Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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 "core/ActionShortcut.h"
      23             : #include "core/ActionWithValue.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "core/PlumedMain.h"
      26             : #include "core/ActionSet.h"
      27             : #include <string>
      28             : #include <cmath>
      29             : 
      30             : //+PLUMEDOC MCOLVAR ALPHABETA
      31             : /*
      32             : Calculate the alpha beta CV
      33             : 
      34             : \par Examples
      35             : 
      36             : 
      37             : */
      38             : //+ENDPLUMEDOC
      39             : 
      40             : namespace PLMD {
      41             : namespace multicolvar {
      42             : 
      43             : class AlphaBeta : public ActionShortcut {
      44             : public:
      45             :   static void registerKeywords(Keywords& keys);
      46             :   explicit AlphaBeta(const ActionOptions&);
      47             : };
      48             : 
      49             : PLUMED_REGISTER_ACTION(AlphaBeta,"ALPHABETA")
      50             : 
      51           4 : void AlphaBeta::registerKeywords(Keywords& keys) {
      52           4 :   ActionShortcut::registerKeywords( keys );
      53           8 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      54           8 :   keys.add("numbered","ATOMS","the atoms involved for each of the torsions you wish to calculate. "
      55             :            "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one torsion will be "
      56             :            "calculated for each ATOM keyword you specify");
      57           8 :   keys.reset_style("ATOMS","atoms");
      58           8 :   keys.add("numbered","REFERENCE","the reference values for each of the torsional angles.  If you use a single REFERENCE value the "
      59             :            "same reference value is used for all torsions");
      60           8 :   keys.add("numbered","COEFFICIENT","the coefficient for each of the torsional angles.  If you use a single COEFFICIENT value the "
      61             :            "same reference value is used for all torsional angles");
      62           4 :   keys.setValueDescription("the alpha beta CV");
      63           4 :   keys.needsAction("CONSTANT");
      64           4 :   keys.needsAction("TORSION");
      65           4 :   keys.needsAction("COMBINE");
      66           4 :   keys.needsAction("CUSTOM");
      67           4 :   keys.needsAction("SUM");
      68           4 : }
      69             : 
      70           2 : AlphaBeta::AlphaBeta(const ActionOptions& ao):
      71             :   Action(ao),
      72           2 :   ActionShortcut(ao) {
      73             :   // Read in the reference value
      74             :   std::string refstr;
      75           4 :   parse("REFERENCE",refstr);
      76             :   unsigned nref=0;
      77           2 :   if( refstr.length()==0 ) {
      78             :     for(unsigned i=0;; ++i) {
      79             :       std::string refval;
      80          18 :       if( !parseNumbered( "REFERENCE", i+1, refval ) ) {
      81             :         break;
      82             :       }
      83           8 :       if( i==0 ) {
      84             :         refstr = refval;
      85             :       } else {
      86          14 :         refstr += "," + refval;
      87             :       }
      88           8 :       nref++;
      89           8 :     }
      90             :   }
      91             :   std::string coeffstr;
      92           4 :   parse("COEFFICIENT",coeffstr);
      93             :   unsigned ncoeff=0;
      94           2 :   if( coeffstr.length()==0 ) {
      95             :     for(unsigned i=0;; ++i) {
      96             :       std::string coeff;
      97           4 :       if( !parseNumbered( "COEFFICIENT", i+1, coeff) ) {
      98             :         break;
      99             :       }
     100           0 :       if( i==0 ) {
     101             :         coeffstr = coeff;
     102             :       } else {
     103           0 :         coeffstr += "," + coeff;
     104             :       }
     105           0 :       ncoeff++;
     106           0 :     }
     107             :   }
     108           2 :   if( coeffstr.length()==0 ) {
     109             :     coeffstr="1";
     110             :   }
     111             :   // Calculate angles
     112           4 :   readInputLine( getShortcutLabel() + "_torsions: TORSION " + convertInputLineToString() );
     113           2 :   ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_torsions" );
     114           2 :   plumed_assert( av && (av->copyOutput(0))->getRank()==1 );
     115           2 :   if( nref==0 ) {
     116           1 :     std::string refval=refstr;
     117           8 :     for(unsigned i=1; i<(av->copyOutput(0))->getShape()[0]; ++i) {
     118          14 :       refstr += "," + refval;
     119             :     }
     120           1 :   } else if( nref!=(av->copyOutput(0))->getShape()[0] ) {
     121           0 :     error("mismatch between number of reference values and number of ATOMS specified");
     122             :   }
     123           2 :   if( ncoeff==0 ) {
     124           2 :     std::string coeff=coeffstr;
     125          16 :     for(unsigned i=1; i<(av->copyOutput(0))->getShape()[0]; ++i) {
     126          28 :       coeffstr += "," + coeff;
     127             :     }
     128           0 :   } else if( ncoeff!=(av->copyOutput(0))->getShape()[0] ) {
     129           0 :     error("mismatch between number of coefficients and number of ATOMS specified");
     130             :   }
     131           4 :   readInputLine( getShortcutLabel() + "_ref: CONSTANT VALUES=" + refstr );
     132           4 :   readInputLine( getShortcutLabel() + "_coeff: CONSTANT VALUES=" + coeffstr );
     133             :   // Caculate difference from reference using combine
     134           4 :   readInputLine( getShortcutLabel() + "_comb: COMBINE ARG=" + getShortcutLabel() + "_torsions," + getShortcutLabel() + "_ref COEFFICIENTS=1,-1 PERIODIC=NO" );
     135             :   // Now matheval for cosine bit
     136           4 :   readInputLine( getShortcutLabel() + "_cos: CUSTOM ARG=" + getShortcutLabel() + "_comb," + getShortcutLabel() + "_coeff FUNC=y*(0.5+0.5*cos(x)) PERIODIC=NO");
     137             :   // And combine to get final value
     138           4 :   readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_cos PERIODIC=NO");
     139           2 : }
     140             : 
     141             : }
     142             : }