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 : #include "VolumeGradientBase.h"
23 : #include "CatomPack.h"
24 :
25 : namespace PLMD {
26 : namespace multicolvar {
27 :
28 35 : void VolumeGradientBase::registerKeywords( Keywords& keys ) {
29 35 : BridgedMultiColvarFunction::registerKeywords( keys );
30 35 : }
31 :
32 29 : VolumeGradientBase::VolumeGradientBase(const ActionOptions&ao):
33 : Action(ao),
34 29 : BridgedMultiColvarFunction(ao)
35 : {
36 29 : }
37 :
38 29 : void VolumeGradientBase::requestAtoms( const std::vector<AtomNumber>& atoms ) {
39 29 : ActionAtomistic::requestAtoms(atoms); bridgeVariable=3*atoms.size();
40 29 : addDependency( getPntrToMultiColvar() );
41 29 : tmpforces.resize( 3*atoms.size()+9 );
42 29 : }
43 :
44 2218 : void VolumeGradientBase::doJobsRequiredBeforeTaskList() {
45 2218 : ActionWithValue::clearDerivatives();
46 2218 : retrieveAtoms(); setupRegions();
47 2218 : ActionWithVessel::doJobsRequiredBeforeTaskList();
48 2218 : }
49 :
50 80527 : void VolumeGradientBase::completeTask( const unsigned& curr, MultiValue& invals, MultiValue& outvals ) const {
51 80527 : if( getPntrToMultiColvar()->isDensity() ) {
52 43404 : outvals.setValue(0, 1.0); outvals.setValue(1, 1.0);
53 : } else {
54 : // Copy derivatives of the colvar and the value of the colvar
55 37158 : invals.copyValues( outvals );
56 37162 : if( derivativesAreRequired() ) invals.copyDerivatives( outvals );
57 : }
58 80562 : calculateAllVolumes( curr, outvals );
59 80553 : }
60 :
61 115292 : void VolumeGradientBase::setNumberInVolume( const unsigned& ivol, const unsigned& curr, const double& weight,
62 : const Vector& wdf, const Tensor& virial, const std::vector<Vector>& refders,
63 : MultiValue& outvals ) const {
64 115292 : MultiColvarBase* mcolv=getPntrToMultiColvar();
65 115355 : if( !mcolv->weightHasDerivatives ) {
66 115355 : outvals.setValue(ivol, weight );
67 115356 : if( derivativesAreRequired() ) {
68 112284 : CatomPack catom( mcolv->getCentralAtomPack( 0, curr ) );
69 252569 : for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
70 140233 : unsigned jatom=3*catom.getIndex(i);
71 140294 : outvals.addDerivative( ivol, jatom+0, catom.getDerivative(i,0,wdf) );
72 140278 : outvals.addDerivative( ivol, jatom+1, catom.getDerivative(i,1,wdf) );
73 140324 : outvals.addDerivative( ivol, jatom+2, catom.getDerivative(i,2,wdf) );
74 : }
75 112339 : unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
76 112381 : for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, virial(i,j) );
77 229486 : for(unsigned i=0; i<refders.size(); ++i) {
78 117108 : unsigned iatom=nmder+3*i;
79 :
80 117108 : outvals.addDerivative( ivol, iatom+0, refders[i][0] );
81 117166 : outvals.addDerivative( ivol, iatom+1, refders[i][1] );
82 117186 : outvals.addDerivative( ivol, iatom+2, refders[i][2] );
83 112329 : }
84 : }
85 0 : } else if(ivol==0) {
86 0 : double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
87 0 : if( derivativesAreRequired() ) {
88 0 : plumed_merror("This needs testing");
89 : CatomPack catom( mcolv->getCentralAtomPack( 0, curr ) );
90 : for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
91 : unsigned jatom=3*catom.getIndex(i);
92 : outvals.addDerivative( ivol, jatom+0, weight*outvals.getDerivative(ivol,jatom+0) + ww*catom.getDerivative(i,0,wdf) );
93 : outvals.addDerivative( ivol, jatom+1, weight*outvals.getDerivative(ivol,jatom+1) + ww*catom.getDerivative(i,1,wdf) );
94 : outvals.addDerivative( ivol, jatom+2, weight*outvals.getDerivative(ivol,jatom+2) + ww*catom.getDerivative(i,2,wdf) );
95 : }
96 : unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
97 : for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );
98 : for(unsigned i=0; i<refders.size(); ++i) {
99 : unsigned iatom=nmder+3*i;
100 : outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
101 : outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
102 : outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
103 : }
104 : }
105 : } else {
106 0 : double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
107 0 : if( derivativesAreRequired() ) {
108 0 : plumed_merror("This needs testing");
109 : CatomPack catom( mcolv->getCentralAtomPack( 0, curr ) );
110 : for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
111 : unsigned jatom=3*catom.getIndex(i);
112 : outvals.addDerivative( ivol, jatom+0, ww*catom.getDerivative(i,0,wdf) );
113 : outvals.addDerivative( ivol, jatom+1, ww*catom.getDerivative(i,1,wdf) );
114 : outvals.addDerivative( ivol, jatom+2, ww*catom.getDerivative(i,2,wdf) );
115 : }
116 : unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
117 : for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );
118 : for(unsigned i=0; i<refders.size(); ++i) {
119 : unsigned iatom=nmder+3*i;
120 : outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
121 : outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
122 : outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
123 : }
124 : }
125 : }
126 115353 : }
127 :
128 0 : void VolumeGradientBase::addBridgeForces( const std::vector<double>& bb ) {
129 : plumed_dbg_assert( bb.size()==tmpforces.size()-9 );
130 : // Forces on local atoms
131 0 : for(unsigned i=0; i<bb.size(); ++i) tmpforces[i]=bb[i];
132 : // Virial contribution is zero
133 0 : for(unsigned i=bb.size(); i<bb.size()+9; ++i) tmpforces[i]=0.0;
134 0 : setForcesOnAtoms( tmpforces, 0 );
135 0 : }
136 :
137 : }
138 2523 : }
|
