Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2019 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 "ActionRegister.h"
      24             : 
      25             : #include <string>
      26             : #include <cmath>
      27             : 
      28             : using namespace std;
      29             : 
      30             : namespace PLMD {
      31             : namespace colvar {
      32             : 
      33             : //+PLUMEDOC COLVAR TEMPLATE
      34             : /*
      35             : This file provides a template for if you want to introduce a new CV.
      36             : 
      37             : <!-----You should add a description of your CV here---->
      38             : 
      39             : \par Examples
      40             : 
      41             : <!---You should put an example of how to use your CV here--->
      42             : 
      43             : \plumedfile
      44             : # This should be a sample input.
      45             : t: TEMPLATE ATOMS=1,2
      46             : PRINT ARG=t STRIDE=100 FILE=COLVAR
      47             : \endplumedfile
      48             : <!---You should reference here the other actions used in this example--->
      49             : (see also \ref PRINT)
      50             : 
      51             : */
      52             : //+ENDPLUMEDOC
      53             : 
      54           0 : class Template : public Colvar {
      55             :   bool pbc;
      56             : 
      57             : public:
      58             :   explicit Template(const ActionOptions&);
      59             : // active methods:
      60             :   virtual void calculate();
      61             :   static void registerKeywords(Keywords& keys);
      62             : };
      63             : 
      64        6452 : PLUMED_REGISTER_ACTION(Template,"TEMPLATE")
      65             : 
      66           1 : void Template::registerKeywords(Keywords& keys) {
      67           1 :   Colvar::registerKeywords(keys);
      68           3 :   keys.addFlag("TEMPLATE_DEFAULT_OFF_FLAG",false,"flags that are by default not performed should be specified like this");
      69           3 :   keys.addFlag("TEMPLATE_DEFAULT_ON_FLAG",true,"flags that are by default performed should be specified like this");
      70           4 :   keys.add("compulsory","TEMPLATE_COMPULSORY","all compulsory keywords should be added like this with a description here");
      71           4 :   keys.add("optional","TEMPLATE_OPTIONAL","all optional keywords that have input should be added like a description here");
      72           4 :   keys.add("atoms","ATOMS","the keyword with which you specify what atoms to use should be added like this");
      73           1 : }
      74             : 
      75           0 : Template::Template(const ActionOptions&ao):
      76             :   PLUMED_COLVAR_INIT(ao),
      77           0 :   pbc(true)
      78             : {
      79             :   vector<AtomNumber> atoms;
      80           0 :   parseAtomList("ATOMS",atoms);
      81           0 :   if(atoms.size()!=2)
      82           0 :     error("Number of specified atoms should be 2");
      83           0 :   bool nopbc=!pbc;
      84           0 :   parseFlag("NOPBC",nopbc);
      85           0 :   pbc=!nopbc;
      86           0 :   checkRead();
      87             : 
      88           0 :   log.printf("  between atoms %d %d\n",atoms[0].serial(),atoms[1].serial());
      89           0 :   if(pbc) log.printf("  using periodic boundary conditions\n");
      90           0 :   else    log.printf("  without periodic boundary conditions\n");
      91             : 
      92           0 :   addValueWithDerivatives(); setNotPeriodic();
      93             : 
      94           0 :   requestAtoms(atoms);
      95           0 : }
      96             : 
      97             : 
      98             : // calculator
      99           0 : void Template::calculate() {
     100             : 
     101           0 :   Vector distance;
     102           0 :   if(pbc) {
     103           0 :     distance=pbcDistance(getPosition(0),getPosition(1));
     104             :   } else {
     105           0 :     distance=delta(getPosition(0),getPosition(1));
     106             :   }
     107           0 :   const double value=distance.modulo();
     108           0 :   const double invvalue=1.0/value;
     109             : 
     110           0 :   setAtomsDerivatives(0,-invvalue*distance);
     111           0 :   setAtomsDerivatives(1,invvalue*distance);
     112           0 :   setBoxDerivatives  (-invvalue*Tensor(distance,distance));
     113           0 :   setValue           (value);
     114           0 : }
     115             : 
     116             : }
     117        4839 : }
     118             : 
     119             : 
     120             :