Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2020 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 "core/ActionRegister.h"
      23             : #include "tools/Pbc.h"
      24             : #include "tools/SwitchingFunction.h"
      25             : #include "ActionVolume.h"
      26             : #include "VolumeShortcut.h"
      27             : 
      28             : //+PLUMEDOC VOLUMES INSPHERE
      29             : /*
      30             : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.
      31             : 
      32             : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
      33             : dimensional space. For example, if we have the coordination numbers for all the atoms in the
      34             : system each coordination number can be assumed to lie on the position of the central atom.
      35             : Because each base quantity can be assigned to a particular point in space we can calculate functions of the
      36             : distribution of base quantities in a particular part of the box by using:
      37             : 
      38             : \f[
      39             : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) \sigma(r) }{ \sum_i \sigma(r) }
      40             : \f]
      41             : 
      42             : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (x_i,y_i,z_i)\f$.
      43             : The function \f$\sigma\f$ is a \ref switchingfunction that acts on the distance between the point at which the
      44             : collective is located \f$(x_i,y_i,z_i)\f$ and the position of the atom that was specified using the ORIGIN keyword.
      45             : In other words:
      46             : \f[
      47             : r = sqrt{ ( x_i - x_0)^2 + ( y_i - y_0)^2 + ( z_i - z_0)^2}
      48             : \f]
      49             : In short this function, \f$\sigma(r_{xy})\f$, measures whether or not the CV is within a sphere that is
      50             : centered on the position of the atom specified using the keyword ORIGIN.
      51             : 
      52             : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.
      53             : 
      54             : When INCYLINDER is used with the \ref DENSITY action the number of atoms in the specified region is calculated
      55             : 
      56             : \par Examples
      57             : 
      58             : The input below can be use to calculate the average coordination numbers for those atoms that are within a sphere
      59             : of radius 1.5 nm that is centered on the position of atom 101.
      60             : 
      61             : \plumedfile
      62             : c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
      63             : d2: INSPHERE ATOM=101 DATA=c1 RADIUS={TANH R_0=1.5} MEAN
      64             : PRINT ARG=d2.* FILE=colvar
      65             : \endplumedfile
      66             : 
      67             : */
      68             : //+ENDPLUMEDOC
      69             : 
      70             : //+PLUMEDOC MCOLVAR INSPHERE_CALC
      71             : /*
      72             : Calculate a vector from the input positions with elements equal to one when the positions are in a particular part of the cell and elements equal to zero otherwise
      73             : 
      74             : \par Examples
      75             : 
      76             : */
      77             : //+ENDPLUMEDOC
      78             : 
      79             : namespace PLMD {
      80             : namespace volumes {
      81             : 
      82             : class VolumeInSphere : public ActionVolume {
      83             : private:
      84             :   Vector origin;
      85             :   SwitchingFunction switchingFunction;
      86             : public:
      87             :   static void registerKeywords( Keywords& keys );
      88             :   explicit VolumeInSphere(const ActionOptions& ao);
      89             :   void setupRegions() override;
      90             :   double calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const override;
      91             : };
      92             : 
      93             : PLUMED_REGISTER_ACTION(VolumeInSphere,"INSPHERE_CALC")
      94             : char glob_sphere[] = "INSPHERE";
      95             : typedef VolumeShortcut<glob_sphere> VolumeInSphereShortcut;
      96             : PLUMED_REGISTER_ACTION(VolumeInSphereShortcut,"INSPHERE")
      97             : 
      98          36 : void VolumeInSphere::registerKeywords( Keywords& keys ) {
      99          36 :   ActionVolume::registerKeywords( keys ); keys.setDisplayName("INSPHERE");
     100          72 :   keys.add("atoms","CENTER","the atom whose vicinity we are interested in examining");
     101          72 :   keys.add("atoms-2","ATOM","the atom whose vicinity we are interested in examining");
     102          72 :   keys.add("compulsory","RADIUS","the switching function that tells us the extent of the sphereical region of interest");
     103          36 :   keys.remove("SIGMA");
     104          36 : }
     105             : 
     106          10 : VolumeInSphere::VolumeInSphere(const ActionOptions& ao):
     107             :   Action(ao),
     108          10 :   ActionVolume(ao)
     109             : {
     110          20 :   std::vector<AtomNumber> atom; parseAtomList("CENTER",atom);
     111          10 :   if( atom.size()==0 ) parseAtomList("ATOM",atom);
     112          10 :   if( atom.size()!=1 ) error("should only be one atom specified");
     113          10 :   log.printf("  center of sphere is at position of atom : %d\n",atom[0].serial() );
     114             : 
     115          20 :   std::string sw, errors; parse("RADIUS",sw);
     116          10 :   if(sw.length()==0) error("missing RADIUS keyword");
     117          10 :   switchingFunction.set(sw,errors);
     118          10 :   if( errors.length()!=0 ) error("problem reading RADIUS keyword : " + errors );
     119          10 :   log.printf("  radius of sphere is given by %s \n", ( switchingFunction.description() ).c_str() );
     120             : 
     121          10 :   checkRead(); requestAtoms(atom);
     122          10 : }
     123             : 
     124         120 : void VolumeInSphere::setupRegions() { }
     125             : 
     126      423194 : double VolumeInSphere::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const {
     127             :   // Calculate position of atom wrt to origin
     128      423194 :   Vector fpos=pbcDistance( getPosition(0), cpos );
     129      423194 :   double dfunc, value = switchingFunction.calculateSqr( fpos.modulo2(), dfunc );
     130      423194 :   derivatives.zero(); derivatives = dfunc*fpos; refders[0] = -derivatives;
     131             :   // Add a virial contribution
     132      423194 :   vir -= Tensor(fpos,derivatives);
     133      423194 :   return value;
     134             : }
     135             : 
     136             : }
     137             : }