Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2019 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 "CubicHarmonicBase.h"
23 : #include "core/ActionRegister.h"
24 :
25 : #include <string>
26 : #include <cmath>
27 :
28 : using namespace std;
29 :
30 : namespace PLMD {
31 : namespace crystallization {
32 :
33 : //+PLUMEDOC MCOLVAR SIMPLECUBIC
34 : /*
35 : Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple
36 : cubic structure.
37 :
38 : We can measure how similar the environment around atom \f$i\f$ is to a simple cubic structure is by evaluating
39 : the following quantity:
40 :
41 : \f[
42 : s_i = \frac{ \sum_{i \ne j} \sigma(r_{ij}) \left[ \frac{ x_{ij}^4 + y_{ij}^4 + z_{ij}^4 }{r_{ij}^4} \right] }{ \sum_{i \ne j} \sigma(r_{ij}) }
43 : \f]
44 :
45 : In this expression \f$x_{ij}\f$, \f$y_{ij}\f$ and \f$z_{ij}\f$ are the \f$x\f$, \f$y\f$ and \f$z\f$ components of the vector connecting atom \f$i\f$ to
46 : atom \f$j\f$ and \f$r_{ij}\f$ is the magnitude of this vector. \f$\sigma(r_{ij})\f$ is a \ref switchingfunction that acts on the distance between atom \f$i\f$ and atom \f$j\f$ and its inclusion in the numerator and the denominator of the above expression as well as the fact that we are summing
47 : over all of the other atoms in the system ensures that we are calculating an average
48 : of the function of \f$x_{ij}\f$, \f$y_{ij}\f$ and \f$z_{ij}\f$ for the atoms in the first coordination sphere around atom \f$i\f$.
49 : This quantity is once again a multicolvar so you can compute it for multiple atoms using a single PLUMED action and then compute
50 : the average value for the atoms in your system, the number of atoms that have an \f$s_i\f$ value that is more that some target and
51 : so on. Notice also that you can rotate the reference frame if you are using a non-standard unit cell.
52 :
53 :
54 : \par Examples
55 :
56 : The following input tells plumed to calculate the simple cubic parameter for the atoms 1-100 with themselves.
57 : The mean value is then calculated.
58 : \plumedfile
59 : SIMPLECUBIC SPECIES=1-100 R_0=1.0 MEAN
60 : \endplumedfile
61 :
62 : The following input tells plumed to look at the ways atoms 1-100 are within 3.0 are arranged about atoms
63 : from 101-110. The number of simple cubic parameters that are greater than 0.8 is then output
64 : \plumedfile
65 : SIMPLECUBIC SPECIESA=101-110 SPECIESB=1-100 R_0=3.0 MORE_THAN={RATIONAL R_0=0.8 NN=6 MM=12 D_0=0}
66 : \endplumedfile
67 :
68 : */
69 : //+ENDPLUMEDOC
70 :
71 :
72 2 : class SimpleCubic : public CubicHarmonicBase {
73 : public:
74 : static void registerKeywords( Keywords& keys );
75 : explicit SimpleCubic(const ActionOptions&);
76 : double calculateCubicHarmonic( const Vector& distance, const double& d2, Vector& myder ) const ;
77 : };
78 :
79 6453 : PLUMED_REGISTER_ACTION(SimpleCubic,"SIMPLECUBIC")
80 :
81 2 : void SimpleCubic::registerKeywords( Keywords& keys ) {
82 2 : CubicHarmonicBase::registerKeywords( keys );
83 2 : }
84 :
85 1 : SimpleCubic::SimpleCubic(const ActionOptions&ao):
86 : Action(ao),
87 1 : CubicHarmonicBase(ao)
88 : {
89 1 : checkRead();
90 1 : }
91 :
92 4032 : double SimpleCubic::calculateCubicHarmonic( const Vector& distance, const double& d2, Vector& myder ) const {
93 4032 : double x2 = distance[0]*distance[0];
94 4032 : double x3 = distance[0]*x2;
95 4032 : double x4 = distance[0]*x3;
96 :
97 4032 : double y2 = distance[1]*distance[1];
98 4032 : double y3 = distance[1]*y2;
99 4032 : double y4 = distance[1]*y3;
100 :
101 4032 : double z2 = distance[2]*distance[2];
102 4032 : double z3 = distance[2]*z2;
103 4032 : double z4 = distance[2]*z3;
104 :
105 4032 : double r4 = pow( d2, 2 );
106 4032 : double tmp = ( x4 + y4 + z4 ) / r4;
107 :
108 4032 : double t1=(x2+y2+z2), t2=t1*t1, t3=(x4+y4+z4)/(t1*t2);
109 4032 : myder[0] = 4*x3/t2-4*distance[0]*t3;
110 4032 : myder[1] = 4*y3/t2-4*distance[1]*t3;
111 4032 : myder[2] = 4*z3/t2-4*distance[2]*t3;
112 4032 : return tmp;
113 : }
114 :
115 : }
116 4839 : }
117 :
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