1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2011-2021 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 "ActionVolume.h"
23
24 namespace PLMD {
25 namespace multicolvar {
26
registerKeywords(Keywords & keys)27 void ActionVolume::registerKeywords( Keywords& keys ) {
28 VolumeGradientBase::registerKeywords( keys );
29 if( keys.reserved("VMEAN") ) keys.use("VMEAN");
30 keys.use("MEAN"); keys.use("LESS_THAN"); keys.use("MORE_THAN");
31 keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("SUM");
32 keys.add("compulsory","SIGMA","the width of the function to be used for kernel density estimation");
33 keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used");
34 keys.addFlag("OUTSIDE",false,"calculate quantities for colvars that are on atoms outside the region of interest");
35 }
36
ActionVolume(const ActionOptions & ao)37 ActionVolume::ActionVolume(const ActionOptions&ao):
38 Action(ao),
39 VolumeGradientBase(ao)
40 {
41 // Find number of quantities
42 if( getPntrToMultiColvar()->isDensity() ) nquantities=2; // Value + weight
43 else if( getPntrToMultiColvar()->getNumberOfQuantities()==2 ) nquantities=2; // Value + weight
44 else nquantities = 1 + getPntrToMultiColvar()->getNumberOfQuantities()-2 + 1; // Norm + vector + weight
45
46 // Output some nice information
47 std::string functype=getPntrToMultiColvar()->getName();
48 std::transform( functype.begin(), functype.end(), functype.begin(), tolower );
49 log.printf(" calculating %s inside region of insterest\n",functype.c_str() );
50
51 parseFlag("OUTSIDE",not_in); sigma=0.0;
52 if( keywords.exists("SIGMA") ) parse("SIGMA",sigma);
53 if( keywords.exists("KERNEL") ) parse("KERNEL",kerneltype);
54
55 if( getPntrToMultiColvar()->isDensity() ) {
56 std::string input;
57 addVessel( "SUM", input, -1 ); // -1 here means that this value will be named getLabel()
58 }
59 readVesselKeywords();
60 }
61
calculateAllVolumes(const unsigned & curr,MultiValue & outvals) const62 void ActionVolume::calculateAllVolumes( const unsigned& curr, MultiValue& outvals ) const {
63 Vector catom_pos=getPntrToMultiColvar()->getCentralAtomPos( curr );
64
65 double weight; Vector wdf; Tensor vir; std::vector<Vector> refders( getNumberOfAtoms() );
66 weight=calculateNumberInside( catom_pos, wdf, vir, refders );
67 if( not_in ) {
68 weight = 1.0 - weight; wdf *= -1.; vir *=-1;
69 for(unsigned i=0; i<refders.size(); ++i) refders[i]*=-1;
70 }
71 setNumberInVolume( 0, curr, weight, wdf, vir, refders, outvals );
72 }
73
inVolumeOfInterest(const unsigned & curr) const74 bool ActionVolume::inVolumeOfInterest( const unsigned& curr ) const {
75 Vector catom_pos=getPntrToMultiColvar()->getCentralAtomPos( curr );
76 Vector wdf; Tensor vir; std::vector<Vector> refders( getNumberOfAtoms() );
77 double weight=calculateNumberInside( catom_pos, wdf, vir, refders );
78 if( not_in ) weight = 1.0 - weight;
79 if( weight<getTolerance() ) return false;
80 return true;
81 }
82
83 }
84 }
85