OpenMD 3.0
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
MagneticField.cpp
1/*
2 * Copyright (c) 2004-present, The University of Notre Dame. All rights
3 * reserved.
4 *
5 * Redistribution and use in source and binary forms, with or without
6 * modification, are permitted provided that the following conditions are met:
7 *
8 * 1. Redistributions of source code must retain the above copyright notice,
9 * this list of conditions and the following disclaimer.
10 *
11 * 2. Redistributions in binary form must reproduce the above copyright notice,
12 * this list of conditions and the following disclaimer in the documentation
13 * and/or other materials provided with the distribution.
14 *
15 * 3. Neither the name of the copyright holder nor the names of its
16 * contributors may be used to endorse or promote products derived from
17 * this software without specific prior written permission.
18 *
19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
23 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
24 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
25 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
26 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
27 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
28 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
29 * POSSIBILITY OF SUCH DAMAGE.
30 *
31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
46
47#include "brains/ForceModifier.hpp"
48#include "nonbonded/NonBondedInteraction.hpp"
50#include "types/FixedChargeAdapter.hpp"
51#include "types/MultipoleAdapter.hpp"
52#include "utils/Constants.hpp"
53
54namespace OpenMD {
55
56 MagneticField::MagneticField(SimInfo* info) :
57 ForceModifier {info}, initialized {false}, doMagneticField {false} {
58 simParams = info_->getSimParams();
59 }
60
61 void MagneticField::initialize() {
62 std::vector<RealType> mf;
63
64 if (simParams->haveMagneticField()) {
65 doMagneticField = true;
66 mf = simParams->getMagneticField();
67 }
68 if (mf.size() != 3) {
69 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
70 "MagneticField: Incorrect number of parameters specified.\n"
71 "\tthere should be 3 parameters, but %lu were specified.\n",
72 mf.size());
73 painCave.isFatal = 1;
74 simError();
75 }
76 MF.x() = mf[0];
77 MF.y() = mf[1];
78 MF.z() = mf[2];
79
80 initialized = true;
81 }
82
83 void MagneticField::modifyForces() {
84 if (!initialized) initialize();
85
86 SimInfo::MoleculeIterator i;
87 Molecule::AtomIterator j;
88 Molecule* mol;
89 Atom* atom;
90 AtomType* atype;
91
92 int l, m, n;
93 RealType C;
94 Vector3d v;
95 Vector3d f;
96 Vector3d r;
97 Vector3d t;
98 Vector3d D;
99 Vector3d AngMomentum;
100 Vector3d omega;
101 Mat3x3d I;
102 bool isCharge;
103
104 if (doMagneticField) {
105 for (mol = info_->beginMolecule(i); mol != NULL;
106 mol = info_->nextMolecule(i)) {
107 for (atom = mol->beginAtom(j); atom != NULL; atom = mol->nextAtom(j)) {
108 isCharge = false;
109 C = 0.0;
110
111 atype = atom->getAtomType();
112 r = atom->getPos();
113 v = atom->getVel();
114
115 FixedChargeAdapter fca = FixedChargeAdapter(atype);
116 if (fca.isFixedCharge()) {
117 isCharge = true;
118 C = fca.getCharge();
119 }
120
121 C *= Constants::chargeFieldConvert;
122
123 if (isCharge) {
124 f = cross(v, MF) * C * Constants::magneticFieldConvert;
125 atom->addFrc(f);
126 }
127
128 MultipoleAdapter ma = MultipoleAdapter(atype);
129 if (ma.isDipole()) {
130 D = atom->getDipole() * Constants::dipoleFieldConvert;
131
132 t = cross(D, cross(v, MF));
133 atom->addTrq(t);
134
135 AngMomentum = atom->getJ();
136 I = atom->getI();
137 if (atom->isLinear()) {
138 l = atom->linearAxis();
139 m = (l + 1) % 3;
140 n = (l + 2) % 3;
141 omega[l] = 0;
142 omega[m] = AngMomentum[m] / I(m, m);
143 omega[n] = AngMomentum[n] / I(n, n);
144 } else {
145 omega = I.inverse() * AngMomentum;
146 }
147
148 f = cross(cross(omega, D), MF);
149 atom->addFrc(f);
150 }
151 }
152 }
153 }
154 }
155} // namespace OpenMD
Uniform Magnetic Field perturbation.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Vector3< Real > cross(const Vector3< Real > &v1, const Vector3< Real > &v2)
Returns the cross product of two Vectors.
Definition Vector3.hpp:136