Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2023 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 "ActionVolume.h"
25 :
26 : //+PLUMEDOC VOLUMES AROUND
27 : /*
28 : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.
29 :
30 : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
31 : dimensional space. For example, if we have the coordination numbers for all the atoms in the
32 : system each coordination number can be assumed to lie on the position of the central atom.
33 : Because each base quantity can be assigned to a particular point in space we can calculate functions of the
34 : distribution of base quantities in a particular part of the box by using:
35 :
36 : \f[
37 : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) w(x_i,y_i,z_i) }{ \sum_i w(x_i,y_i,z_i) }
38 : \f]
39 :
40 : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (x_i,y_i,z_i)\f$.
41 : The function \f$ w(x_i,y_i,z_i) \f$ measures whether or not the system is in the subregion of interest. It
42 : is equal to:
43 :
44 : \f[
45 : w(x_i,y_i,z_i) = \int_{xl}^{xu} \int_{yl}^{yu} \int_{zl}^{zu} \textrm{d}x\textrm{d}y\textrm{d}z K\left( \frac{x - x_i}{\sigma} \right)K\left( \frac{y - y_i}{\sigma} \right)K\left( \frac{z - z_i}{\sigma} \right)
46 : \f]
47 :
48 : where \f$K\f$ is one of the kernel functions described on \ref histogrambead and \f$\sigma\f$ is a bandwidth parameter.
49 : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.
50 :
51 : When AROUND is used with the \ref DENSITY action the number of atoms in the specified region is calculated
52 :
53 : \par Examples
54 :
55 : The following commands tell plumed to calculate the average coordination number for the atoms
56 : that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The final value will be labeled s.mean.
57 : \plumedfile
58 : COM ATOMS=1-100 LABEL=c1
59 : COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 LABEL=c
60 : AROUND DATA=c ATOM=c1 XLOWER=-2.0 XUPPER=2.0 SIGMA=0.1 MEAN LABEL=s
61 : \endplumedfile
62 :
63 : */
64 : //+ENDPLUMEDOC
65 :
66 : namespace PLMD {
67 : namespace multicolvar {
68 :
69 : class VolumeAround : public ActionVolume {
70 : private:
71 : Vector origin;
72 : bool dox, doy, doz;
73 : double xlow, xhigh;
74 : double ylow, yhigh;
75 : double zlow, zhigh;
76 : public:
77 : static void registerKeywords( Keywords& keys );
78 : explicit VolumeAround(const ActionOptions& ao);
79 : void setupRegions() override;
80 : double calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const override;
81 : };
82 :
83 13829 : PLUMED_REGISTER_ACTION(VolumeAround,"AROUND")
84 :
85 26 : void VolumeAround::registerKeywords( Keywords& keys ) {
86 26 : ActionVolume::registerKeywords( keys );
87 52 : keys.add("atoms","ATOM","the atom whose vicinity we are interested in examining");
88 52 : keys.add("compulsory","XLOWER","0.0","the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).");
89 52 : keys.add("compulsory","XUPPER","0.0","the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).");
90 52 : keys.add("compulsory","YLOWER","0.0","the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).");
91 52 : keys.add("compulsory","YUPPER","0.0","the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).");
92 52 : keys.add("compulsory","ZLOWER","0.0","the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).");
93 52 : keys.add("compulsory","ZUPPER","0.0","the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).");
94 26 : }
95 :
96 22 : VolumeAround::VolumeAround(const ActionOptions& ao):
97 : Action(ao),
98 22 : ActionVolume(ao) {
99 : std::vector<AtomNumber> atom;
100 44 : parseAtomList("ATOM",atom);
101 22 : if( atom.size()!=1 ) {
102 0 : error("should only be one atom specified");
103 : }
104 22 : log.printf(" boundaries for region are calculated based on positions of atom : %d\n",atom[0].serial() );
105 :
106 22 : dox=true;
107 22 : parse("XLOWER",xlow);
108 22 : parse("XUPPER",xhigh);
109 22 : doy=true;
110 22 : parse("YLOWER",ylow);
111 22 : parse("YUPPER",yhigh);
112 22 : doz=true;
113 22 : parse("ZLOWER",zlow);
114 22 : parse("ZUPPER",zhigh);
115 22 : if( xlow==0.0 && xhigh==0.0 ) {
116 6 : dox=false;
117 : }
118 22 : if( ylow==0.0 && yhigh==0.0 ) {
119 14 : doy=false;
120 : }
121 22 : if( zlow==0.0 && zhigh==0.0 ) {
122 14 : doz=false;
123 : }
124 22 : if( !dox && !doy && !doz ) {
125 0 : error("no subregion defined use XLOWER, XUPPER, YLOWER, YUPPER, ZLOWER, ZUPPER");
126 : }
127 22 : log.printf(" boundaries for region (region of interest about atom) : x %f %f, y %f %f, z %f %f \n",xlow,xhigh,ylow,yhigh,zlow,zhigh);
128 22 : checkRead();
129 22 : requestAtoms(atom);
130 22 : }
131 :
132 317 : void VolumeAround::setupRegions() { }
133 :
134 56393 : double VolumeAround::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const {
135 : // Setup the histogram bead
136 56393 : HistogramBead bead;
137 : bead.isNotPeriodic();
138 56393 : bead.setKernelType( getKernelType() );
139 :
140 : // Calculate position of atom wrt to origin
141 56393 : Vector fpos=pbcDistance( getPosition(0), cpos );
142 : double xcontr, ycontr, zcontr, xder, yder, zder;
143 56393 : if( dox ) {
144 32393 : bead.set( xlow, xhigh, getSigma() );
145 32393 : xcontr=bead.calculate( fpos[0], xder );
146 : } else {
147 : xcontr=1.;
148 24000 : xder=0.;
149 : }
150 56393 : if( doy ) {
151 32000 : bead.set( ylow, yhigh, getSigma() );
152 32000 : ycontr=bead.calculate( fpos[1], yder );
153 : } else {
154 : ycontr=1.;
155 24393 : yder=0.;
156 : }
157 56393 : if( doz ) {
158 32000 : bead.set( zlow, zhigh, getSigma() );
159 32000 : zcontr=bead.calculate( fpos[2], zder );
160 : } else {
161 : zcontr=1.;
162 24393 : zder=0.;
163 : }
164 56393 : derivatives[0]=xder*ycontr*zcontr;
165 56393 : derivatives[1]=xcontr*yder*zcontr;
166 56393 : derivatives[2]=xcontr*ycontr*zder;
167 : // Add derivatives wrt to position of origin atom
168 56393 : refders[0] = -derivatives;
169 : // Add virial contribution
170 56393 : vir -= Tensor(fpos,derivatives);
171 56393 : return xcontr*ycontr*zcontr;
172 : }
173 :
174 : }
175 : }
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