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 : std::vector<double> coord;
55 : public:
56 : explicit Ghost(const ActionOptions&ao);
57 : void calculate() override;
58 : static void registerKeywords( Keywords& keys );
59 : };
60 :
61 13791 : PLUMED_REGISTER_ACTION(Ghost,"GHOST")
62 :
63 7 : void Ghost::registerKeywords(Keywords& keys) {
64 7 : ActionWithVirtualAtom::registerKeywords(keys);
65 14 : keys.add("atoms","COORDINATES","coordinates of the ghost atom in the local reference frame");
66 7 : }
67 :
68 3 : Ghost::Ghost(const ActionOptions&ao):
69 : Action(ao),
70 3 : ActionWithVirtualAtom(ao) {
71 : std::vector<AtomNumber> atoms;
72 6 : parseAtomList("ATOMS",atoms);
73 3 : if(atoms.size()!=3) {
74 0 : error("ATOMS should contain a list of three atoms");
75 : }
76 :
77 6 : parseVector("COORDINATES",coord);
78 3 : if(coord.size()!=3) {
79 0 : error("COORDINATES should be a list of three real numbers");
80 : }
81 :
82 3 : checkRead();
83 3 : log.printf(" of atoms");
84 12 : for(unsigned i=0; i<atoms.size(); ++i) {
85 9 : log.printf(" %d",atoms[i].serial());
86 : }
87 3 : log.printf("\n");
88 3 : requestAtoms(atoms);
89 3 : }
90 :
91 7 : void Ghost::calculate() {
92 7 : Vector pos;
93 7 : std::vector<Tensor> deriv(getNumberOfAtoms());
94 : std::vector<Vector> n;
95 :
96 : // first versor
97 7 : Vector n01 = delta(getPosition(0), getPosition(1));
98 14 : n.push_back(n01/n01.modulo());
99 :
100 : // auxiliary vector
101 7 : Vector n02 = delta(getPosition(0), getPosition(2));
102 :
103 : // second versor
104 7 : Vector n03 = crossProduct(n[0],n02);
105 7 : double n03_norm = n03.modulo();
106 14 : n.push_back(n03/n03_norm);
107 :
108 : // third versor
109 14 : n.push_back(crossProduct(n[0],n[1]));
110 :
111 : // origin of the reference system
112 7 : pos = getPosition(0);
113 :
114 28 : for(unsigned i=0; i<3; ++i) {
115 21 : pos += coord[i] * n[i];
116 : }
117 :
118 : setPosition(pos);
119 : setMass(1.0);
120 : setCharge(0.0);
121 :
122 : // some useful tensors for derivatives
123 7 : Tensor dn0d0 = (-Tensor::identity()+Tensor(n[0],n[0]))/n01.modulo();
124 7 : Tensor dn0d1 = (+Tensor::identity()-Tensor(n[0],n[0]))/n01.modulo();
125 7 : Tensor dn02d0 = -Tensor::identity();
126 7 : Tensor dn02d2 = Tensor::identity();
127 :
128 : // derivative of n1 = n0 x n02
129 7 : Tensor dn1d0, dn1d1, dn1d2;
130 7 : Vector aux0, aux1, aux2;
131 :
132 28 : for(unsigned j=0; j<3; ++j) {
133 : // derivative of n0 x n02 with respect to point 0, coordinate j
134 21 : Vector tmp00 = Vector( dn0d0(j,0), dn0d0(j,1), dn0d0(j,2));
135 21 : Vector tmp020 = Vector(dn02d0(j,0), dn02d0(j,1), dn02d0(j,2));
136 21 : Vector tmp0 = crossProduct(tmp00,n02) + crossProduct(n[0],tmp020);
137 21 : aux0[j] = dotProduct(tmp0,n[1]);
138 : // derivative of n0 x n02 with respect to point 1, coordinate j
139 21 : Vector tmp01 = Vector( dn0d1(j,0), dn0d1(j,1), dn0d1(j,2));
140 21 : Vector tmp1 = crossProduct(tmp01,n02);
141 21 : aux1[j] = dotProduct(tmp1,n[1]);
142 : // derivative of n0 x n02 with respect to point 2, coordinate j
143 21 : Vector tmp022 = Vector(dn02d2(j,0), dn02d2(j,1), dn02d2(j,2));
144 21 : Vector tmp2 = crossProduct(n[0],tmp022);
145 21 : aux2[j] = dotProduct(tmp2,n[1]);
146 : // derivative of n1 = (n0 x n02) / || (n0 x n02) ||
147 84 : for(unsigned i=0; i<3; ++i) {
148 63 : dn1d0(j,i) = ( tmp0[i] - aux0[j] * n[1][i] ) / n03_norm;
149 63 : dn1d1(j,i) = ( tmp1[i] - aux1[j] * n[1][i] ) / n03_norm;
150 63 : dn1d2(j,i) = ( tmp2[i] - aux2[j] * n[1][i] ) / n03_norm;
151 : }
152 : }
153 :
154 : // Derivative of the last versor n2 = n0 x n1 = ( n0( n0 n02 ) - n02 ) / || n0 x n02 ||
155 : // Scalar product and derivatives
156 7 : double n0_n02 = dotProduct(n[0],n02);
157 7 : Vector dn0_n02d0, dn0_n02d1, dn0_n02d2;
158 :
159 28 : for(unsigned j=0; j<3; ++j) {
160 84 : for(unsigned i=0; i<3; ++i) {
161 63 : dn0_n02d0[j] += dn0d0(j,i)*n02[i] + n[0][i]*dn02d0(j,i);
162 63 : dn0_n02d1[j] += dn0d1(j,i)*n02[i];
163 63 : dn0_n02d2[j] += n[0][i]*dn02d2(j,i);
164 : }
165 : }
166 :
167 7 : Tensor dn2d0, dn2d1, dn2d2;
168 28 : for(unsigned j=0; j<3; ++j) {
169 84 : for(unsigned i=0; i<3; ++i) {
170 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;
171 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;
172 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;
173 : }
174 : }
175 :
176 : // Finally, the derivative tensor
177 7 : deriv[0] = Tensor::identity() + coord[0]*dn0d0 + coord[1]*dn1d0 + coord[2]*dn2d0;
178 7 : deriv[1] = coord[0]*dn0d1 + coord[1]*dn1d1 + coord[2]*dn2d1;
179 7 : deriv[2] = coord[1]*dn1d2 + coord[2]*dn2d2;
180 :
181 : setAtomsDerivatives(deriv);
182 :
183 : // Virial contribution
184 7 : setBoxDerivativesNoPbc();
185 7 : }
186 :
187 : }
188 : }
|
