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root/OpenMD/trunk/src/brains/Thermo.cpp
Revision: 998
Committed: Mon Jul 3 13:18:43 2006 UTC (18 years, 10 months ago) by chrisfen
File size: 7684 byte(s)
Log Message:
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants

File Contents

# Content
1 /*
2 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 *
4 * The University of Notre Dame grants you ("Licensee") a
5 * non-exclusive, royalty free, license to use, modify and
6 * redistribute this software in source and binary code form, provided
7 * that the following conditions are met:
8 *
9 * 1. Acknowledgement of the program authors must be made in any
10 * publication of scientific results based in part on use of the
11 * program. An acceptable form of acknowledgement is citation of
12 * the article in which the program was described (Matthew
13 * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 * Parallel Simulation Engine for Molecular Dynamics,"
16 * J. Comput. Chem. 26, pp. 252-271 (2005))
17 *
18 * 2. Redistributions of source code must retain the above copyright
19 * notice, this list of conditions and the following disclaimer.
20 *
21 * 3. Redistributions in binary form must reproduce the above copyright
22 * notice, this list of conditions and the following disclaimer in the
23 * documentation and/or other materials provided with the
24 * distribution.
25 *
26 * This software is provided "AS IS," without a warranty of any
27 * kind. All express or implied conditions, representations and
28 * warranties, including any implied warranty of merchantability,
29 * fitness for a particular purpose or non-infringement, are hereby
30 * excluded. The University of Notre Dame and its licensors shall not
31 * be liable for any damages suffered by licensee as a result of
32 * using, modifying or distributing the software or its
33 * derivatives. In no event will the University of Notre Dame or its
34 * licensors be liable for any lost revenue, profit or data, or for
35 * direct, indirect, special, consequential, incidental or punitive
36 * damages, however caused and regardless of the theory of liability,
37 * arising out of the use of or inability to use software, even if the
38 * University of Notre Dame has been advised of the possibility of
39 * such damages.
40 */
41
42 #include <math.h>
43 #include <iostream>
44
45 #ifdef IS_MPI
46 #include <mpi.h>
47 #endif //is_mpi
48
49 #include "brains/Thermo.hpp"
50 #include "primitives/Molecule.hpp"
51 #include "utils/simError.h"
52 #include "utils/OOPSEConstant.hpp"
53
54 namespace oopse {
55
56 RealType Thermo::getKinetic() {
57 SimInfo::MoleculeIterator miter;
58 std::vector<StuntDouble*>::iterator iiter;
59 Molecule* mol;
60 StuntDouble* integrableObject;
61 Vector3d vel;
62 Vector3d angMom;
63 Mat3x3d I;
64 int i;
65 int j;
66 int k;
67 RealType mass;
68 RealType kinetic = 0.0;
69 RealType kinetic_global = 0.0;
70
71 for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72 for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73 integrableObject = mol->nextIntegrableObject(iiter)) {
74
75 mass = integrableObject->getMass();
76 vel = integrableObject->getVel();
77
78 kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
79
80 if (integrableObject->isDirectional()) {
81 angMom = integrableObject->getJ();
82 I = integrableObject->getI();
83
84 if (integrableObject->isLinear()) {
85 i = integrableObject->linearAxis();
86 j = (i + 1) % 3;
87 k = (i + 2) % 3;
88 kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
89 } else {
90 kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
91 + angMom[2]*angMom[2]/I(2, 2);
92 }
93 }
94
95 }
96 }
97
98 #ifdef IS_MPI
99
100 MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101 MPI_COMM_WORLD);
102 kinetic = kinetic_global;
103
104 #endif //is_mpi
105
106 kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
107
108 return kinetic;
109 }
110
111 RealType Thermo::getPotential() {
112 RealType potential = 0.0;
113 Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114 RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115
116 // Get total potential for entire system from MPI.
117
118 #ifdef IS_MPI
119
120 MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121 MPI_COMM_WORLD);
122 potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123
124 #else
125
126 potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127
128 #endif // is_mpi
129
130 return potential;
131 }
132
133 RealType Thermo::getTotalE() {
134 RealType total;
135
136 total = this->getKinetic() + this->getPotential();
137 return total;
138 }
139
140 RealType Thermo::getTemperature() {
141
142 RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
143 return temperature;
144 }
145
146 RealType Thermo::getVolume() {
147 Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148 return curSnapshot->getVolume();
149 }
150
151 RealType Thermo::getPressure() {
152
153 // Relies on the calculation of the full molecular pressure tensor
154
155
156 Mat3x3d tensor;
157 RealType pressure;
158
159 tensor = getPressureTensor();
160
161 pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162
163 return pressure;
164 }
165
166 RealType Thermo::getPressure(int direction) {
167
168 // Relies on the calculation of the full molecular pressure tensor
169
170
171 Mat3x3d tensor;
172 RealType pressure;
173
174 tensor = getPressureTensor();
175
176 pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
177
178 return pressure;
179 }
180
181 Mat3x3d Thermo::getPressureTensor() {
182 // returns pressure tensor in units amu*fs^-2*Ang^-1
183 // routine derived via viral theorem description in:
184 // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
185 Mat3x3d pressureTensor;
186 Mat3x3d p_local(0.0);
187 Mat3x3d p_global(0.0);
188
189 SimInfo::MoleculeIterator i;
190 std::vector<StuntDouble*>::iterator j;
191 Molecule* mol;
192 StuntDouble* integrableObject;
193 for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194 for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195 integrableObject = mol->nextIntegrableObject(j)) {
196
197 RealType mass = integrableObject->getMass();
198 Vector3d vcom = integrableObject->getVel();
199 p_local += mass * outProduct(vcom, vcom);
200 }
201 }
202
203 #ifdef IS_MPI
204 MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205 #else
206 p_global = p_local;
207 #endif // is_mpi
208
209 RealType volume = this->getVolume();
210 Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211 Mat3x3d tau = curSnapshot->statData.getTau();
212
213 pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume;
214
215 return pressureTensor;
216 }
217
218
219 void Thermo::saveStat(){
220 Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221 Stats& stat = currSnapshot->statData;
222
223 stat[Stats::KINETIC_ENERGY] = getKinetic();
224 stat[Stats::POTENTIAL_ENERGY] = getPotential();
225 stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
226 stat[Stats::TEMPERATURE] = getTemperature();
227 stat[Stats::PRESSURE] = getPressure();
228 stat[Stats::VOLUME] = getVolume();
229
230 Mat3x3d tensor =getPressureTensor();
231 stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);
232 stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);
233 stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);
234
235
236 /**@todo need refactorying*/
237 //Conserved Quantity is set by integrator and time is set by setTime
238
239 }
240
241 } //end namespace oopse