Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 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 "core/ActionRegister.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace bias {
      27             : 
      28             : //+PLUMEDOC BIAS BIASVALUE
      29             : /*
      30             : Takes the value of one variable and use it as a bias
      31             : 
      32             : This is the simplest possible bias: when you use this method the bias potential is set equal to the scalar-valued argument that was input.
      33             : This action is useful for creating custom biasing potential, e.g. if you apply a function (see [function module](module_function.md))
      34             : to some collective variable then use the value of this function directly as a bias.
      35             : 
      36             : This action is also useful for testing that forces are being calculated correctly.  If I wanted to test whether the derivatives calculated
      37             : by the [DISTANCE](DISTANCE.md) action are computed correctly I would write a PLUMED input like this one:
      38             : 
      39             : ```plumed
      40             : d1: DISTANCE ATOMS=1,2
      41             : BIASVALUE ARG=d1
      42             : ```
      43             : 
      44             : I would then run a calculation using [driver](driver.md) with the following input:
      45             : 
      46             : ```plumed
      47             : plumed driver --ixyz traj.xyz --debug-forces forces.num
      48             : ```
      49             : 
      50             : This outputs a file with two columns that both contain the forces that are acting upon the atoms.  The first set of forces output are the
      51             : analytic forces that are implemented within PLUMED.  The second set of forces are calcluated numerically using finite difference.  If you
      52             : method is implemented correctly these two sets of forces should be the same.
      53             : 
      54             : ## Examples
      55             : 
      56             : The following input tells plumed to use the value of the distance between atoms 3 and 5
      57             : and the value of the distance between atoms 2 and 4 as biases.
      58             : It then tells plumed to print the energy of the restraint
      59             : 
      60             : ```plumed
      61             : DISTANCE ATOMS=3,5 LABEL=d1
      62             : DISTANCE ATOMS=3,6 LABEL=d2
      63             : BIASVALUE ARG=d1,d2 LABEL=b
      64             : PRINT ARG=d1,d2,b.d1_bias,b.d2_bias
      65             : ```
      66             : 
      67             : Another thing one can do is ask the system to follow a circle in sin/cos in accordance with a time dependence
      68             : 
      69             : ```plumed
      70             : t: TIME
      71             : # this just print cos and sin of time
      72             : cos: MATHEVAL ARG=t VAR=t FUNC=cos(t) PERIODIC=NO
      73             : sin: MATHEVAL ARG=t VAR=t FUNC=sin(t) PERIODIC=NO
      74             : c1: COM ATOMS=1,2
      75             : c2: COM ATOMS=3,4
      76             : d: DISTANCE COMPONENTS ATOMS=c1,c2
      77             : PRINT ARG=t,cos,sin,d.x,d.y,d.z STRIDE=1 FILE=colvar FMT=%8.4f
      78             : # this calculates sine and cosine of a projected component of distance
      79             : mycos:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=x/sqrt(x*x+y*y) PERIODIC=NO
      80             : mysin:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=y/sqrt(x*x+y*y) PERIODIC=NO
      81             : # this creates a moving spring so that the system follows a circle-like dynamics
      82             : # but it is not a bias, it is a simple value now
      83             : vv1:  MATHEVAL ARG=mycos,mysin,cos,sin VAR=mc,ms,c,s  FUNC=100*((mc-c)^2+(ms-s)^2) PERIODIC=NO
      84             : # this takes the value calculated with matheval and uses as a bias
      85             : cc: BIASVALUE ARG=vv1
      86             : # some printout
      87             : PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.vv1_bias STRIDE=1 FILE=colvar FMT=%8.4f
      88             : ```
      89             : 
      90             : */
      91             : //+ENDPLUMEDOC
      92             : 
      93             : class BiasValue : public Bias {
      94             : public:
      95             :   explicit BiasValue(const ActionOptions&);
      96             :   void calculate() override;
      97             :   static void registerKeywords(Keywords& keys);
      98             : };
      99             : 
     100             : PLUMED_REGISTER_ACTION(BiasValue,"BIASVALUE")
     101             : 
     102         687 : void BiasValue::registerKeywords(Keywords& keys) {
     103         687 :   Bias::registerKeywords(keys);
     104        1374 :   keys.addInputKeyword("compulsory","ARG","scalar/vector","the labels of the scalar arguments whose values will be used as a bias on the system (a vector must have a single element)");
     105             :   // Should be _bias below
     106        1374 :   keys.addOutputComponent("_bias","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
     107             :                           "these quantities will named with  the arguments of the bias followed by "
     108             :                           "the character string _bias. These quantities tell the user how much the bias is "
     109             :                           "due to each of the colvars.");
     110        1374 :   keys.reset_style("NUMERICAL_DERIVATIVES","hidden");
     111         687 : }
     112             : 
     113         669 : BiasValue::BiasValue(const ActionOptions&ao):
     114         669 :   PLUMED_BIAS_INIT(ao) {
     115         668 :   checkRead();
     116             :   // add one bias for each argument
     117        1368 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     118         700 :     std::string ss=getPntrToArgument(i)->getName()+"_bias";
     119         700 :     addComponent(ss);
     120         700 :     componentIsNotPeriodic(ss);
     121             :   }
     122         669 : }
     123             : 
     124       43378 : void BiasValue::calculate() {
     125             :   double bias=0.0;
     126       95028 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     127             :     double val;
     128       51650 :     val=getArgument(i);
     129       51650 :     getPntrToComponent(i+1)->set(val);
     130       51650 :     setOutputForce(i,-1.);
     131       51650 :     bias+=val;
     132             :   }
     133       43378 :   setBias(bias);
     134       43378 : }
     135             : 
     136             : }
     137             : }