Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2015-2018 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/SwitchingFunction.h"
25 : #include "ActionVolume.h"
26 :
27 : //+PLUMEDOC VOLUMES INSPHERE
28 : /*
29 : This quantity can be used to calculate functions of the distribution of collective
30 : variables for the atoms that lie in a particular, user-specified part of of the cell.
31 :
32 : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
33 : dimensional space. For example, if we have the coordination numbers for all the atoms in the
34 : system each coordination number can be assumed to lie on the position of the central atom.
35 : Because each base quantity can be assigned to a particular point in space we can calculate functions of the
36 : distribution of base quantities in a particular part of the box by using:
37 :
38 : \f[
39 : \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) }
40 : \f]
41 :
42 : 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$.
43 : The function \f$ w(x_i,y_i,z_i) \f$ measures whether or not the system is in the subregion of interest. It
44 : is equal to:
45 :
46 : \f[
47 : w(x_i,y_i,z_i) =
48 : \f]
49 :
50 : where \f$\sigma\f$ is a \ref switchingfunction.
51 : 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.
52 :
53 : When INCYLINDER is used with the \ref DENSITY action the number of atoms in the specified region is calculated
54 :
55 : \par Examples
56 :
57 : The input below can be use to calculate the average coordination numbers for those atoms that are within a sphere
58 : of radius 1.5 nm that is centered on the position of atom 101.
59 :
60 : \verbatim
61 : c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
62 : d2: INSPHERE ATOM=101 DATA=d1 RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 MEAN
63 : PRINT ARG=d2.* FILE=colvar
64 : \endverbatim
65 :
66 : */
67 : //+ENDPLUMEDOC
68 :
69 : namespace PLMD {
70 : namespace multicolvar {
71 :
72 4 : class VolumeInSphere : public ActionVolume {
73 : private:
74 : Vector origin;
75 : SwitchingFunction switchingFunction;
76 : public:
77 : static void registerKeywords( Keywords& keys );
78 : explicit VolumeInSphere(const ActionOptions& ao);
79 : void setupRegions();
80 : double calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const ;
81 : };
82 :
83 2525 : PLUMED_REGISTER_ACTION(VolumeInSphere,"INSPHERE")
84 :
85 3 : void VolumeInSphere::registerKeywords( Keywords& keys ) {
86 3 : ActionVolume::registerKeywords( keys );
87 3 : keys.add("atoms","ATOM","the atom whose vicinity we are interested in examining");
88 3 : keys.add("compulsory","RADIUS","the switching function that tells us the extent of the sphereical region of interest");
89 3 : keys.remove("SIGMA");
90 3 : }
91 :
92 2 : VolumeInSphere::VolumeInSphere(const ActionOptions& ao):
93 : Action(ao),
94 2 : ActionVolume(ao)
95 : {
96 2 : std::vector<AtomNumber> atom;
97 2 : parseAtomList("ATOM",atom);
98 2 : if( atom.size()!=1 ) error("should only be one atom specified");
99 2 : log.printf(" center of sphere is at position of atom : %d\n",atom[0].serial() );
100 :
101 4 : std::string sw, errors; parse("RADIUS",sw);
102 2 : if(sw.length()==0) error("missing RADIUS keyword");
103 2 : switchingFunction.set(sw,errors);
104 2 : if( errors.length()!=0 ) error("problem reading RADIUS keyword : " + errors );
105 2 : log.printf(" radius of sphere is given by %s \n", ( switchingFunction.description() ).c_str() );
106 :
107 4 : checkRead(); requestAtoms(atom);
108 2 : }
109 :
110 40 : void VolumeInSphere::setupRegions() { }
111 :
112 68470 : double VolumeInSphere::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const {
113 : // Calculate position of atom wrt to origin
114 68470 : Vector fpos=pbcDistance( getPosition(0), cpos );
115 68473 : double dfunc, value = switchingFunction.calculateSqr( fpos.modulo2(), dfunc );
116 68473 : derivatives.zero(); derivatives = dfunc*fpos; refders[0] = -derivatives;
117 : // Add a virial contribution
118 68473 : vir -= Tensor(fpos,derivatives);
119 68471 : return value;
120 : }
121 :
122 : }
123 2523 : }
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