Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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 "SingleDomainRMSD.h"
      23             : #include "tools/PDB.h"
      24             : #include "DRMSD.h"
      25             : 
      26             : namespace PLMD {
      27             : 
      28         527 : SingleDomainRMSD::SingleDomainRMSD( const ReferenceConfigurationOptions& ro ):
      29             :   ReferenceConfiguration(ro),
      30         527 :   ReferenceAtoms(ro) {
      31         527 : }
      32             : 
      33         458 : void SingleDomainRMSD::readReference( const PDB& pdb ) {
      34         458 :   readAtomsFromPDB( pdb );
      35             :   double wa=0, wd=0;
      36        9071 :   for(unsigned i=0; i<pdb.size(); ++i) {
      37        8613 :     wa+=align[i];
      38        8613 :     wd+=displace[i];
      39             :   }
      40             : 
      41         458 :   if(wa>epsilon) {
      42         456 :     double w=1.0/wa;
      43        9039 :     for(unsigned i=0; i<pdb.size(); ++i) {
      44        8583 :       align[i] *= w;
      45             :     }
      46             :   } else {
      47           2 :     double w=1.0/pdb.size();
      48          32 :     for(unsigned i=0; i<pdb.size(); ++i) {
      49          30 :       align[i] = w;
      50             :     }
      51             :   }
      52             : 
      53         458 :   if(wd>epsilon) {
      54         456 :     double w=1.0/wd;
      55        9039 :     for(unsigned i=0; i<pdb.size(); ++i) {
      56        8583 :       displace[i] *= w;
      57             :     }
      58             :   } else {
      59           2 :     double w=1.0/pdb.size();
      60          32 :     for(unsigned i=0; i<pdb.size(); ++i) {
      61          30 :       displace[i] = w;
      62             :     }
      63             :   }
      64             : 
      65         458 :   Vector center;
      66        9071 :   for(unsigned i=0; i<pdb.size(); ++i) {
      67        8613 :     center+=reference_atoms[i]*align[i];
      68             :   }
      69        9071 :   for(unsigned i=0; i<pdb.size(); ++i) {
      70        8613 :     reference_atoms[i]-=center;
      71             :   }
      72         458 : }
      73             : 
      74          72 : void SingleDomainRMSD::setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in ) {
      75          72 :   reference_atoms.resize( conf.size() );
      76          72 :   align.resize( conf.size() );
      77          72 :   displace.resize( conf.size() );
      78          72 :   atom_der_index.resize( conf.size() );
      79             :   double wa=0, wd=0;
      80        1991 :   for(unsigned i=0; i<conf.size(); ++i) {
      81        1919 :     wa+=align_in[i];
      82        1919 :     wd+=displace_in[i];
      83             :   }
      84             : 
      85          72 :   if(wa>epsilon) {
      86          71 :     double w=1.0/wa;
      87        1982 :     for(unsigned i=0; i<conf.size(); ++i) {
      88        1911 :       align[i] = align_in[i] * w;
      89             :     }
      90             :   } else {
      91           1 :     double w=1.0/conf.size();
      92           9 :     for(unsigned i=0; i<conf.size(); ++i) {
      93           8 :       align[i] = w;
      94             :     }
      95             :   }
      96             : 
      97          72 :   if(wd>epsilon) {
      98          71 :     double w=1.0/wd;
      99        1983 :     for(unsigned i=0; i<conf.size(); ++i) {
     100        1912 :       displace[i] = displace_in[i] * w;
     101             :     }
     102             :   } else {
     103           1 :     double w=1.0/conf.size();
     104           8 :     for(unsigned i=0; i<conf.size(); ++i) {
     105           7 :       displace[i] = w;
     106             :     }
     107             :   }
     108             : 
     109          72 :   Vector center;
     110        1991 :   for(unsigned i=0; i<conf.size(); ++i) {
     111        1919 :     center+=conf[i]*align[i];
     112        1919 :     atom_der_index[i]=i;
     113             :   }
     114        1991 :   for(unsigned i=0; i<conf.size(); ++i) {
     115        1919 :     reference_atoms[i]=conf[i]-center;
     116             :   }
     117          72 :   setupRMSDObject();
     118          72 : }
     119             : 
     120      130838 : double SingleDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
     121      130838 :   return calc( pos, pbc, myder, squared );
     122             : }
     123             : 
     124      140941 : double SingleDomainRMSD::calc( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals, const std::vector<double>& arg,
     125             :                                ReferenceValuePack& myder, const bool& squared ) const {
     126             :   plumed_dbg_assert( vals.size()==0 && pos.size()==getNumberOfAtoms() && arg.size()==0 );
     127      140941 :   return calc( pos, pbc, myder, squared );
     128             : }
     129             : 
     130             : }