Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2018 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 "RMSDBase.h"
23 : #include "MetricRegister.h"
24 : #include "tools/RMSD.h"
25 :
26 : namespace PLMD {
27 :
28 58 : class SimpleRMSD : public RMSDBase {
29 : private:
30 : RMSD myrmsd;
31 : public:
32 : explicit SimpleRMSD( const ReferenceConfigurationOptions& ro );
33 : void read( const PDB& );
34 : double calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const ;
35 3 : bool pcaIsEnabledForThisReference() { return true; }
36 67 : void setupPCAStorage( ReferenceValuePack& mypack ) {
37 67 : mypack.switchOnPCAOption(); mypack.getAtomsDisplacementVector().resize( getNumberOfAtoms() );
38 67 : }
39 : double projectAtomicDisplacementOnVector( const unsigned& iv, const Matrix<Vector>& vecs, const std::vector<Vector>& pos, ReferenceValuePack& mypack ) const ;
40 : };
41 :
42 2552 : PLUMED_REGISTER_METRIC(SimpleRMSD,"SIMPLE")
43 :
44 29 : SimpleRMSD::SimpleRMSD( const ReferenceConfigurationOptions& ro ):
45 : ReferenceConfiguration( ro ),
46 29 : RMSDBase( ro )
47 : {
48 29 : }
49 :
50 23 : void SimpleRMSD::read( const PDB& pdb ) {
51 23 : readReference( pdb );
52 23 : }
53 :
54 148 : double SimpleRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const {
55 148 : if( myder.getAtomsDisplacementVector().size()!=pos.size() ) myder.getAtomsDisplacementVector().resize( pos.size() );
56 148 : double d=myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), myder.getAtomVector(), myder.getAtomsDisplacementVector(), squared );
57 148 : myder.clear(); for(unsigned i=0; i<pos.size(); ++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );
58 148 : if( !myder.updateComplete() ) myder.updateDynamicLists();
59 148 : return d;
60 : }
61 :
62 66 : double SimpleRMSD::projectAtomicDisplacementOnVector( const unsigned& iv, const Matrix<Vector>& vecs, const std::vector<Vector>& pos, ReferenceValuePack& mypack ) const {
63 66 : plumed_dbg_assert( mypack.calcUsingPCAOption() ); Vector comder; comder.zero();
64 374 : for(unsigned j=0; j<pos.size(); ++j) {
65 308 : for(unsigned k=0; k<3; ++k) comder[k] += getAlign()[j]*vecs(iv,j)[k];
66 : }
67 :
68 66 : double proj=0; mypack.clear();
69 374 : for(unsigned j=0; j<pos.size(); ++j) {
70 1232 : for(unsigned k=0; k<3; ++k) {
71 924 : proj += vecs(iv,j)[k]*mypack.getAtomsDisplacementVector()[j][k];
72 : }
73 308 : mypack.setAtomDerivatives( j, vecs(iv,j) - comder );
74 : }
75 66 : if( !mypack.updateComplete() ) mypack.updateDynamicLists();
76 66 : return proj;
77 : }
78 :
79 2523 : }
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