BiasValue.cpp

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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2013 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed-code.org for more information.

   This file is part of plumed, version 2.0.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "Bias.h"
#include "ActionRegister.h"


using namespace std;


namespace PLMD{
namespace bias{

//+PLUMEDOC BIAS BIASVALUE 
/*
Takes the value of one variable and use it as a bias

This is the simplest possible bias: the bias potential is equal to a collective variable.
It is useful to create custom biasing potential, e.g. applying a function (see \ref Function)
to some collective variable then using the value of this function directly as a bias.

\par Examples

The following input tells plumed to use the value of the distance between atoms 3 and 5
and the value of the distance between atoms 2 and 4 as biases. 
It then tells plumed to print the energy of the restraint
\verbatim
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=3,6 LABEL=d2
BIASVALUE ARG=d1,d2 LABEL=b
PRINT ARG=d1,d2,b.d1,b.d2
\endverbatim
(See also \ref DISTANCE and \ref PRINT).

Another thing one can do is asking one system to follow  
a circle in sin/cos according a  time dependence

\verbatim
t: TIME
# this just print cos and sin of time
cos: MATHEVAL ARG=t VAR=t FUNC=cos(t) PERIODIC=NO 
sin: MATHEVAL ARG=t VAR=t FUNC=sin(t) PERIODIC=NO
c1: COM ATOMS=1,2
c2: COM ATOMS=3,4
d: DISTANCE COMPONENTS ATOMS=c1,c2
PRINT ARG=t,cos,sin,d.x,d.y,d.z STRIDE=1 FILE=colvar FMT=%8.4f
# this calculates sine and cosine of a projected component of distance
mycos:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=x/sqrt(x*x+y*y) PERIODIC=NO
mysin:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=y/sqrt(x*x+y*y) PERIODIC=NO
# this creates a moving spring so that the system follows a circle-like dynamics 
# but it is not a bias, it is a simple value now
vv1:  MATHEVAL ARG=mycos,mysin,cos,sin VAR=mc,ms,c,s  FUNC=100*((mc-c)^2+(ms-s)^2) PERIODIC=NO
# this takes the value calculated with matheval and uses as a bias 
cc: BIASVALUE ARG=vv1 
# some printout
PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.bias.vv1 STRIDE=1 FILE=colvar FMT=%8.4f
\endverbatim
(see also \ref TIME, \ref MATHEVAL, \ref COM, \ref DISTANCE, and \ref PRINT).


*/
//+ENDPLUMEDOC

class BiasValue : public Bias{
public:
  BiasValue(const ActionOptions&);
  void calculate();
  static void registerKeywords(Keywords& keys);
};

PLUMED_REGISTER_ACTION(BiasValue,"BIASVALUE")

void BiasValue::registerKeywords(Keywords& keys){
  Bias::registerKeywords(keys);
  keys.use("ARG");
  componentsAreNotOptional(keys);
  // Should be _bias below
  keys.addOutputComponent("bias.","default","one or multiple instances of this quantity will be refereceable elsewhere in the input file. "
                                            "these quantities will named with  the arguments of the bias followed by "
                                            "the character string _bias. These quantities tell the user how much the bias is "
                                            "due to each of the colvars.");
  keys.addOutputComponent("bias","default","total bias");
}

BiasValue::BiasValue(const ActionOptions&ao):
PLUMED_BIAS_INIT(ao)
{
  checkRead();
  // add one bias for each argument  
 // addComponent("bias");
  for(unsigned i=0;i<getNumberOfArguments();++i){ 
        //log<<getPntrToArgument(i)->getName()<<"\n";
        string ss;
        ss="bias."+getPntrToArgument(i)->getName();
//        ss=getPntrToArgument(i)->getName()+"_bias";
        addComponent(ss); componentIsNotPeriodic(ss);
  }
  addComponent("bias"); componentIsNotPeriodic("bias");
}

void BiasValue::calculate(){
  double bias=0.0;
for(unsigned i=0;i< getNumberOfArguments() ;++i){
  double val; val=getArgument(i); 
//  log<<"BIAS "<<val<<"\n";
  getPntrToComponent(i)->set(val);
  setOutputForce(i,-1.);
  bias+=val;
}
  getPntrToComponent(getNumberOfArguments())->set(bias);
}

}
}