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 "core/ActionRegister.h"
24 : #include "tools/Vector.h"
25 : #include "tools/Exception.h"
26 : #include <array>
27 :
28 : namespace PLMD {
29 : namespace vatom {
30 :
31 : //+PLUMEDOC VATOM GHOST
32 : /*
33 : Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms.
34 :
35 : The computed ghost atom is stored as a virtual atom that can be accessed in
36 : an atom list through the the label for the GHOST action that creates it.
37 :
38 : When running with periodic boundary conditions, the atoms should be
39 : in the proper periodic image. This is done automatically since PLUMED 2.10,
40 : by considering the ordered list of atoms and rebuilding the molecule using a procedure
41 : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that
42 : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES
43 : which actually modifies the coordinates stored in PLUMED.
44 :
45 : In case you want to recover the old behavior you should use the NOPBC flag.
46 : In that case you need to take care that atoms are in the correct
47 : periodic image.
48 :
49 : \par Examples
50 :
51 : The following input instructs plumed to print the distance between the
52 : ghost atom and the center of mass for atoms 15,20:
53 : \plumedfile
54 : c1: GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0
55 : c2: COM ATOMS=15,20
56 : d1: DISTANCE ATOMS=c1,c2
57 : PRINT ARG=d1
58 : \endplumedfile
59 :
60 : */
61 : //+ENDPLUMEDOC
62 :
63 :
64 : class Ghost:
65 : public ActionWithVirtualAtom
66 : {
67 : std::vector<double> coord;
68 : std::vector<Tensor> deriv;
69 : bool nopbc=false;
70 : public:
71 : explicit Ghost(const ActionOptions&ao);
72 : void calculate() override;
73 : static void registerKeywords( Keywords& keys );
74 : };
75 :
76 : PLUMED_REGISTER_ACTION(Ghost,"GHOST")
77 :
78 711 : void Ghost::registerKeywords(Keywords& keys) {
79 711 : ActionWithVirtualAtom::registerKeywords(keys);
80 1422 : keys.add("atoms","COORDINATES","coordinates of the ghost atom in the local reference frame");
81 1422 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
82 711 : }
83 :
84 709 : Ghost::Ghost(const ActionOptions&ao):
85 : Action(ao),
86 709 : ActionWithVirtualAtom(ao)
87 : {
88 : std::vector<AtomNumber> atoms;
89 1418 : parseAtomList("ATOMS",atoms);
90 709 : if(atoms.size()!=3) error("ATOMS should contain a list of three atoms");
91 :
92 1418 : parseVector("COORDINATES",coord);
93 709 : if(coord.size()!=3) error("COORDINATES should be a list of three real numbers");
94 :
95 709 : parseFlag("NOPBC",nopbc);
96 :
97 709 : checkRead();
98 709 : log.printf(" of atoms");
99 2836 : for(unsigned i=0; i<atoms.size(); ++i) log.printf(" %d",atoms[i].serial());
100 709 : log.printf("\n");
101 :
102 709 : if(nopbc) {
103 4 : log<<" PBC will be ignored\n";
104 : } else {
105 705 : log<<" broken molecules will be rebuilt assuming atoms are in the proper order\n";
106 : }
107 709 : requestAtoms(atoms);
108 709 : }
109 :
110 1413 : void Ghost::calculate() {
111 :
112 1413 : if(!nopbc) makeWhole();
113 :
114 1413 : Vector pos;
115 1413 : deriv.resize(getNumberOfAtoms());
116 1413 : std::array<Vector,3> n;
117 :
118 : // first versor
119 1413 : Vector n01 = delta(getPosition(0), getPosition(1));
120 1413 : n[0]=n01/n01.modulo();
121 :
122 : // auxiliary vector
123 1413 : Vector n02 = delta(getPosition(0), getPosition(2));
124 :
125 : // second versor
126 1413 : Vector n03 = crossProduct(n[0],n02);
127 1413 : double n03_norm = n03.modulo();
128 1413 : n[1]=n03/n03_norm;
129 :
130 : // third versor
131 1413 : n[2]=crossProduct(n[0],n[1]);
132 :
133 : // origin of the reference system
134 1413 : pos = getPosition(0);
135 :
136 5652 : for(unsigned i=0; i<3; ++i) {
137 4239 : pos += coord[i] * n[i];
138 : }
139 :
140 1413 : setPosition(pos);
141 1413 : setMass(1.0);
142 1413 : setCharge(0.0);
143 :
144 : // some useful tensors for derivatives
145 1413 : Tensor dn0d0 = (-Tensor::identity()+Tensor(n[0],n[0]))/n01.modulo();
146 1413 : Tensor dn0d1 = (+Tensor::identity()-Tensor(n[0],n[0]))/n01.modulo();
147 1413 : Tensor dn02d0 = -Tensor::identity();
148 1413 : Tensor dn02d2 = Tensor::identity();
149 :
150 : // derivative of n1 = n0 x n02
151 1413 : Tensor dn1d0, dn1d1, dn1d2;
152 1413 : Vector aux0, aux1, aux2;
153 :
154 5652 : for(unsigned j=0; j<3; ++j) {
155 : // derivative of n0 x n02 with respect to point 0, coordinate j
156 4239 : Vector tmp00 = Vector( dn0d0(j,0), dn0d0(j,1), dn0d0(j,2));
157 4239 : Vector tmp020 = Vector(dn02d0(j,0), dn02d0(j,1), dn02d0(j,2));
158 4239 : Vector tmp0 = crossProduct(tmp00,n02) + crossProduct(n[0],tmp020);
159 4239 : aux0[j] = dotProduct(tmp0,n[1]);
160 : // derivative of n0 x n02 with respect to point 1, coordinate j
161 4239 : Vector tmp01 = Vector( dn0d1(j,0), dn0d1(j,1), dn0d1(j,2));
162 4239 : Vector tmp1 = crossProduct(tmp01,n02);
163 4239 : aux1[j] = dotProduct(tmp1,n[1]);
164 : // derivative of n0 x n02 with respect to point 2, coordinate j
165 4239 : Vector tmp022 = Vector(dn02d2(j,0), dn02d2(j,1), dn02d2(j,2));
166 4239 : Vector tmp2 = crossProduct(n[0],tmp022);
167 4239 : aux2[j] = dotProduct(tmp2,n[1]);
168 : // derivative of n1 = (n0 x n02) / || (n0 x n02) ||
169 16956 : for(unsigned i=0; i<3; ++i) {
170 12717 : dn1d0(j,i) = ( tmp0[i] - aux0[j] * n[1][i] ) / n03_norm;
171 12717 : dn1d1(j,i) = ( tmp1[i] - aux1[j] * n[1][i] ) / n03_norm;
172 12717 : dn1d2(j,i) = ( tmp2[i] - aux2[j] * n[1][i] ) / n03_norm;
173 : }
174 : }
175 :
176 : // Derivative of the last versor n2 = n0 x n1 = ( n0( n0 n02 ) - n02 ) / || n0 x n02 ||
177 : // Scalar product and derivatives
178 1413 : double n0_n02 = dotProduct(n[0],n02);
179 1413 : Vector dn0_n02d0, dn0_n02d1, dn0_n02d2;
180 :
181 5652 : for(unsigned j=0; j<3; ++j) {
182 16956 : for(unsigned i=0; i<3; ++i) {
183 12717 : dn0_n02d0[j] += dn0d0(j,i)*n02[i] + n[0][i]*dn02d0(j,i);
184 12717 : dn0_n02d1[j] += dn0d1(j,i)*n02[i];
185 12717 : dn0_n02d2[j] += n[0][i]*dn02d2(j,i);
186 : }
187 : }
188 :
189 1413 : Tensor dn2d0, dn2d1, dn2d2;
190 5652 : for(unsigned j=0; j<3; ++j) {
191 16956 : for(unsigned i=0; i<3; ++i) {
192 12717 : 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;
193 12717 : 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;
194 12717 : 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;
195 : }
196 : }
197 :
198 : // Finally, the derivative tensor
199 1413 : deriv[0] = Tensor::identity() + coord[0]*dn0d0 + coord[1]*dn1d0 + coord[2]*dn2d0;
200 1413 : deriv[1] = coord[0]*dn0d1 + coord[1]*dn1d1 + coord[2]*dn2d1;
201 1413 : deriv[2] = coord[1]*dn1d2 + coord[2]*dn2d2;
202 :
203 1413 : setAtomsDerivatives(deriv);
204 :
205 : // Virial contribution
206 1413 : setBoxDerivativesNoPbc();
207 1413 : }
208 :
209 : }
210 : }
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