1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2014-2021 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 "BridgedMultiColvarFunction.h"
23 #include "core/PlumedMain.h"
24 #include "core/ActionSet.h"
25 #include "CatomPack.h"
26
27 namespace PLMD {
28 namespace multicolvar {
29
registerKeywords(Keywords & keys)30 void BridgedMultiColvarFunction::registerKeywords( Keywords& keys ) {
31 MultiColvarBase::registerKeywords( keys );
32 keys.add("compulsory","DATA","The multicolvar that calculates the set of base quantities that we are interested in");
33 }
34
BridgedMultiColvarFunction(const ActionOptions & ao)35 BridgedMultiColvarFunction::BridgedMultiColvarFunction(const ActionOptions&ao):
36 Action(ao),
37 MultiColvarBase(ao)
38 {
39 std::string mlab; parse("DATA",mlab);
40 mycolv = plumed.getActionSet().selectWithLabel<MultiColvarBase*>(mlab);
41 if(!mycolv) error("action labeled " + mlab + " does not exist or is not a multicolvar");
42
43 // When using numerical derivatives here we must use numerical derivatives
44 // in base multicolvar
45 if( checkNumericalDerivatives() ) mycolv->useNumericalDerivatives();
46
47 myBridgeVessel = mycolv->addBridgingVessel( this ); addDependency(mycolv);
48 weightHasDerivatives=true; usespecies=mycolv->usespecies;
49 // Number of tasks is the same as the number in the underlying MultiColvar
50 for(unsigned i=0; i<mycolv->getFullNumberOfTasks(); ++i) addTaskToList( mycolv->getTaskCode(i) );
51 }
52
turnOnDerivatives()53 void BridgedMultiColvarFunction::turnOnDerivatives() {
54 BridgedMultiColvarFunction* check = dynamic_cast<BridgedMultiColvarFunction*>( mycolv );
55 if( check ) {
56 if( check->getNumberOfAtoms()>0 ) error("cannot calculate required derivatives of this quantity");
57 }
58 MultiColvarBase::turnOnDerivatives();
59 }
60
transformBridgedDerivatives(const unsigned & current,MultiValue & invals,MultiValue & outvals) const61 void BridgedMultiColvarFunction::transformBridgedDerivatives( const unsigned& current, MultiValue& invals, MultiValue& outvals ) const {
62 completeTask( current, invals, outvals );
63
64 // Now update the outvals derivatives lists
65 if( derivativesAreRequired() ) {
66 outvals.emptyActiveMembers();
67 if( mycolv->isDensity() ) {
68 for(unsigned j=0; j<3; ++j) outvals.putIndexInActiveArray( 3*current+j );
69 for(unsigned j=invals.getNumberOfDerivatives()-9; j<invals.getNumberOfDerivatives(); ++j) outvals.putIndexInActiveArray(j);
70 } else {
71 for(unsigned j=0; j<invals.getNumberActive(); ++j) outvals.putIndexInActiveArray( invals.getActiveIndex(j) );
72 }
73 for(unsigned j=invals.getNumberOfDerivatives(); j<outvals.getNumberOfDerivatives(); ++j) outvals.putIndexInActiveArray( j );
74 outvals.completeUpdate();
75 }
76 }
77
performTask(const unsigned & taskIndex,const unsigned & current,MultiValue & myvals) const78 void BridgedMultiColvarFunction::performTask( const unsigned& taskIndex, const unsigned& current, MultiValue& myvals ) const {
79 // This allows us to speed up the code as we don't need to reallocate memory on every call of perform task
80 MultiValue& invals=myBridgeVessel->getTemporyMultiValue();
81 if( invals.getNumberOfValues()!=mycolv->getNumberOfQuantities() ||
82 invals.getNumberOfDerivatives()!=mycolv->getNumberOfDerivatives() ) {
83 invals.resize( mycolv->getNumberOfQuantities(), mycolv->getNumberOfDerivatives() );
84 }
85 invals.clearAll(); mycolv->performTask( taskIndex, current, invals );
86 transformBridgedDerivatives( taskIndex, invals, myvals );
87 }
88
calculateNumericalDerivatives(ActionWithValue * a)89 void BridgedMultiColvarFunction::calculateNumericalDerivatives( ActionWithValue* a ) {
90 if(!a) {
91 a=dynamic_cast<ActionWithValue*>(this);
92 plumed_massert(a,"cannot compute numerical derivatives for an action without values");
93 }
94 if( myBridgeVessel ) {
95 myBridgeVessel->completeNumericalDerivatives();
96 } else {
97 error("numerical derivatives are not implemented");
98 }
99 }
100
applyBridgeForces(const std::vector<double> & bb)101 void BridgedMultiColvarFunction::applyBridgeForces( const std::vector<double>& bb ) {
102 if( getNumberOfAtoms()==0 ) return ;
103
104 std::vector<Vector>& f( modifyForces() );
105 for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
106 f[i][0]+=bb[3*i+0]; f[i][1]+=bb[3*i+1]; f[i][2]+=bb[3*i+2];
107 }
108 applyForces();
109 }
110
isPeriodic()111 bool BridgedMultiColvarFunction::isPeriodic() {
112 return mycolv->isPeriodic();
113 }
114
deactivate_task(const unsigned & taskno)115 void BridgedMultiColvarFunction::deactivate_task( const unsigned& taskno ) {
116 plumed_merror("This should never be called");
117 }
118
getCentralAtomPack(const unsigned & basn,const unsigned & curr,CatomPack & mypack)119 void BridgedMultiColvarFunction::getCentralAtomPack( const unsigned& basn, const unsigned& curr, CatomPack& mypack ) {
120 return mycolv->getCentralAtomPack( basn, curr, mypack );
121 }
122
123 }
124 }
125