Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "Colvar.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace colvar {
      27             : 
      28             : //+PLUMEDOC COLVAR TEMPLATE
      29             : /*
      30             : This file provides a template for if you want to introduce a new CV.
      31             : 
      32             : The descrition of the CV that you include here will appear in the further details and examples
      33             : section of the manual
      34             : 
      35             : You can (and should) include examples showing how to use your CV as follows:
      36             : 
      37             : ```plumed
      38             : # This should be a sample input.
      39             : t: TEMPLATE ATOMS=1,2
      40             : PRINT ARG=t STRIDE=100 FILE=COLVAR
      41             : ```
      42             : 
      43             : */
      44             : //+ENDPLUMEDOC
      45             : 
      46             : class Template : public Colvar {
      47             :   bool pbc;
      48             : 
      49             : public:
      50             :   explicit Template(const ActionOptions&);
      51             : // active methods:
      52             :   void calculate() override;
      53             :   static void registerKeywords(Keywords& keys);
      54             : };
      55             : 
      56             : PLUMED_REGISTER_ACTION(Template,"TEMPLATE")
      57             : 
      58           2 : void Template::registerKeywords(Keywords& keys) {
      59           2 :   Colvar::registerKeywords(keys);
      60           2 :   keys.addFlag("TEMPLATE_DEFAULT_OFF_FLAG",false,"flags that are by default not performed should be specified like this");
      61           2 :   keys.add("compulsory","TEMPLATE_COMPULSORY","all compulsory keywords should be added like this with a description here");
      62           2 :   keys.add("optional","TEMPLATE_OPTIONAL","all optional keywords that have input should be added like a description here");
      63           2 :   keys.add("atoms","ATOMS","the keyword with which you specify what atoms to use should be added like this");
      64           4 :   keys.setValueDescription("scalar","a description of the value that is computed by this colvar should be included here");
      65           2 : }
      66             : 
      67           0 : Template::Template(const ActionOptions&ao):
      68             :   PLUMED_COLVAR_INIT(ao),
      69           0 :   pbc(true) {
      70             :   std::vector<AtomNumber> atoms;
      71           0 :   parseAtomList("ATOMS",atoms);
      72           0 :   if(atoms.size()!=2) {
      73           0 :     error("Number of specified atoms should be 2");
      74             :   }
      75           0 :   bool nopbc=!pbc;
      76           0 :   parseFlag("NOPBC",nopbc);
      77           0 :   pbc=!nopbc;
      78           0 :   checkRead();
      79             : 
      80           0 :   log.printf("  between atoms %d %d\n",atoms[0].serial(),atoms[1].serial());
      81           0 :   if(pbc) {
      82           0 :     log.printf("  using periodic boundary conditions\n");
      83             :   } else {
      84           0 :     log.printf("  without periodic boundary conditions\n");
      85             :   }
      86             : 
      87           0 :   addValueWithDerivatives();
      88           0 :   setNotPeriodic();
      89             : 
      90           0 :   requestAtoms(atoms);
      91           0 : }
      92             : 
      93             : 
      94             : // calculator
      95           0 : void Template::calculate() {
      96             : 
      97           0 :   Vector distance;
      98           0 :   if(pbc) {
      99           0 :     distance=pbcDistance(getPosition(0),getPosition(1));
     100             :   } else {
     101           0 :     distance=delta(getPosition(0),getPosition(1));
     102             :   }
     103           0 :   const double value=distance.modulo();
     104           0 :   const double invvalue=1.0/value;
     105             : 
     106           0 :   setAtomsDerivatives(0,-invvalue*distance);
     107           0 :   setAtomsDerivatives(1,invvalue*distance);
     108           0 :   setBoxDerivatives  (-invvalue*Tensor(distance,distance));
     109           0 :   setValue           (value);
     110           0 : }
     111             : 
     112             : }
     113             : }
     114             : 
     115             : 
     116             :