Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2019 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 "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
29 : variables for the atoms that lie in a particular, user-specified part of of the cell.
30 :
31 : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
32 : dimensional space. For example, if we have the coordination numbers for all the atoms in the
33 : system each coordination number can be assumed to lie on the position of the central atom.
34 : Because each base quantity can be assigned to a particular point in space we can calculate functions of the
35 : distribution of base quantities in a particular part of the box by using:
36 :
37 : \f[
38 : \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) }
39 : \f]
40 :
41 : 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$.
42 : The function \f$ w(x_i,y_i,z_i) \f$ measures whether or not the system is in the subregion of interest. It
43 : is equal to:
44 :
45 : \f[
46 : 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)
47 : \f]
48 :
49 : where \f$K\f$ is one of the kernel functions described on \ref histogrambead and \f$\sigma\f$ is a bandwidth parameter.
50 : 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.
51 :
52 : When AROUND is used with the \ref DENSITY action the number of atoms in the specified region is calculated
53 :
54 : \par Examples
55 :
56 : The following commands tell plumed to calculate the average coordination number for the atoms
57 : that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The final value will be labeled s.mean.
58 : \plumedfile
59 : COM ATOMS=1-100 LABEL=c1
60 : COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 LABEL=c
61 : AROUND DATA=c ORIGIN=c1 XLOWER=-2.0 XUPPER=2.0 SIGMA=0.1 MEAN LABEL=s
62 : \endplumedfile
63 :
64 : */
65 : //+ENDPLUMEDOC
66 :
67 : namespace PLMD {
68 : namespace multicolvar {
69 :
70 44 : class VolumeAround : public ActionVolume {
71 : private:
72 : Vector origin;
73 : bool dox, doy, doz;
74 : double xlow, xhigh;
75 : double ylow, yhigh;
76 : double zlow, zhigh;
77 : public:
78 : static void registerKeywords( Keywords& keys );
79 : explicit VolumeAround(const ActionOptions& ao);
80 : void setupRegions();
81 : double calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const ;
82 : };
83 :
84 6474 : PLUMED_REGISTER_ACTION(VolumeAround,"AROUND")
85 :
86 23 : void VolumeAround::registerKeywords( Keywords& keys ) {
87 23 : ActionVolume::registerKeywords( keys );
88 92 : keys.add("atoms","ATOM","the atom whose vicinity we are interested in examining");
89 115 : 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).");
90 115 : 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).");
91 115 : 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).");
92 115 : 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).");
93 115 : 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).");
94 115 : 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).");
95 23 : }
96 :
97 22 : VolumeAround::VolumeAround(const ActionOptions& ao):
98 : Action(ao),
99 22 : ActionVolume(ao)
100 : {
101 : std::vector<AtomNumber> atom;
102 44 : parseAtomList("ATOM",atom);
103 22 : if( atom.size()!=1 ) error("should only be one atom specified");
104 44 : log.printf(" boundaries for region are calculated based on positions of atom : %d\n",atom[0].serial() );
105 :
106 66 : dox=true; parse("XLOWER",xlow); parse("XUPPER",xhigh);
107 66 : doy=true; parse("YLOWER",ylow); parse("YUPPER",yhigh);
108 66 : doz=true; parse("ZLOWER",zlow); parse("ZUPPER",zhigh);
109 22 : if( xlow==0.0 && xhigh==0.0 ) dox=false;
110 22 : if( ylow==0.0 && yhigh==0.0 ) doy=false;
111 22 : if( zlow==0.0 && zhigh==0.0 ) doz=false;
112 22 : if( !dox && !doy && !doz ) error("no subregion defined use XLOWER, XUPPER, YLOWER, YUPPER, ZLOWER, ZUPPER");
113 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);
114 22 : checkRead(); requestAtoms(atom);
115 22 : }
116 :
117 317 : void VolumeAround::setupRegions() { }
118 :
119 56393 : double VolumeAround::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const {
120 : // Setup the histogram bead
121 169179 : HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( getKernelType() );
122 :
123 : // Calculate position of atom wrt to origin
124 112786 : Vector fpos=pbcDistance( getPosition(0), cpos );
125 : double xcontr, ycontr, zcontr, xder, yder, zder;
126 56393 : if( dox ) {
127 32393 : bead.set( xlow, xhigh, getSigma() );
128 32393 : xcontr=bead.calculate( fpos[0], xder );
129 : } else {
130 24000 : xcontr=1.; xder=0.;
131 : }
132 56393 : if( doy ) {
133 32000 : bead.set( ylow, yhigh, getSigma() );
134 32000 : ycontr=bead.calculate( fpos[1], yder );
135 : } else {
136 24393 : ycontr=1.; yder=0.;
137 : }
138 56393 : if( doz ) {
139 32000 : bead.set( zlow, zhigh, getSigma() );
140 32000 : zcontr=bead.calculate( fpos[2], zder );
141 : } else {
142 24393 : zcontr=1.; zder=0.;
143 : }
144 56393 : derivatives[0]=xder*ycontr*zcontr;
145 56393 : derivatives[1]=xcontr*yder*zcontr;
146 56393 : derivatives[2]=xcontr*ycontr*zder;
147 : // Add derivatives wrt to position of origin atom
148 56393 : refders[0] = -derivatives;
149 : // Add virial contribution
150 56393 : vir -= Tensor(fpos,derivatives);
151 56393 : return xcontr*ycontr*zcontr;
152 : }
153 :
154 : }
155 4839 : }
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