OpenMD 3.0
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
StuntDouble.cpp
Go to the documentation of this file.
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
45/**
46 * @file StuntDouble.cpp
47 * @author tlin
48 * @date 10/22/2004
49 * @version 1.0
50 */
51
53
54#include <cassert>
55#include <memory>
56
57namespace OpenMD {
58
59 StuntDouble::StuntDouble(ObjectType objType, DataStoragePointer storage) :
60 objType_(objType), storage_(storage), snapshotMan_(NULL), linear_(false),
61 linearAxis_(-1), globalIndex_(-1), globalIntegrableObjectIndex_(-1),
62 localIndex_(-1) {}
63
64 void StuntDouble::zeroForcesAndTorques() {
65 int sl = (snapshotMan_->getCurrentSnapshot()->*storage_).getStorageLayout();
66
67 if (sl & DataStorage::dslForce) setFrc(V3Zero);
68 if (sl & DataStorage::dslTorque) setTrq(V3Zero);
69 if (sl & DataStorage::dslParticlePot) setParticlePot(0.0);
70 if (sl & DataStorage::dslFlucQForce) setFlucQFrc(0.0);
71 if (sl & DataStorage::dslElectricField) setElectricField(V3Zero);
72 if (sl & DataStorage::dslSitePotential) setSitePotential(0.0);
73 }
74
75 void StuntDouble::combineForcesAndTorques(Snapshot* snapA, Snapshot* snapB,
76 RealType multA, RealType multB) {
77 int sl = (snapshotMan_->getCurrentSnapshot()->*storage_).getStorageLayout();
78
79 assert(sl == (snapA->*storage_).getStorageLayout());
80 assert(sl == (snapB->*storage_).getStorageLayout());
81
82 if (sl & DataStorage::dslForce) {
83 Vector3d forceA = (snapA->*storage_).force[localIndex_];
84 Vector3d forceB = (snapB->*storage_).force[localIndex_];
85
86 ((snapshotMan_->getCurrentSnapshot())->*storage_).force[localIndex_] =
87 multA * forceA + multB * forceB;
88 }
89
90 if (sl & DataStorage::dslTorque) {
91 Vector3d torqueA = (snapA->*storage_).torque[localIndex_];
92 Vector3d torqueB = (snapB->*storage_).torque[localIndex_];
93
94 ((snapshotMan_->getCurrentSnapshot())->*storage_).torque[localIndex_] =
95 multA * torqueA + multB * torqueB;
96 }
97
98 if (sl & DataStorage::dslParticlePot) {
99 RealType particlePotA = (snapA->*storage_).particlePot[localIndex_];
100 RealType particlePotB = (snapB->*storage_).particlePot[localIndex_];
101
102 ((snapshotMan_->getCurrentSnapshot())->*storage_)
103 .particlePot[localIndex_] =
104 multA * particlePotA + multB * particlePotB;
105 }
106
107 if (sl & DataStorage::dslFlucQForce) {
108 RealType flucQFrcA = (snapA->*storage_).flucQFrc[localIndex_];
109 RealType flucQFrcB = (snapB->*storage_).flucQFrc[localIndex_];
110
111 ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQFrc[localIndex_] =
112 multA * flucQFrcA + multB * flucQFrcB;
113 }
114
115 if (sl & DataStorage::dslElectricField) {
116 Vector3d electricFieldA = (snapA->*storage_).electricField[localIndex_];
117 Vector3d electricFieldB = (snapB->*storage_).electricField[localIndex_];
118
119 ((snapshotMan_->getCurrentSnapshot())->*storage_)
120 .electricField[localIndex_] =
121 multA * electricFieldA + multB * electricFieldB;
122 }
123
124 if (sl & DataStorage::dslSitePotential) {
125 RealType sitePotentialA = (snapA->*storage_).sitePotential[localIndex_];
126 RealType sitePotentialB = (snapB->*storage_).sitePotential[localIndex_];
127
128 ((snapshotMan_->getCurrentSnapshot())->*storage_)
129 .sitePotential[localIndex_] =
130 multA * sitePotentialA + multB * sitePotentialB;
131 }
132 }
133
134 void StuntDouble::addProperty(std::shared_ptr<GenericData> genData) {
135 properties_.addProperty(genData);
136 }
137
138 void StuntDouble::removeProperty(const std::string& propName) {
139 properties_.removeProperty(propName);
140 }
141
142 std::vector<std::string> StuntDouble::getPropertyNames() {
143 return properties_.getPropertyNames();
144 }
145
146 std::vector<std::shared_ptr<GenericData>> StuntDouble::getProperties() {
147 return properties_.getProperties();
148 }
149
150 std::shared_ptr<GenericData> StuntDouble::getPropertyByName(
151 const std::string& propName) {
152 return properties_.getPropertyByName(propName);
153 }
154
155} // namespace OpenMD
The Snapshot class is a repository storing dynamic data during a Simulation.
Definition Snapshot.hpp:147
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.