Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2018 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 "VesselRegister.h"
      23             : #include "FunctionVessel.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace vesselbase {
      27             : 
      28           4 : class AltMin : public vesselbase::FunctionVessel {
      29             : private:
      30             :   double beta;
      31             : public:
      32             :   static void registerKeywords( Keywords& keys );
      33             :   static void reserveKeyword( Keywords& keys );
      34             :   explicit AltMin( const vesselbase::VesselOptions& da );
      35             :   std::string value_descriptor();
      36             :   double calcTransform( const double& val, double& dv ) const ;
      37             :   double finalTransform( const double& val, double& dv );
      38             : };
      39             : 
      40        2525 : PLUMED_REGISTER_VESSEL(AltMin,"ALT_MIN")
      41             : 
      42           2 : void AltMin::registerKeywords( Keywords& keys ) {
      43           2 :   FunctionVessel::registerKeywords(keys);
      44           2 :   keys.add("compulsory","BETA","the value of beta for the equation in the manual");
      45           2 : }
      46             : 
      47         841 : void AltMin::reserveKeyword( Keywords& keys ) {
      48             :   keys.reserve("vessel","ALT_MIN","calculate the minimum value. "
      49             :                "To make this quantity continuous the minimum is calculated using "
      50             :                "\\f$ \\textrm{min} = -\\frac{1}{\\beta} \\log \\sum_i \\exp\\left( -\\beta s_i \\right)  \\f$ "
      51         841 :                "The value of \\f$\\beta\\f$ in this function is specified using (BETA=\\f$\\beta\\f$).");
      52             :   keys.addOutputComponent("altmin","ALT_MIN","the minimum value. This is calculated using the formula described in the description of the "
      53         841 :                           "keyword so as to make it continuous.");
      54         841 : }
      55             : 
      56           2 : AltMin::AltMin( const vesselbase::VesselOptions& da ):
      57           2 :   FunctionVessel(da)
      58             : {
      59           2 :   if( getAction()->isPeriodic() ) error("MIN is not a meaningful option for periodic variables");
      60           2 :   parse("BETA",beta); usetol=true;
      61           2 : }
      62             : 
      63           2 : std::string AltMin::value_descriptor() {
      64           2 :   std::string str_beta; Tools::convert( beta, str_beta );
      65           2 :   return "the minimum value. Beta is equal to " + str_beta;
      66             : }
      67             : 
      68          10 : double AltMin::calcTransform( const double& val, double& dv ) const {
      69          10 :   double f = exp( -beta*val ); dv = -beta*f; return f;
      70             : }
      71             : 
      72           5 : double AltMin::finalTransform( const double& val, double& dv ) {
      73           5 :   dv = - 1.0 /(beta*val); return -std::log( val ) / beta;
      74             : }
      75             : 
      76             : }
      77        2523 : }