Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2020 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 "MultiColvarBase.h"
      23             : #include "AtomValuePack.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : #include <string>
      27             : #include <cmath>
      28             : 
      29             : using namespace std;
      30             : 
      31             : namespace PLMD {
      32             : namespace multicolvar {
      33             : 
      34             : //+PLUMEDOC MCOLVAR DENSITY
      35             : /*
      36             : Calculate functions of the density of atoms as a function of the box.  This allows one to calculate
      37             :  the number of atoms in half the box.
      38             : 
      39             : \par Examples
      40             : 
      41             : The following example calculates the number of atoms in one half of the simulation box.
      42             : 
      43             : \plumedfile
      44             : DENSITY SPECIES=1-100 LABEL=d
      45             : AROUND ATOM=101 DATA=d SIGMA=0.1 XLOWER=0.0 XUPPER=0.5 LABEL=d1
      46             : PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f
      47             : \endplumedfile
      48             : 
      49             : */
      50             : //+ENDPLUMEDOC
      51             : 
      52             : 
      53          22 : class Density : public MultiColvarBase {
      54             : public:
      55             :   static void registerKeywords( Keywords& keys );
      56             :   explicit Density(const ActionOptions&);
      57             : // active methods:
      58             :   virtual double compute( const unsigned& tindex, AtomValuePack& myatoms ) const ;
      59             :   /// Returns the number of coordinates of the field
      60           4 :   bool isPeriodic() { return false; }
      61      200687 :   bool isDensity() const { return true; }
      62           0 :   bool hasDifferentiableOrientation() const { return true; }
      63             : //  void addOrientationDerivativesToBase( const unsigned& iatom, const unsigned& jstore, const unsigned& base_cv_no,
      64             : //                                        const std::vector<double>& weight, MultiColvarFunction* func ){}
      65             :   void getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices );
      66             : //  unsigned getNumberOfQuantities();
      67             :   void getValueForTask( const unsigned& iatom, std::vector<double>& vals );
      68             : };
      69             : 
      70        7378 : PLUMED_REGISTER_ACTION(Density,"DENSITY")
      71             : 
      72          12 : void Density::registerKeywords( Keywords& keys ) {
      73          12 :   MultiColvarBase::registerKeywords( keys );
      74          24 :   keys.use("SPECIES");
      75          12 : }
      76             : 
      77          11 : Density::Density(const ActionOptions&ao):
      78             :   Action(ao),
      79          11 :   MultiColvarBase(ao)
      80             : {
      81          22 :   std::vector<AtomNumber> all_atoms; parseMultiColvarAtomList("SPECIES", -1, all_atoms);
      82          22 :   ablocks.resize(1); ablocks[0].resize( atom_lab.size() );
      83         978 :   for(unsigned i=0; i<atom_lab.size(); ++i) { addTaskToList(i); ablocks[0][i]=i; }
      84          11 :   setupMultiColvarBase( all_atoms );
      85             :   // And check everything has been read in correctly
      86          11 :   checkRead();
      87          11 : }
      88             : 
      89       15950 : double Density::compute( const unsigned& tindex, AtomValuePack& myvals ) const {
      90       15950 :   return 1.0;
      91             : }
      92             : 
      93           0 : void Density::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ) {
      94           0 :   indices[jstore]=0;
      95           0 : }
      96             : 
      97             : // unsigned Density::getNumberOfQuantities(){
      98             : //    return 2;
      99             : // }
     100             : 
     101           0 : void Density::getValueForTask( const unsigned& iatom, std::vector<double>& vals ) {
     102           0 :   plumed_dbg_assert( vals.size()==2 ); vals[0]=vals[1]=1.0;
     103           0 : }
     104             : 
     105             : }
     106        5517 : }
     107             :