Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2019 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 "VolumeGradientBase.h"
23 : #include "core/PlumedMain.h"
24 : #include "core/ActionSet.h"
25 : #include "CatomPack.h"
26 :
27 : namespace PLMD {
28 : namespace multicolvar {
29 :
30 37 : void VolumeGradientBase::registerKeywords( Keywords& keys ) {
31 37 : BridgedMultiColvarFunction::registerKeywords( keys );
32 37 : }
33 :
34 30 : VolumeGradientBase::VolumeGradientBase(const ActionOptions&ao):
35 : Action(ao),
36 30 : BridgedMultiColvarFunction(ao)
37 : {
38 30 : }
39 :
40 30 : void VolumeGradientBase::requestAtoms( const std::vector<AtomNumber>& atoms ) {
41 60 : ActionAtomistic::requestAtoms(atoms); bridgeVariable=3*atoms.size();
42 : std::map<std::string,bool> checklabs;
43 66 : for(const auto & p : getDependencies() ) checklabs.insert(std::pair<std::string,bool>(p->getLabel(),false));
44 132 : for(const auto & p : plumed.getActionSet() ) {
45 306 : if( p->getLabel()==getPntrToMultiColvar()->getLabel() ) break;
46 6 : if( checklabs.count(p->getLabel()) ) checklabs[p->getLabel()]=true;
47 : }
48 33 : for(const auto & p : checklabs ) {
49 3 : if( !p.second ) error("the input for the virtual atoms used in the input for this action must appear in the input file before the input multicolvar");
50 : }
51 60 : addDependency( getPntrToMultiColvar() );
52 60 : tmpforces.resize( 3*atoms.size()+9 );
53 30 : }
54 :
55 2239 : void VolumeGradientBase::doJobsRequiredBeforeTaskList() {
56 2239 : ActionWithValue::clearDerivatives();
57 2239 : retrieveAtoms(); setupRegions();
58 2239 : ActionWithVessel::doJobsRequiredBeforeTaskList();
59 2239 : }
60 :
61 80958 : void VolumeGradientBase::completeTask( const unsigned& curr, MultiValue& invals, MultiValue& outvals ) const {
62 80958 : if( getPntrToMultiColvar()->isDensity() ) {
63 : outvals.setValue(0, 1.0); outvals.setValue(1, 1.0);
64 : } else {
65 : // Copy derivatives of the colvar and the value of the colvar
66 37538 : invals.copyValues( outvals );
67 37538 : if( derivativesAreRequired() ) invals.copyDerivatives( outvals );
68 : }
69 80958 : calculateAllVolumes( curr, outvals );
70 80958 : }
71 :
72 115758 : void VolumeGradientBase::setNumberInVolume( const unsigned& ivol, const unsigned& curr, const double& weight,
73 : const Vector& wdf, const Tensor& virial, const std::vector<Vector>& refders,
74 : MultiValue& outvals ) const {
75 : MultiColvarBase* mcolv=getPntrToMultiColvar();
76 115758 : if( !mcolv->weightHasDerivatives ) {
77 : outvals.setValue(ivol, weight );
78 115758 : if( derivativesAreRequired() ) {
79 225450 : CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
80 506900 : for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
81 140725 : unsigned jatom=3*catom.getIndex(i);
82 140725 : outvals.addDerivative( ivol, jatom+0, catom.getDerivative(i,0,wdf) );
83 140725 : outvals.addDerivative( ivol, jatom+1, catom.getDerivative(i,1,wdf) );
84 140725 : outvals.addDerivative( ivol, jatom+2, catom.getDerivative(i,2,wdf) );
85 : }
86 112725 : unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
87 450900 : 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) );
88 578205 : for(unsigned i=0; i<refders.size(); ++i) {
89 117585 : unsigned iatom=nmder+3*i;
90 :
91 117585 : outvals.addDerivative( ivol, iatom+0, refders[i][0] );
92 117585 : outvals.addDerivative( ivol, iatom+1, refders[i][1] );
93 117585 : outvals.addDerivative( ivol, iatom+2, refders[i][2] );
94 : }
95 : }
96 0 : } else if(ivol==0) {
97 0 : double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
98 0 : if( derivativesAreRequired() ) {
99 0 : plumed_merror("This needs testing");
100 : CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
101 : for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
102 : unsigned jatom=3*catom.getIndex(i);
103 : outvals.addDerivative( ivol, jatom+0, weight*outvals.getDerivative(ivol,jatom+0) + ww*catom.getDerivative(i,0,wdf) );
104 : outvals.addDerivative( ivol, jatom+1, weight*outvals.getDerivative(ivol,jatom+1) + ww*catom.getDerivative(i,1,wdf) );
105 : outvals.addDerivative( ivol, jatom+2, weight*outvals.getDerivative(ivol,jatom+2) + ww*catom.getDerivative(i,2,wdf) );
106 : }
107 : unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
108 : 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) );
109 : for(unsigned i=0; i<refders.size(); ++i) {
110 : unsigned iatom=nmder+3*i;
111 : outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
112 : outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
113 : outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
114 : }
115 : }
116 : } else {
117 0 : double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
118 0 : if( derivativesAreRequired() ) {
119 0 : plumed_merror("This needs testing");
120 : CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
121 : for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
122 : unsigned jatom=3*catom.getIndex(i);
123 : outvals.addDerivative( ivol, jatom+0, ww*catom.getDerivative(i,0,wdf) );
124 : outvals.addDerivative( ivol, jatom+1, ww*catom.getDerivative(i,1,wdf) );
125 : outvals.addDerivative( ivol, jatom+2, ww*catom.getDerivative(i,2,wdf) );
126 : }
127 : unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
128 : 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) );
129 : for(unsigned i=0; i<refders.size(); ++i) {
130 : unsigned iatom=nmder+3*i;
131 : outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
132 : outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
133 : outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
134 : }
135 : }
136 : }
137 115758 : }
138 :
139 0 : void VolumeGradientBase::addBridgeForces( const std::vector<double>& bb ) {
140 : plumed_dbg_assert( bb.size()==tmpforces.size()-9 );
141 : // Forces on local atoms
142 0 : for(unsigned i=0; i<bb.size(); ++i) tmpforces[i]=bb[i];
143 : // Virial contribution is zero
144 0 : for(unsigned i=bb.size(); i<bb.size()+9; ++i) tmpforces[i]=0.0;
145 0 : setForcesOnAtoms( tmpforces, 0 );
146 0 : }
147 :
148 : }
149 4839 : }
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