Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2019 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 "ActionWithVirtualAtom.h"
23 : #include "ActionRegister.h"
24 : #include "tools/Vector.h"
25 : #include "tools/Exception.h"
26 :
27 : using namespace std;
28 :
29 : namespace PLMD {
30 : namespace vatom {
31 :
32 : //+PLUMEDOC VATOM GHOST
33 : /*
34 : Calculate the absolute position of a ghost atom with fixed coordinates
35 : in the local reference frame formed by three atoms.
36 : The computed ghost atom is stored as a virtual atom that can be accessed in
37 : an atom list through the the label for the GHOST action that creates it.
38 :
39 : \par Examples
40 :
41 : The following input instructs plumed to print the distance between the
42 : ghost atom and the center of mass for atoms 15,20:
43 : \plumedfile
44 : c1: GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0
45 : c2: COM ATOMS=15,20
46 : d1: DISTANCE ATOMS=c1,c2
47 : PRINT ARG=d1
48 : \endplumedfile
49 :
50 : */
51 : //+ENDPLUMEDOC
52 :
53 :
54 9 : class Ghost:
55 : public ActionWithVirtualAtom
56 : {
57 : vector<double> coord;
58 : public:
59 : explicit Ghost(const ActionOptions&ao);
60 : void calculate();
61 : static void registerKeywords( Keywords& keys );
62 : };
63 :
64 6455 : PLUMED_REGISTER_ACTION(Ghost,"GHOST")
65 :
66 4 : void Ghost::registerKeywords(Keywords& keys) {
67 4 : ActionWithVirtualAtom::registerKeywords(keys);
68 16 : keys.add("atoms","COORDINATES","coordinates of the ghost atom in the local reference frame");
69 4 : }
70 :
71 3 : Ghost::Ghost(const ActionOptions&ao):
72 : Action(ao),
73 3 : ActionWithVirtualAtom(ao)
74 : {
75 : vector<AtomNumber> atoms;
76 6 : parseAtomList("ATOMS",atoms);
77 3 : if(atoms.size()!=3) error("ATOMS should contain a list of three atoms");
78 :
79 6 : parseVector("COORDINATES",coord);
80 3 : if(coord.size()!=3) error("COORDINATES should be a list of three real numbers");
81 :
82 3 : checkRead();
83 3 : log.printf(" of atoms");
84 33 : for(unsigned i=0; i<atoms.size(); ++i) log.printf(" %d",atoms[i].serial());
85 3 : log.printf("\n");
86 3 : requestAtoms(atoms);
87 3 : }
88 :
89 7 : void Ghost::calculate() {
90 7 : Vector pos;
91 7 : vector<Tensor> deriv(getNumberOfAtoms());
92 : vector<Vector> n;
93 :
94 : // first versor
95 7 : Vector n01 = delta(getPosition(0), getPosition(1));
96 14 : n.push_back(n01/n01.modulo());
97 :
98 : // auxiliary vector
99 7 : Vector n02 = delta(getPosition(0), getPosition(2));
100 :
101 : // second versor
102 7 : Vector n03 = crossProduct(n[0],n02);
103 7 : double n03_norm = n03.modulo();
104 14 : n.push_back(n03/n03_norm);
105 :
106 : // third versor
107 14 : n.push_back(crossProduct(n[0],n[1]));
108 :
109 : // origin of the reference system
110 7 : pos = getPosition(0);
111 :
112 49 : for(unsigned i=0; i<3; ++i) {
113 42 : pos += coord[i] * n[i];
114 : }
115 :
116 : setPosition(pos);
117 : setMass(1.0);
118 : setCharge(0.0);
119 :
120 : // some useful tensors for derivatives
121 14 : Tensor dn0d0 = (-Tensor::identity()+Tensor(n[0],n[0]))/n01.modulo();
122 14 : Tensor dn0d1 = (+Tensor::identity()-Tensor(n[0],n[0]))/n01.modulo();
123 7 : Tensor dn02d0 = -Tensor::identity();
124 7 : Tensor dn02d2 = Tensor::identity();
125 :
126 : // derivative of n1 = n0 x n02
127 7 : Tensor dn1d0, dn1d1, dn1d2;
128 7 : Vector aux0, aux1, aux2;
129 :
130 49 : for(unsigned j=0; j<3; ++j) {
131 : // derivative of n0 x n02 with respect to point 0, coordinate j
132 21 : Vector tmp00 = Vector( dn0d0(j,0), dn0d0(j,1), dn0d0(j,2));
133 21 : Vector tmp020 = Vector(dn02d0(j,0), dn02d0(j,1), dn02d0(j,2));
134 21 : Vector tmp0 = crossProduct(tmp00,n02) + crossProduct(n[0],tmp020);
135 21 : aux0[j] = dotProduct(tmp0,n[1]);
136 : // derivative of n0 x n02 with respect to point 1, coordinate j
137 21 : Vector tmp01 = Vector( dn0d1(j,0), dn0d1(j,1), dn0d1(j,2));
138 21 : Vector tmp1 = crossProduct(tmp01,n02);
139 21 : aux1[j] = dotProduct(tmp1,n[1]);
140 : // derivative of n0 x n02 with respect to point 2, coordinate j
141 21 : Vector tmp022 = Vector(dn02d2(j,0), dn02d2(j,1), dn02d2(j,2));
142 21 : Vector tmp2 = crossProduct(n[0],tmp022);
143 21 : aux2[j] = dotProduct(tmp2,n[1]);
144 : // derivative of n1 = (n0 x n02) / || (n0 x n02) ||
145 147 : for(unsigned i=0; i<3; ++i) {
146 126 : dn1d0(j,i) = ( tmp0[i] - aux0[j] * n[1][i] ) / n03_norm;
147 126 : dn1d1(j,i) = ( tmp1[i] - aux1[j] * n[1][i] ) / n03_norm;
148 126 : dn1d2(j,i) = ( tmp2[i] - aux2[j] * n[1][i] ) / n03_norm;
149 : }
150 : }
151 :
152 : // Derivative of the last versor n2 = n0 x n1 = ( n0( n0 n02 ) - n02 ) / || n0 x n02 ||
153 : // Scalar product and derivatives
154 7 : double n0_n02 = dotProduct(n[0],n02);
155 7 : Vector dn0_n02d0, dn0_n02d1, dn0_n02d2;
156 :
157 49 : for(unsigned j=0; j<3; ++j) {
158 147 : for(unsigned i=0; i<3; ++i) {
159 126 : dn0_n02d0[j] += dn0d0(j,i)*n02[i] + n[0][i]*dn02d0(j,i);
160 63 : dn0_n02d1[j] += dn0d1(j,i)*n02[i];
161 63 : dn0_n02d2[j] += n[0][i]*dn02d2(j,i);
162 : }
163 : }
164 :
165 7 : Tensor dn2d0, dn2d1, dn2d2;
166 49 : for(unsigned j=0; j<3; ++j) {
167 147 : for(unsigned i=0; i<3; ++i) {
168 126 : dn2d0(j,i) = ( dn0d0(j,i) * n0_n02 + n[0][i] * dn0_n02d0[j] - dn02d0(j,i) - ( n[0][i] * n0_n02 - n02[i] ) * aux0[j] / n03_norm ) / n03_norm;
169 126 : dn2d1(j,i) = ( dn0d1(j,i) * n0_n02 + n[0][i] * dn0_n02d1[j] - ( n[0][i] * n0_n02 - n02[i] ) * aux1[j] / n03_norm ) / n03_norm;
170 63 : dn2d2(j,i) = ( n[0][i] * dn0_n02d2[j] - dn02d2(j,i) - ( n[0][i] * n0_n02 - n02[i] ) * aux2[j] / n03_norm ) / n03_norm;
171 : }
172 : }
173 :
174 : // Finally, the derivative tensor
175 28 : deriv[0] = Tensor::identity() + coord[0]*dn0d0 + coord[1]*dn1d0 + coord[2]*dn2d0;
176 28 : deriv[1] = coord[0]*dn0d1 + coord[1]*dn1d1 + coord[2]*dn2d1;
177 21 : deriv[2] = coord[1]*dn1d2 + coord[2]*dn2d2;
178 :
179 : setAtomsDerivatives(deriv);
180 :
181 : // Virial contribution
182 7 : setBoxDerivativesNoPbc();
183 7 : }
184 :
185 : }
186 4839 : }
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