Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2023 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 : namespace PLMD {
28 : namespace vatom {
29 :
30 : //+PLUMEDOC VATOM GHOST
31 : /*
32 : Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms.
33 :
34 : The computed ghost atom is stored as a virtual atom that can be accessed in
35 : an atom list through the the label for the GHOST action that creates it.
36 :
37 : \par Examples
38 :
39 : The following input instructs plumed to print the distance between the
40 : ghost atom and the center of mass for atoms 15,20:
41 : \plumedfile
42 : c1: GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0
43 : c2: COM ATOMS=15,20
44 : d1: DISTANCE ATOMS=c1,c2
45 : PRINT ARG=d1
46 : \endplumedfile
47 :
48 : */
49 : //+ENDPLUMEDOC
50 :
51 :
52 : class Ghost:
53 : public ActionWithVirtualAtom
54 : {
55 : std::vector<double> coord;
56 : public:
57 : explicit Ghost(const ActionOptions&ao);
58 : void calculate() override;
59 : static void registerKeywords( Keywords& keys );
60 : };
61 :
62 10425 : PLUMED_REGISTER_ACTION(Ghost,"GHOST")
63 :
64 4 : void Ghost::registerKeywords(Keywords& keys) {
65 4 : ActionWithVirtualAtom::registerKeywords(keys);
66 8 : keys.add("atoms","COORDINATES","coordinates of the ghost atom in the local reference frame");
67 4 : }
68 :
69 3 : Ghost::Ghost(const ActionOptions&ao):
70 : Action(ao),
71 3 : ActionWithVirtualAtom(ao)
72 : {
73 : std::vector<AtomNumber> atoms;
74 6 : parseAtomList("ATOMS",atoms);
75 3 : if(atoms.size()!=3) error("ATOMS should contain a list of three atoms");
76 :
77 6 : parseVector("COORDINATES",coord);
78 3 : if(coord.size()!=3) error("COORDINATES should be a list of three real numbers");
79 :
80 3 : checkRead();
81 3 : log.printf(" of atoms");
82 12 : for(unsigned i=0; i<atoms.size(); ++i) log.printf(" %d",atoms[i].serial());
83 3 : log.printf("\n");
84 3 : requestAtoms(atoms);
85 3 : }
86 :
87 7 : void Ghost::calculate() {
88 7 : Vector pos;
89 7 : std::vector<Tensor> deriv(getNumberOfAtoms());
90 : std::vector<Vector> n;
91 :
92 : // first versor
93 7 : Vector n01 = delta(getPosition(0), getPosition(1));
94 14 : n.push_back(n01/n01.modulo());
95 :
96 : // auxiliary vector
97 7 : Vector n02 = delta(getPosition(0), getPosition(2));
98 :
99 : // second versor
100 7 : Vector n03 = crossProduct(n[0],n02);
101 7 : double n03_norm = n03.modulo();
102 14 : n.push_back(n03/n03_norm);
103 :
104 : // third versor
105 14 : n.push_back(crossProduct(n[0],n[1]));
106 :
107 : // origin of the reference system
108 7 : pos = getPosition(0);
109 :
110 28 : for(unsigned i=0; i<3; ++i) {
111 21 : pos += coord[i] * n[i];
112 : }
113 :
114 : setPosition(pos);
115 : setMass(1.0);
116 : setCharge(0.0);
117 :
118 : // some useful tensors for derivatives
119 7 : Tensor dn0d0 = (-Tensor::identity()+Tensor(n[0],n[0]))/n01.modulo();
120 7 : Tensor dn0d1 = (+Tensor::identity()-Tensor(n[0],n[0]))/n01.modulo();
121 7 : Tensor dn02d0 = -Tensor::identity();
122 7 : Tensor dn02d2 = Tensor::identity();
123 :
124 : // derivative of n1 = n0 x n02
125 7 : Tensor dn1d0, dn1d1, dn1d2;
126 7 : Vector aux0, aux1, aux2;
127 :
128 28 : for(unsigned j=0; j<3; ++j) {
129 : // derivative of n0 x n02 with respect to point 0, coordinate j
130 21 : Vector tmp00 = Vector( dn0d0(j,0), dn0d0(j,1), dn0d0(j,2));
131 21 : Vector tmp020 = Vector(dn02d0(j,0), dn02d0(j,1), dn02d0(j,2));
132 21 : Vector tmp0 = crossProduct(tmp00,n02) + crossProduct(n[0],tmp020);
133 21 : aux0[j] = dotProduct(tmp0,n[1]);
134 : // derivative of n0 x n02 with respect to point 1, coordinate j
135 21 : Vector tmp01 = Vector( dn0d1(j,0), dn0d1(j,1), dn0d1(j,2));
136 21 : Vector tmp1 = crossProduct(tmp01,n02);
137 21 : aux1[j] = dotProduct(tmp1,n[1]);
138 : // derivative of n0 x n02 with respect to point 2, coordinate j
139 21 : Vector tmp022 = Vector(dn02d2(j,0), dn02d2(j,1), dn02d2(j,2));
140 21 : Vector tmp2 = crossProduct(n[0],tmp022);
141 21 : aux2[j] = dotProduct(tmp2,n[1]);
142 : // derivative of n1 = (n0 x n02) / || (n0 x n02) ||
143 84 : for(unsigned i=0; i<3; ++i) {
144 63 : dn1d0(j,i) = ( tmp0[i] - aux0[j] * n[1][i] ) / n03_norm;
145 63 : dn1d1(j,i) = ( tmp1[i] - aux1[j] * n[1][i] ) / n03_norm;
146 63 : dn1d2(j,i) = ( tmp2[i] - aux2[j] * n[1][i] ) / n03_norm;
147 : }
148 : }
149 :
150 : // Derivative of the last versor n2 = n0 x n1 = ( n0( n0 n02 ) - n02 ) / || n0 x n02 ||
151 : // Scalar product and derivatives
152 7 : double n0_n02 = dotProduct(n[0],n02);
153 7 : Vector dn0_n02d0, dn0_n02d1, dn0_n02d2;
154 :
155 28 : for(unsigned j=0; j<3; ++j) {
156 84 : for(unsigned i=0; i<3; ++i) {
157 63 : dn0_n02d0[j] += dn0d0(j,i)*n02[i] + n[0][i]*dn02d0(j,i);
158 63 : dn0_n02d1[j] += dn0d1(j,i)*n02[i];
159 63 : dn0_n02d2[j] += n[0][i]*dn02d2(j,i);
160 : }
161 : }
162 :
163 7 : Tensor dn2d0, dn2d1, dn2d2;
164 28 : for(unsigned j=0; j<3; ++j) {
165 84 : for(unsigned i=0; i<3; ++i) {
166 63 : 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;
167 63 : 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;
168 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;
169 : }
170 : }
171 :
172 : // Finally, the derivative tensor
173 7 : deriv[0] = Tensor::identity() + coord[0]*dn0d0 + coord[1]*dn1d0 + coord[2]*dn2d0;
174 7 : deriv[1] = coord[0]*dn0d1 + coord[1]*dn1d1 + coord[2]*dn2d1;
175 7 : deriv[2] = coord[1]*dn1d2 + coord[2]*dn2d2;
176 :
177 : setAtomsDerivatives(deriv);
178 :
179 : // Virial contribution
180 7 : setBoxDerivativesNoPbc();
181 7 : }
182 :
183 : }
184 : }
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