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