Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2023 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 "DistanceFromContourBase.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC COLVAR DISTANCE_FROM_SPHERICAL_CONTOUR
      26             : /*
      27             : Calculate the perpendicular distance from a Willard-Chandler dividing surface.
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace contour {
      36             : 
      37             : class DistanceFromSphericalContour : public DistanceFromContourBase {
      38             : public:
      39             :   static void registerKeywords( Keywords& keys );
      40             :   explicit DistanceFromSphericalContour( const ActionOptions& );
      41             :   void calculate();
      42             :   void evaluateDerivatives( const Vector& root1, const double& root2 );
      43             : };
      44             : 
      45             : PLUMED_REGISTER_ACTION(DistanceFromSphericalContour,"DISTANCE_FROM_SPHERICAL_CONTOUR")
      46             : 
      47           3 : void DistanceFromSphericalContour::registerKeywords( Keywords& keys ) {
      48           3 :   DistanceFromContourBase::registerKeywords( keys );
      49           6 :   keys.addOutputComponent("dist","default","the distance between the reference atom and the nearest contour");
      50           6 :   keys.addOutputComponent("radius","default","the radial distance from the center of the contour to the edge");
      51           6 :   keys.add("atoms","ORIGIN","The position of the center of the region that the contour encloses");
      52           3 : }
      53             : 
      54           1 : DistanceFromSphericalContour::DistanceFromSphericalContour( const ActionOptions& ao ):
      55             :   Action(ao),
      56           1 :   DistanceFromContourBase(ao)
      57             : {
      58             :   // Create the values
      59             :   std::vector<unsigned> shape;
      60           2 :   addComponentWithDerivatives("dist", shape ); componentIsNotPeriodic("dist");
      61           3 :   addComponent("radius", shape ); componentIsNotPeriodic("radius");
      62           1 : }
      63             : 
      64          17 : void DistanceFromSphericalContour::calculate() {
      65             :   // Check box is orthorhombic
      66          17 :   if( !getPbc().isOrthorombic() ) error("cell box must be orthorhombic");
      67             : 
      68             :   // Calculate the director of the vector connecting the center of the sphere to the molecule of interest
      69          17 :   Vector dirv = pbcDistance( getPosition(getNumberOfAtoms()-1), getPosition(getNumberOfAtoms()-2) );
      70          17 :   double len=dirv.modulo(); dirv /= len;
      71             :   // Now work out which atoms need to be considered explicitly
      72          17 :   Vector myvec = pbcDistance( getPosition(getNumberOfAtoms()-1), getPosition(0) );
      73          17 :   nactive=1; active_list[0]=0;
      74        8704 :   for(unsigned j=1; j<getNumberOfAtoms()-2; ++j) {
      75        8687 :     if( getNumberOfArguments()==1 ) {
      76        8687 :       if( getPntrToArgument(0)->get(j)<epsilon ) continue;
      77             :     }
      78        6698 :     active_list[nactive]=j; nactive++;
      79        6698 :     Vector distance=pbcDistance( getPosition(getNumberOfAtoms()-1), getPosition(j) );
      80        6698 :     double dp = dotProduct( distance, dirv ); double cp = distance.modulo2() - dp*dp;
      81        6698 :     if( cp<rcut2 ) { active_list[nactive]=j; nactive++; }
      82             :   }
      83             :   // Get maximum length to fit in box
      84          17 :   double hbox = 0.5*getBox()(0,0);
      85          17 :   if( 0.5*getBox()(1,1)<hbox ) hbox = 0.5*getBox()(1,1);
      86          17 :   if( 0.5*getBox()(2,2)<hbox ) hbox = 0.5*getBox()(2,2);
      87             :   // Set initial guess for position of contour to position of closest molecule in region
      88          17 :   std::vector<double> pos1(3), dirv2(3);
      89          68 :   for(unsigned k=0; k<3; ++k) { dirv2[k]=hbox*dirv[k]; pos1[k]=0; }
      90             :   // Now do a search for the contours
      91             :   findContour( dirv2, pos1 );
      92             :   // Now find the distance between the center of the sphere and the contour
      93          17 :   double rad = sqrt( pos1[0]*pos1[0] + pos1[1]*pos1[1] + pos1[2]*pos1[2] );
      94             :   // Set the radius
      95          17 :   getPntrToComponent("radius")->set( rad );
      96             :   // Set the distance between the contour and the molecule
      97          17 :   getPntrToComponent("dist")->set( len - rad );
      98             : 
      99             :   // Now calculate the derivatives
     100          17 :   if( !doNotCalculateDerivatives() ) plumed_merror("derivatives not implemented");
     101          17 : }
     102             : 
     103           0 : void DistanceFromSphericalContour::evaluateDerivatives( const Vector& root1, const double& root2 ) {
     104           0 :   plumed_error();
     105             : }
     106             : 
     107             : }
     108             : }