1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2017-2021 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 "core/ActionRegister.h"
23 #include "tools/Pbc.h"
24 #include "tools/KernelFunctions.h"
25 #include "tools/SwitchingFunction.h"
26 #include "ActionVolume.h"
27 #include <memory>
28
29 //+PLUMEDOC VOLUMES INENVELOPE
30 /*
31 This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a region where the density of a certain type of atom is high.
32
33 This collective variable can be used to determine whether colvars are within region where the density
34 of a particular atom is high. This is achieved by calculating the following function at the point where
35 the atom is located \f$(x,y,z)\f$:
36
37 \f[
38 w_j = 1 - \sigma\left[ \sum_{i=1}^N K\left( \frac{x-x_i}{\sigma_x},\frac{y-y_i}{\sigma_y},\frac{z-z_i}{\sigma_z} \right) \right]
39 \f]
40
41 Here \f$\sigma\f$ is a \ref switchingfunction and \f$K\f$ is a \ref kernelfunctions. The sum runs over the atoms
42 specified using the ATOMS keyword and a \f$w_j\f$ value is calculated for each of the central atoms of the input
43 multicolvar.
44
45 \par Examples
46
47 The input below calculates a density field from the positions of atoms 1-14400. The number of the atoms
48 that are specified in the DENSITY action that are within a region where the density field is greater than
49 2.0 is then calculated.
50
51 \plumedfile
52 d1: DENSITY SPECIES=14401-74134:3 LOWMEM
53 fi: INENVELOPE DATA=d1 ATOMS=1-14400 CONTOUR={RATIONAL D_0=2.0 R_0=1.0} BANDWIDTH=0.1,0.1,0.1 LOWMEM
54 PRINT ARG=fi FILE=colvar
55 \endplumedfile
56
57 */
58 //+ENDPLUMEDOC
59
60 namespace PLMD {
61 namespace multicolvar {
62
63 class VolumeInEnvelope : public ActionVolume {
64 private:
65 LinkCells mylinks;
66 std::unique_ptr<KernelFunctions> kernel;
67 std::vector<std::unique_ptr<Value>> pos;
68 std::vector<Vector> ltmp_pos;
69 std::vector<unsigned> ltmp_ind;
70 SwitchingFunction sfunc;
71 public:
72 static void registerKeywords( Keywords& keys );
73 explicit VolumeInEnvelope(const ActionOptions& ao);
74 void setupRegions() override;
75 double calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const override;
76 };
77
78 PLUMED_REGISTER_ACTION(VolumeInEnvelope,"INENVELOPE")
79
registerKeywords(Keywords & keys)80 void VolumeInEnvelope::registerKeywords( Keywords& keys ) {
81 ActionVolume::registerKeywords( keys ); keys.remove("SIGMA");
82 keys.add("atoms","ATOMS","the atom whose positions we are constructing a field from");
83 keys.add("compulsory","BANDWIDTH","the bandwidths for kernel density estimation");
84 keys.add("compulsory","CONTOUR","a switching function that tells PLUMED how large the density should be");
85 }
86
VolumeInEnvelope(const ActionOptions & ao)87 VolumeInEnvelope::VolumeInEnvelope(const ActionOptions& ao):
88 Action(ao),
89 ActionVolume(ao),
90 mylinks(comm)
91 {
92 std::vector<AtomNumber> atoms; parseAtomList("ATOMS",atoms);
93 log.printf(" creating density field from atoms : ");
94 for(unsigned i=0; i<atoms.size(); ++i) log.printf("%d ",atoms[i].serial() );
95 log.printf("\n"); ltmp_ind.resize( atoms.size() ); ltmp_pos.resize( atoms.size() );
96 for(unsigned i=0; i<atoms.size(); ++i) ltmp_ind[i]=i;
97
98 std::string sw, errors; parse("CONTOUR",sw);
99 if(sw.length()==0) error("missing CONTOURkeyword");
100 sfunc.set(sw,errors);
101 if( errors.length()!=0 ) error("problem reading RADIUS keyword : " + errors );
102 log.printf(" density at atom must be larger than %s \n", ( sfunc.description() ).c_str() );
103
104 std::vector<double> pp(3,0.0), bandwidth(3); parseVector("BANDWIDTH",bandwidth);
105 log.printf(" using %s kernel with bandwidths %f %f %f \n",getKernelType().c_str(),bandwidth[0],bandwidth[1],bandwidth[2] );
106 kernel.reset( new KernelFunctions( pp, bandwidth, getKernelType(), "DIAGONAL", 1.0 ) );
107 for(unsigned i=0; i<3; ++i) { pos.emplace_back(new Value()); pos[i]->setNotPeriodic(); }
108 std::vector<double> csupport( kernel->getContinuousSupport() );
109 double maxs = csupport[0];
110 for(unsigned i=1; i<csupport.size(); ++i) {
111 if( csupport[i]>maxs ) maxs = csupport[i];
112 }
113 checkRead(); requestAtoms(atoms); mylinks.setCutoff( maxs );
114 }
115
setupRegions()116 void VolumeInEnvelope::setupRegions() {
117 for(unsigned i=0; i<ltmp_ind.size(); ++i) { ltmp_pos[i]=getPosition(i); }
118 mylinks.buildCellLists( ltmp_pos, ltmp_ind, getPbc() );
119 }
120
calculateNumberInside(const Vector & cpos,Vector & derivatives,Tensor & vir,std::vector<Vector> & refders) const121 double VolumeInEnvelope::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const {
122 unsigned ncells_required=0, natoms=1; std::vector<unsigned> cells_required( mylinks.getNumberOfCells() ), indices( 1 + getNumberOfAtoms() );
123 mylinks.addRequiredCells( mylinks.findMyCell( cpos ), ncells_required, cells_required );
124 indices[0]=getNumberOfAtoms(); mylinks.retrieveAtomsInCells( ncells_required, cells_required, natoms, indices );
125 double value=0; std::vector<double> der(3); Vector tder;
126
127 // convert pointer once
128 auto pos_ptr=Tools::unique2raw(pos);
129
130 for(unsigned i=1; i<natoms; ++i) {
131 Vector dist = getSeparation( cpos, getPosition( indices[i] ) );
132 for(unsigned j=0; j<3; ++j) pos[j]->set( dist[j] );
133 value += kernel->evaluate( pos_ptr, der, true );
134 for(unsigned j=0; j<3; ++j) {
135 derivatives[j] -= der[j]; refders[ indices[i] ][j] += der[j]; tder[j]=der[j];
136 }
137 vir -= Tensor( tder, dist );
138 }
139 double deriv, fval = sfunc.calculate( value, deriv );
140 derivatives *= -deriv*value; vir *= -deriv*value;
141 for(unsigned i=1; i<natoms; ++i) refders[ indices[i] ] *= -deriv*value;
142 return 1.0 - fval;
143 }
144
145 }
146 }
147