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 "MultiColvarBase.h"
      23             : #include "AtomValuePack.h"
      24             : #include "tools/SwitchingFunction.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "vesselbase/LessThan.h"
      27             : #include "vesselbase/Between.h"
      28             : #include "tools/Angle.h"
      29             : 
      30             : #include <string>
      31             : #include <cmath>
      32             : 
      33             : using namespace std;
      34             : 
      35             : namespace PLMD {
      36             : namespace multicolvar {
      37             : 
      38             : //+PLUMEDOC MCOLVAR INPLANEDISTANCES
      39             : /*
      40             : Calculate distances in the plane perpendicular to an axis
      41             : 
      42             : Each quantity calculated in this CV uses the positions of two atoms, this indices of which are specified using the VECTORSTART and VECTOREND keywords, to specify the
      43             : orientation of a vector, \f$\mathbf{n}\f$.  The perpendicular distance between this vector and the position of some third atom is then computed using:
      44             : \f[
      45             :  x_j = |\mathbf{r}_{j}| \sin (\theta_j)
      46             : \f]
      47             : where \f$\mathbf{r}_j\f$ is the distance between one of the two atoms that define the vector \f$\mathbf{n}\f$ and a third atom (atom \f$j\f$) and where \f$\theta_j\f$
      48             : is the angle between the vector \f$\mathbf{n}\f$ and the vector \f$\mathbf{r}_{j}\f$.  The \f$x_j\f$ values for each of the atoms specified using the GROUP keyword are calculated.
      49             : Keywords such as MORE_THAN and LESS_THAN can then be used to calculate the number of these quantities that are more or less than a given cutoff.
      50             : 
      51             : \par Examples
      52             : 
      53             : The following input can be used to calculate the number of atoms that have indices greater than 3 and less than 101 that
      54             : are within a cylinder with a radius of 0.3 nm that has its long axis aligned with the vector connecting atoms 1 and 2.
      55             : 
      56             : \plumedfile
      57             : d1: INPLANEDISTANCES VECTORSTART=1 VECTOREND=2 GROUP=3-100 LESS_THAN={RATIONAL D_0=0.2 R_0=0.1}
      58             : PRINT ARG=d1.lessthan FILE=colvar
      59             : \endplumedfile
      60             : 
      61             : 
      62             : */
      63             : //+ENDPLUMEDOC
      64             : 
      65           0 : class InPlaneDistances : public MultiColvarBase {
      66             : public:
      67             :   static void registerKeywords( Keywords& keys );
      68             :   explicit InPlaneDistances(const ActionOptions&);
      69             : // active methods:
      70             :   virtual double compute(const unsigned& tindex, AtomValuePack& myatoms ) const ;
      71           0 :   bool isPeriodic() { return false; }
      72             : };
      73             : 
      74        7356 : PLUMED_REGISTER_ACTION(InPlaneDistances,"INPLANEDISTANCES")
      75             : 
      76           1 : void InPlaneDistances::registerKeywords( Keywords& keys ) {
      77           1 :   MultiColvarBase::registerKeywords( keys );
      78           4 :   keys.use("ALT_MIN"); keys.use("LOWEST"); keys.use("HIGHEST");
      79           5 :   keys.use("MEAN"); keys.use("MIN"); keys.use("MAX"); keys.use("LESS_THAN");
      80           5 :   keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
      81           4 :   keys.add("atoms","VECTORSTART","The first atom position that is used to define the normal to the plane of interest");
      82           4 :   keys.add("atoms","VECTOREND","The second atom position that is used to define the normal to the plane of interest");
      83           4 :   keys.add("atoms-2","GROUP","The set of atoms for which you wish to calculate the in plane distance ");
      84           1 : }
      85             : 
      86           0 : InPlaneDistances::InPlaneDistances(const ActionOptions&ao):
      87             :   Action(ao),
      88           0 :   MultiColvarBase(ao)
      89             : {
      90             :   // Read in the atoms
      91             :   std::vector<AtomNumber> all_atoms;
      92           0 :   readThreeGroups("GROUP","VECTORSTART","VECTOREND",false,false,all_atoms);
      93           0 :   setupMultiColvarBase( all_atoms );
      94             : 
      95             :   // Setup the multicolvar base
      96           0 :   setupMultiColvarBase( all_atoms ); readVesselKeywords();
      97             :   // Check atoms are OK
      98           0 :   if( getFullNumberOfTasks()!=getNumberOfAtoms()-2 ) error("you should specify one atom for VECTORSTART and one atom for VECTOREND only");
      99             :   // And check everything has been read in correctly
     100           0 :   checkRead();
     101             : 
     102             : // Now check if we can use link cells
     103           0 :   if( getNumberOfVessels()>0 ) {
     104             :     bool use_link=false; double rcut;
     105           0 :     vesselbase::LessThan* lt=dynamic_cast<vesselbase::LessThan*>( getPntrToVessel(0) );
     106           0 :     if( lt ) {
     107           0 :       use_link=true; rcut=lt->getCutoff();
     108             :     } else {
     109           0 :       vesselbase::Between* bt=dynamic_cast<vesselbase::Between*>( getPntrToVessel(0) );
     110           0 :       if( bt ) {
     111           0 :         use_link=true; rcut=bt->getCutoff();
     112             :       }
     113             :     }
     114             :     if( use_link ) {
     115           0 :       for(unsigned i=1; i<getNumberOfVessels(); ++i) {
     116           0 :         vesselbase::LessThan* lt2=dynamic_cast<vesselbase::LessThan*>( getPntrToVessel(i) );
     117           0 :         vesselbase::Between* bt=dynamic_cast<vesselbase::Between*>( getPntrToVessel(i) );
     118           0 :         if( lt2 ) {
     119           0 :           double tcut=lt2->getCutoff();
     120           0 :           if( tcut>rcut ) rcut=tcut;
     121           0 :         } else if( bt ) {
     122           0 :           double tcut=bt->getCutoff();
     123           0 :           if( tcut>rcut ) rcut=tcut;
     124             :         } else {
     125             :           use_link=false;
     126             :         }
     127             :       }
     128             :     }
     129           0 :     if( use_link ) setLinkCellCutoff( rcut );
     130             :   }
     131           0 : }
     132             : 
     133           0 : double InPlaneDistances::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
     134           0 :   Vector normal=getSeparation( myatoms.getPosition(1), myatoms.getPosition(2) );
     135           0 :   Vector dir=getSeparation( myatoms.getPosition(1), myatoms.getPosition(0) );
     136           0 :   PLMD::Angle a; Vector ddij, ddik; double angle=a.compute(normal,dir,ddij,ddik);
     137           0 :   double sangle=sin(angle), cangle=cos(angle);
     138           0 :   double dd=dir.modulo(), invdd=1.0/dd, val=dd*sangle;
     139             : 
     140           0 :   addAtomDerivatives( 1, 0, dd*cangle*ddik + sangle*invdd*dir, myatoms );
     141           0 :   addAtomDerivatives( 1, 1, -dd*cangle*(ddik+ddij) - sangle*invdd*dir, myatoms );
     142           0 :   addAtomDerivatives( 1, 2, dd*cangle*ddij, myatoms );
     143           0 :   myatoms.addBoxDerivatives( 1, -dd*cangle*(Tensor(normal,ddij)+Tensor(dir,ddik)) - sangle*invdd*Tensor(dir,dir) );
     144             : 
     145           0 :   return val;
     146             : }
     147             : 
     148             : }
     149        5517 : }