG");
      79         840 :   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");
      80         840 :   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");
      81         672 :   keys.add("compulsory","AT","the position of the restraint");
      82         672 :   keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
      83         168 : }
      84             : 
      85         167 : Restraint::Restraint(const ActionOptions&ao):
      86             :   PLUMED_BIAS_INIT(ao),
      87             :   at(getNumberOfArguments()),
      88             :   kappa(getNumberOfArguments(),0.0),
      89         659 :   slope(getNumberOfArguments(),0.0)
      90             : {
      91         328 :   parseVector("SLOPE",slope);
      92         328 :   parseVector("KAPPA",kappa);
      93         328 :   parseVector("AT",at);
      94         164 :   checkRead();
      95             : 
      96         164 :   log.printf("  at");
      97         919 :   for(unsigned i=0; i<at.size(); i++) log.printf(" %f",at[i]);
      98         164 :   log.printf("\n");
      99         164 :   log.printf("  with harmonic force constant");
     100         919 :   for(unsigned i=0; i<kappa.size(); i++) log.printf(" %f",kappa[i]);
     101         164 :   log.printf("\n");
     102         164 :   log.printf("  and linear force constant");
     103         919 :   for(unsigned i=0; i<slope.size(); i++) log.printf(" %f",slope[i]);
     104         164 :   log.printf("\n");
     105             : 
     106         328 :   addComponent("force2");
     107         328 :   componentIsNotPeriodic("force2");
     108         328 :   valueForce2=getPntrToComponent("force2");
     109         164 : }
     110             : 
     111             : 
     112        4503 : void Restraint::calculate() {
     113             :   double ene=0.0;
     114             :   double totf2=0.0;
     115       14037 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     116        4767 :     const double cv=difference(i,at[i],getArgument(i));
     117        4767 :     const double k=kappa[i];
     118        4767 :     const double m=slope[i];
     119        4767 :     const double f=-(k*cv+m);
     120        4767 :     ene+=0.5*k*cv*cv+m*cv;
     121             :     setOutputForce(i,f);
     122        4767 :     totf2+=f*f;
     123             :   }
     124             :   setBias(ene);
     125        4503 :   valueForce2->set(totf2);
     126        4503 : }
     127             : 
     128             : }
     129             : 
     130             : 
     131        5517 : }