Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2017 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 "MoreThan.h"
      23             : #include "FunctionShortcut.h"
      24             : #include "FunctionOfVector.h"
      25             : #include "FunctionOfMatrix.h"
      26             : #include "core/ActionRegister.h"
      27             : 
      28             : #include <cmath>
      29             : 
      30             : namespace PLMD {
      31             : namespace function {
      32             : 
      33             : //+PLUMEDOC FUNCTION MORE_THAN
      34             : /*
      35             : Use a switching function to determine how many of the input variables are more than a certain cutoff.
      36             : 
      37             : \par Examples
      38             : 
      39             : */
      40             : //+ENDPLUMEDOC
      41             : 
      42             : //+PLUMEDOC FUNCTION MORE_THAN_VECTOR
      43             : /*
      44             : Use a switching function to determine how many of elements in the input vector are more than a certain cutoff.
      45             : 
      46             : \par Examples
      47             : 
      48             : */
      49             : //+ENDPLUMEDOC
      50             : 
      51             : //+PLUMEDOC COLVAR MORE_THAN_MATRIX
      52             : /*
      53             : Transform all the elements of a matrix using a switching function that is one when the input value is larger than a threshold
      54             : 
      55             : \par Examples
      56             : 
      57             : */
      58             : //+ENDPLUMEDOC
      59             : 
      60             : typedef FunctionShortcut<MoreThan> MoreThanShortcut;
      61             : PLUMED_REGISTER_ACTION(MoreThanShortcut,"MORE_THAN")
      62             : typedef FunctionOfVector<MoreThan> VectorMoreThan;
      63             : PLUMED_REGISTER_ACTION(VectorMoreThan,"MORE_THAN_VECTOR")
      64             : typedef FunctionOfMatrix<MoreThan> MatrixMoreThan;
      65             : PLUMED_REGISTER_ACTION(MatrixMoreThan,"MORE_THAN_MATRIX")
      66             : 
      67         246 : void MoreThan::registerKeywords(Keywords& keys) {
      68         492 :   keys.add("compulsory","NN","6","The n parameter of the switching function ");
      69         492 :   keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN");
      70         492 :   keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
      71         492 :   keys.add("compulsory","R_0","The r_0 parameter of the switching function");
      72         492 :   keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
      73             :            "The following provides information on the \\ref switchingfunction that are available. "
      74             :            "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
      75         492 :   keys.addFlag("SQUARED",false,"is the input quantity the square of the value that you would like to apply the switching function to");
      76         492 :   keys.setValueDescription("scalar/vector/matrix","a function that is one if the if the input is more than a threshold");
      77         246 : }
      78             : 
      79          68 : void MoreThan::read( ActionWithArguments* action ) {
      80          68 :   if( action->getNumberOfArguments()!=1 ) action->error("should only be one argument to more_than actions");
      81          68 :   if( action->getPntrToArgument(0)->isPeriodic() ) action->error("cannot use this function on periodic functions");
      82             : 
      83             : 
      84             :   std::string sw,errors;
      85         136 :   action->parse("SWITCH",sw);
      86          68 :   if(sw.length()>0) {
      87          68 :     switchingFunction.set(sw,errors);
      88          68 :     if( errors.length()!=0 ) action->error("problem reading SWITCH keyword : " + errors );
      89             :   } else {
      90           0 :     int nn=6; int mm=0; double d0=0.0; double r0=0.0; action->parse("R_0",r0);
      91           0 :     if(r0<=0.0) action->error("R_0 should be explicitly specified and positive");
      92           0 :     action->parse("D_0",d0); action->parse("NN",nn); action->parse("MM",mm);
      93           0 :     switchingFunction.set(nn,mm,r0,d0);
      94             :   }
      95          68 :   action->log<<"  using switching function with cutoff "<<switchingFunction.description()<<"\n";
      96          68 :   action->parseFlag("SQUARED",squared);
      97          68 :   if( squared ) action->log<<"  input quantity is square of quantity that switching function acts upon\n";
      98          68 : }
      99             : 
     100      556662 : void MoreThan::calc( const ActionWithArguments* action, const std::vector<double>& args, std::vector<double>& vals, Matrix<double>& derivatives ) const {
     101             :   plumed_dbg_assert( args.size()==1 );
     102      556662 :   if( squared ) vals[0] = 1.0 - switchingFunction.calculateSqr( args[0], derivatives(0,0) );
     103       87550 :   else vals[0] = 1.0 - switchingFunction.calculate( args[0], derivatives(0,0) );
     104      556662 :   derivatives(0,0) = -args[0]*derivatives(0,0);
     105      556662 : }
     106             : 
     107             : }
     108             : }
     109             : 
     110             :