Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2018 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 : #ifndef __PLUMED_multicolvar_AtomValuePack_h
23 : #define __PLUMED_multicolvar_AtomValuePack_h
24 :
25 : #include "tools/MultiValue.h"
26 : #include "MultiColvarBase.h"
27 :
28 : namespace PLMD {
29 :
30 : class LinkCells;
31 :
32 : namespace multicolvar {
33 :
34 : class CatomPack;
35 :
36 : class AtomValuePack {
37 : friend class MultiColvarBase;
38 : friend class LocalAverage;
39 : private:
40 : /// Copy of the values that we are adding to
41 : MultiValue& myvals;
42 : /// Copy of the underlying multicolvar
43 : MultiColvarBase const * mycolv;
44 : /// Number of atoms at the moment
45 : unsigned natoms;
46 : /// Atom indices
47 : std::vector<unsigned>& indices;
48 : /// This is used to sort the atom indices
49 : std::vector<unsigned>& sort_vector;
50 : /// This holds atom positions
51 : std::vector<Vector>& myatoms;
52 : ///
53 : void addDerivative( const unsigned&, const unsigned&, const double& );
54 : ///
55 : void addAtomsDerivatives( const unsigned&, const unsigned&, const Vector& );
56 : ///
57 : void addTemporyAtomsDerivatives( const unsigned& jder, const Vector& der );
58 : public:
59 : AtomValuePack( MultiValue& vals, MultiColvarBase const * mcolv );
60 : /// Set the number of atoms
61 : void setNumberOfAtoms( const unsigned& );
62 : /// Set the index for one of the atoms
63 : void setIndex( const unsigned&, const unsigned& );
64 : ///
65 : void setAtomIndex( const unsigned& j, const unsigned& ind );
66 : ///
67 : void setAtom( const unsigned& j, const unsigned& ind );
68 : ///
69 : unsigned setupAtomsFromLinkCells( const std::vector<unsigned>& cind, const Vector& cpos, const LinkCells& linkcells );
70 : ///
71 : unsigned getIndex( const unsigned& j ) const ;
72 : ///
73 : unsigned getNumberOfAtoms() const ;
74 : ///
75 : unsigned getNumberOfDerivatives() const ;
76 : /// Get the position of the ith atom
77 : Vector& getPosition( const unsigned& );
78 : ///
79 : void setValue( const unsigned&, const double& );
80 : ///
81 : void addValue( const unsigned& ival, const double& vv );
82 : ///
83 : double getValue( const unsigned& ) const ;
84 : ///
85 : void addBoxDerivatives( const unsigned&, const Tensor& );
86 : ///
87 : void addTemporyBoxDerivatives( const Tensor& vir );
88 : ///
89 : void updateUsingIndices();
90 : ///
91 : void updateDynamicList();
92 : ///
93 : void addComDerivatives( const int&, const Vector&, CatomPack& );
94 : ///
95 : MultiValue& getUnderlyingMultiValue();
96 : };
97 :
98 : inline
99 232072 : void AtomValuePack::setNumberOfAtoms( const unsigned& nat ) {
100 232072 : natoms=nat;
101 232072 : }
102 :
103 : inline
104 13120755 : unsigned AtomValuePack::getNumberOfAtoms() const {
105 13120755 : return natoms;
106 : }
107 :
108 : inline
109 100 : unsigned AtomValuePack::getNumberOfDerivatives() const {
110 100 : return myvals.getNumberOfDerivatives();
111 : }
112 :
113 : inline
114 : void AtomValuePack::setIndex( const unsigned& j, const unsigned& ind ) {
115 : plumed_dbg_assert( j<natoms ); indices[j]=ind;
116 : }
117 :
118 : inline
119 580194 : void AtomValuePack::setAtomIndex( const unsigned& j, const unsigned& ind ) {
120 580194 : plumed_dbg_assert( j<natoms ); indices[j]=ind;
121 580364 : }
122 :
123 : inline
124 554528 : void AtomValuePack::setAtom( const unsigned& j, const unsigned& ind ) {
125 554528 : setAtomIndex( j, ind ); myatoms[j]=mycolv->getPositionOfAtomForLinkCells( ind );
126 554833 : }
127 :
128 : inline
129 125825812 : unsigned AtomValuePack::getIndex( const unsigned& j ) const {
130 125825812 : plumed_dbg_assert( j<natoms ); return indices[j];
131 : }
132 :
133 : inline
134 15951473 : Vector& AtomValuePack::getPosition( const unsigned& iatom ) {
135 : plumed_dbg_assert( iatom<natoms );
136 15951473 : return myatoms[iatom];
137 : }
138 :
139 : inline
140 642539 : void AtomValuePack::setValue( const unsigned& ival, const double& vv ) {
141 642539 : myvals.setValue( ival, vv );
142 642689 : }
143 :
144 : inline
145 56323659 : void AtomValuePack::addValue( const unsigned& ival, const double& vv ) {
146 56323659 : myvals.addValue( ival, vv );
147 56323065 : }
148 :
149 : inline
150 4642757 : double AtomValuePack::getValue( const unsigned& ival ) const {
151 4642757 : return myvals.get( ival );
152 : }
153 :
154 : inline
155 60782592 : void AtomValuePack::addDerivative( const unsigned& ival, const unsigned& jder, const double& der ) {
156 60782592 : myvals.addDerivative( ival, jder, der );
157 60782592 : }
158 :
159 : inline
160 101655360 : void AtomValuePack::addAtomsDerivatives( const unsigned& ival, const unsigned& jder, const Vector& der ) {
161 : plumed_dbg_assert( jder<natoms );
162 101655360 : myvals.addDerivative( ival, 3*indices[jder] + 0, der[0] );
163 101658279 : myvals.addDerivative( ival, 3*indices[jder] + 1, der[1] );
164 101657005 : myvals.addDerivative( ival, 3*indices[jder] + 2, der[2] );
165 101656581 : }
166 :
167 : inline
168 4371940 : void AtomValuePack::addTemporyAtomsDerivatives( const unsigned& jder, const Vector& der ) {
169 : plumed_dbg_assert( jder<natoms );
170 4371940 : myvals.addTemporyDerivative( 3*indices[jder] + 0, der[0] );
171 4371976 : myvals.addTemporyDerivative( 3*indices[jder] + 1, der[1] );
172 4371976 : myvals.addTemporyDerivative( 3*indices[jder] + 2, der[2] );
173 4371978 : }
174 :
175 : inline
176 2203667 : void AtomValuePack::addTemporyBoxDerivatives( const Tensor& vir ) {
177 2203667 : unsigned nvir=3*mycolv->getNumberOfAtoms();
178 2203666 : for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) myvals.addTemporyDerivative( nvir + 3*i+j, vir(i,j) );
179 2203669 : }
180 :
181 : inline
182 50912166 : void AtomValuePack::addBoxDerivatives( const unsigned& ival, const Tensor& vir ) {
183 50912166 : unsigned nvir=3*mycolv->getNumberOfAtoms();
184 50908210 : for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) myvals.addDerivative( ival, nvir + 3*i+j, vir(i,j) );
185 50911351 : }
186 :
187 : inline
188 137920 : void AtomValuePack::updateDynamicList() {
189 275840 : if( myvals.updateComplete() ) return;
190 137483 : myvals.updateDynamicList();
191 : }
192 :
193 : inline
194 4453822 : MultiValue& AtomValuePack::getUnderlyingMultiValue() {
195 4453822 : return myvals;
196 : }
197 :
198 : }
199 : }
200 : #endif
201 :
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