Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2017-2019 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 "OrientationSphere.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC MCOLVARF POLYMER_ANGLES
      26             : /*
      27             : Calculate a function to investigate the relative orientations of polymer angles
      28             : 
      29             : This CV takes the vectors calculated by a \ref PLANES action as input and computes the following function
      30             : of the relative angles, \f$\theta\f$, between the normals of pairs of input vectors:
      31             : 
      32             : \f[
      33             : s = \frac{ 3 \cos \theta - 1 }{ 2 }
      34             : \f]
      35             : 
      36             : This average of this quantity over all the vectors in the first coordination sphere around each of the PLANES specified
      37             : is then calculated.
      38             : 
      39             : \par Examples
      40             : 
      41             : The example below calculates a set of vectors using the \ref PLANES action.  The average number for the function \f$s\f$
      42             : defined above is then computed over the first coordination sphere of each of the centers of mass of the molecules that were
      43             : used to define the planes.  Finally the average of these quantities is computed an printed to a file.
      44             : 
      45             : \plumedfile
      46             : PLANES ...
      47             : MOL1=9,10,11
      48             : MOL2=89,90,91
      49             : MOL3=473,474,475
      50             : MOL4=1161,1162,1163
      51             : MOL5=1521,1522,1523
      52             : MOL6=1593,1594,1595
      53             : MOL7=1601,1602,1603
      54             : MOL8=2201,2202,2203
      55             : LABEL=m3
      56             : ... PLANES
      57             : 
      58             : s3: POLYMER_ANGLES SPECIES=m3 LOWMEM SWITCH={RATIONAL R_0=0.6} MEAN
      59             : PRINT ARG=s3.mean FILE=colvar
      60             : \endplumedfile
      61             : 
      62             : */
      63             : //+ENDPLUMEDOC
      64             : 
      65             : namespace PLMD {
      66             : namespace crystallization {
      67             : 
      68           2 : class PolymerAngles : public OrientationSphere {
      69             : public:
      70             :   static void registerKeywords( Keywords& keys );
      71             :   explicit PolymerAngles(const ActionOptions& ao);
      72             :   double computeVectorFunction( const Vector& conn, const std::vector<double>& vec1, const std::vector<double>& vec2,
      73             :                                 Vector& dconn, std::vector<double>& dvec1, std::vector<double>& dvec2 ) const ;
      74             : };
      75             : 
      76        6453 : PLUMED_REGISTER_ACTION(PolymerAngles,"POLYMER_ANGLES")
      77             : 
      78           2 : void PolymerAngles::registerKeywords( Keywords& keys ) {
      79           2 :   OrientationSphere::registerKeywords(keys);
      80           2 : }
      81             : 
      82           1 : PolymerAngles::PolymerAngles(const ActionOptions& ao):
      83             :   Action(ao),
      84           1 :   OrientationSphere(ao)
      85             : {
      86           1 :   if( mybasemulticolvars.size()==0 ) error("SMAC must take multicolvar as input");
      87           5 :   for(unsigned i=0; i<mybasemulticolvars.size(); ++i) {
      88           1 :     if( (mybasemulticolvars[i]->getNumberOfQuantities()-2)%3!=0 ) error("POLYMER_ANGLES is only possible with three dimensional vectors");
      89             :   }
      90           1 : }
      91             : 
      92         616 : double PolymerAngles::computeVectorFunction( const Vector& conn, const std::vector<double>& vec1, const std::vector<double>& vec2,
      93             :     Vector& dconn, std::vector<double>& dvec1, std::vector<double>& dvec2 ) const {
      94             : 
      95         616 :   plumed_assert( (vec1.size()-2)==3 );
      96        6160 :   double dot = 0; for(unsigned k=0; k<3; ++k) dot += vec1[2+k]*vec2[2+k];
      97        8008 :   double ans = 1.5*dot - 0.5; for(unsigned k=0; k<3; ++k) { dvec1[2+k]=1.5*vec2[2+k]; dvec2[2+k]=1.5*vec1[2+k]; }
      98         616 :   return ans;
      99             : }
     100             : 
     101             : }
     102        4839 : }