1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2013-2021 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 "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 PLUMED_REGISTER_ACTION(VolumeAround,"AROUND")
84
registerKeywords(Keywords & keys)85 void VolumeAround::registerKeywords( Keywords& keys ) {
86 ActionVolume::registerKeywords( keys );
87 keys.add("atoms","ATOM","the atom whose vicinity we are interested in examining");
88 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 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 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 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 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 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 }
95
VolumeAround(const ActionOptions & ao)96 VolumeAround::VolumeAround(const ActionOptions& ao):
97 Action(ao),
98 ActionVolume(ao)
99 {
100 std::vector<AtomNumber> atom;
101 parseAtomList("ATOM",atom);
102 if( atom.size()!=1 ) error("should only be one atom specified");
103 log.printf(" boundaries for region are calculated based on positions of atom : %d\n",atom[0].serial() );
104
105 dox=true; parse("XLOWER",xlow); parse("XUPPER",xhigh);
106 doy=true; parse("YLOWER",ylow); parse("YUPPER",yhigh);
107 doz=true; parse("ZLOWER",zlow); parse("ZUPPER",zhigh);
108 if( xlow==0.0 && xhigh==0.0 ) dox=false;
109 if( ylow==0.0 && yhigh==0.0 ) doy=false;
110 if( zlow==0.0 && zhigh==0.0 ) doz=false;
111 if( !dox && !doy && !doz ) error("no subregion defined use XLOWER, XUPPER, YLOWER, YUPPER, ZLOWER, ZUPPER");
112 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);
113 checkRead(); requestAtoms(atom);
114 }
115
setupRegions()116 void VolumeAround::setupRegions() { }
117
calculateNumberInside(const Vector & cpos,Vector & derivatives,Tensor & vir,std::vector<Vector> & refders) const118 double VolumeAround::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const {
119 // Setup the histogram bead
120 HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( getKernelType() );
121
122 // Calculate position of atom wrt to origin
123 Vector fpos=pbcDistance( getPosition(0), cpos );
124 double xcontr, ycontr, zcontr, xder, yder, zder;
125 if( dox ) {
126 bead.set( xlow, xhigh, getSigma() );
127 xcontr=bead.calculate( fpos[0], xder );
128 } else {
129 xcontr=1.; xder=0.;
130 }
131 if( doy ) {
132 bead.set( ylow, yhigh, getSigma() );
133 ycontr=bead.calculate( fpos[1], yder );
134 } else {
135 ycontr=1.; yder=0.;
136 }
137 if( doz ) {
138 bead.set( zlow, zhigh, getSigma() );
139 zcontr=bead.calculate( fpos[2], zder );
140 } else {
141 zcontr=1.; zder=0.;
142 }
143 derivatives[0]=xder*ycontr*zcontr;
144 derivatives[1]=xcontr*yder*zcontr;
145 derivatives[2]=xcontr*ycontr*zder;
146 // Add derivatives wrt to position of origin atom
147 refders[0] = -derivatives;
148 // Add virial contribution
149 vir -= Tensor(fpos,derivatives);
150 return xcontr*ycontr*zcontr;
151 }
152
153 }
154 }
155