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root/OpenMD/branches/development/src/brains/Thermo.cpp

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trunk/src/brains/Thermo.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
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. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
12	+	* 2. Redistributions in binary form must reproduce the above copyright
13	+	*    notice, this list of conditions and the following disclaimer in the
14	+	*    documentation and/or other materials provided with the
15	+	*    distribution.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
28	+	* arising out of the use of or inability to use software, even if the
29	+	* University of Notre Dame has been advised of the possibility of
30	+	* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40	+	*/
41	+
42		#include <math.h>
43		#include <iostream>
3	–	using namespace std;
44
45		#ifdef IS_MPI
46		#include <mpi.h>
47		#endif //is_mpi
48
49		#include "brains/Thermo.hpp"
50	<	#include "primitives/SRI.hpp"
11	<	#include "integrators/Integrator.hpp"
50	>	#include "primitives/Molecule.hpp"
51		#include "utils/simError.h"
52	<	#include "math/MatVec3.h"
52	>	#include "utils/PhysicalConstants.hpp"
53
54	<	#ifdef IS_MPI
16	<	#define __C
17	<	#include "brains/mpiSimulation.hpp"
18	<	#endif // is_mpi
54	>	namespace OpenMD {
55
56	<	inline double roundMe( double x ){
57	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
58	<	}
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	<	Thermo::Thermo( SimInfo* the_info ) {
85	<	info = the_info;
86	<	int baseSeed = the_info->getSeed();
87	<
88	<	gaussStream = new gaussianSPRNG( baseSeed );
89	<	}
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	<	Thermo::~Thermo(){
101	<	delete gaussStream;
102	<	}
100	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	>	MPI_COMM_WORLD);
102	>	kinetic = kinetic_global;
103
104	<	double Thermo::getKinetic(){
104	>	#endif //is_mpi
105
106	<	const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
38	<	double kinetic;
39	<	double amass;
40	<	double aVel[3], aJ[3], I[3][3];
41	<	int i, j, k, kl;
106	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
107
108	<	double kinetic_global;
109	<	vector<StuntDouble *> integrableObjects = info->integrableObjects;
45	<
46	<	kinetic = 0.0;
47	<	kinetic_global = 0.0;
108	>	return kinetic;
109	>	}
110
111	<	for (kl=0; kl<integrableObjects.size(); kl++) {
112	<	integrableObjects[kl]->getVel(aVel);
113	<	amass = integrableObjects[kl]->getMass();
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	<	for(j=0; j<3; j++)
54	<	kinetic += amass*aVel[j]*aVel[j];
116	>	// Get total potential for entire system from MPI.
117
56	–	if (integrableObjects[kl]->isDirectional()){
57	–
58	–	integrableObjects[kl]->getJ( aJ );
59	–	integrableObjects[kl]->getI( I );
60	–
61	–	if (integrableObjects[kl]->isLinear()) {
62	–	i = integrableObjects[kl]->linearAxis();
63	–	j = (i+1)%3;
64	–	k = (i+2)%3;
65	–	kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
66	–	} else {
67	–	for (j=0; j<3; j++)
68	–	kinetic += aJ[j]*aJ[j] / I[j][j];
69	–	}
70	–	}
71	–	}
118		#ifdef IS_MPI
73	–	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
74	–	MPI_SUM, MPI_COMM_WORLD);
75	–	kinetic = kinetic_global;
76	–	#endif //is_mpi
77	–
78	–	kinetic = kinetic * 0.5 / e_convert;
119
120	<	return kinetic;
121	<	}
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	<	double Thermo::getPotential(){
84	<
85	<	double potential_local;
86	<	double potential;
87	<	int el, nSRI;
88	<	Molecule* molecules;
124	>	#else
125
126	<	molecules = info->molecules;
91	<	nSRI = info->n_SRI;
126	>	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127
128	<	potential_local = 0.0;
94	<	potential = 0.0;
95	<	potential_local += info->lrPot;
128	>	#endif // is_mpi
129
130	<	for( el=0; el<info->n_mol; el++ ){
98	<	potential_local += molecules[el].getPotential();
130	>	return potential;
131		}
132
133	<	// Get total potential for entire system from MPI.
134	<	#ifdef IS_MPI
103	<	MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
104	<	MPI_SUM, MPI_COMM_WORLD);
105	<	#else
106	<	potential = potential_local;
107	<	#endif // is_mpi
133	>	RealType Thermo::getTotalE() {
134	>	RealType total;
135
136	<	return potential;
137	<	}
136	>	total = this->getKinetic() + this->getPotential();
137	>	return total;
138	>	}
139
140	<	double Thermo::getTotalE(){
140	>	RealType Thermo::getTemperature() {
141	>
142	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143	>	return temperature;
144	>	}
145
146	<	double total;
146	>	RealType Thermo::getVolume() {
147	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148	>	return curSnapshot->getVolume();
149	>	}
150
151	<	total = this->getKinetic() + this->getPotential();
117	<	return total;
118	<	}
151	>	RealType Thermo::getPressure() {
152
153	<	double Thermo::getTemperature(){
153	>	// Relies on the calculation of the full molecular pressure tensor
154
122	–	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123	–	double temperature;
155
156	<	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
157	<	return temperature;
127	<	}
156	>	Mat3x3d tensor;
157	>	RealType pressure;
158
159	<	double Thermo::getVolume() {
159	>	tensor = getPressureTensor();
160
161	<	return info->boxVol;
132	<	}
161	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162
163	<	double Thermo::getPressure() {
163	>	return pressure;
164	>	}
165
166	<	// Relies on the calculation of the full molecular pressure tensor
137	<
138	<	const double p_convert = 1.63882576e8;
139	<	double press[3][3];
140	<	double pressure;
166	>	RealType Thermo::getPressure(int direction) {
167
168	<	this->getPressureTensor(press);
168	>	// Relies on the calculation of the full molecular pressure tensor
169
170	<	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
170	>
171	>	Mat3x3d tensor;
172	>	RealType pressure;
173
174	<	return pressure;
147	<	}
174	>	tensor = getPressureTensor();
175
176	<	double Thermo::getPressureX() {
176	>	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
177
178	<	// Relies on the calculation of the full molecular pressure tensor
179	<
153	<	const double p_convert = 1.63882576e8;
154	<	double press[3][3];
155	<	double pressureX;
178	>	return pressure;
179	>	}
180
181	<	this->getPressureTensor(press);
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	<	pressureX = p_convert * press[0][0];
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	<	return pressureX;
198	<	}
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	<	double Thermo::getPressureY() {
209	>	RealType volume = this->getVolume();
210	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211	>	Mat3x3d tau = curSnapshot->statData.getTau();
212
213	<	// Relies on the calculation of the full molecular pressure tensor
214	<
215	<	const double p_convert = 1.63882576e8;
216	<	double press[3][3];
170	<	double pressureY;
213	>	pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
214	>
215	>	return pressureTensor;
216	>	}
217
172	–	this->getPressureTensor(press);
218
219	<	pressureY = p_convert * press[1][1];
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	<	return pressureY;
231	<	}
230	>	Mat3x3d tensor =getPressureTensor();
231	>	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
232	>	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
233	>	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
234	>	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
235	>	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
236	>	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
237	>	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
238	>	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
239	>	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
240
179	–	double Thermo::getPressureZ() {
241
242	<	// Relies on the calculation of the full molecular pressure tensor
182	<
183	<	const double p_convert = 1.63882576e8;
184	<	double press[3][3];
185	<	double pressureZ;
242	>	Globals* simParams = info_->getSimParams();
243
244	<	this->getPressureTensor(press);
244	>	if (simParams->haveTaggedAtomPair() &&
245	>	simParams->havePrintTaggedPairDistance()) {
246	>	if ( simParams->getPrintTaggedPairDistance()) {
247	>
248	>	std::pair<int, int> tap = simParams->getTaggedAtomPair();
249	>	Vector3d pos1, pos2, rab;
250
251	<	pressureZ = p_convert * press[2][2];
251	>	#ifdef IS_MPI
252	>	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
253
254	<	return pressureZ;
255	<	}
254	>	int mol1 = info_->getGlobalMolMembership(tap.first);
255	>	int mol2 = info_->getGlobalMolMembership(tap.second);
256	>	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
257
258	+	int proc1 = info_->getMolToProc(mol1);
259	+	int proc2 = info_->getMolToProc(mol2);
260
261	<	void Thermo::getPressureTensor(double press[3][3]){
196	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
197	<	// routine derived via viral theorem description in:
198	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
261	>	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
262
263	<	const double e_convert = 4.184e-4;
263	>	RealType data[3];
264	>	if (proc1 == worldRank) {
265	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
266	>	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
267	>	pos1 = sd1->getPos();
268	>	data[0] = pos1.x();
269	>	data[1] = pos1.y();
270	>	data[2] = pos1.z();
271	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
272	>	} else {
273	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
274	>	pos1 = Vector3d(data);
275	>	}
276
202	–	double molmass, volume;
203	–	double vcom[3];
204	–	double p_local[9], p_global[9];
205	–	int i, j, k;
277
278	<	for (i=0; i < 9; i++) {
279	<	p_local[i] = 0.0;
280	<	p_global[i] = 0.0;
281	<	}
282	<
283	<	// use velocities of integrableObjects and their masses:
284	<
285	<	for (i=0; i < info->integrableObjects.size(); i++) {
286	<
287	<	molmass = info->integrableObjects[i]->getMass();
288	<
289	<	info->integrableObjects[i]->getVel(vcom);
219	<
220	<	p_local[0] += molmass * (vcom[0] * vcom[0]);
221	<	p_local[1] += molmass * (vcom[0] * vcom[1]);
222	<	p_local[2] += molmass * (vcom[0] * vcom[2]);
223	<	p_local[3] += molmass * (vcom[1] * vcom[0]);
224	<	p_local[4] += molmass * (vcom[1] * vcom[1]);
225	<	p_local[5] += molmass * (vcom[1] * vcom[2]);
226	<	p_local[6] += molmass * (vcom[2] * vcom[0]);
227	<	p_local[7] += molmass * (vcom[2] * vcom[1]);
228	<	p_local[8] += molmass * (vcom[2] * vcom[2]);
229	<
230	<	}
231	<
232	<	// Get total for entire system from MPI.
233	<
234	<	#ifdef IS_MPI
235	<	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
278	>	if (proc2 == worldRank) {
279	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
280	>	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
281	>	pos2 = sd2->getPos();
282	>	data[0] = pos2.x();
283	>	data[1] = pos2.y();
284	>	data[2] = pos2.z();
285	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
286	>	} else {
287	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
288	>	pos2 = Vector3d(data);
289	>	}
290		#else
291	<	for (i=0; i<9; i++) {
292	<	p_global[i] = p_local[i];
293	<	}
294	<	#endif // is_mpi
295	<
296	<	volume = this->getVolume();
297	<
298	<
299	<
246	<	for(i = 0; i < 3; i++) {
247	<	for (j = 0; j < 3; j++) {
248	<	k = 3*i + j;
249	<	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
291	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
292	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
293	>	pos1 = at1->getPos();
294	>	pos2 = at2->getPos();
295	>	#endif
296	>	rab = pos2 - pos1;
297	>	currSnapshot->wrapVector(rab);
298	>	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
299	>	}
300		}
251	–	}
252	–	}
253	–
254	–	void Thermo::velocitize() {
255	–
256	–	double aVel[3], aJ[3], I[3][3];
257	–	int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
258	–	double vdrift[3];
259	–	double vbar;
260	–	const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
261	–	double av2;
262	–	double kebar;
263	–	double temperature;
264	–	int nobj;
265	–
266	–	if (!info->have_target_temp) {
267	–	sprintf( painCave.errMsg,
268	–	"You can't resample the velocities without a targetTemp!\n"
269	–	);
270	–	painCave.isFatal = 1;
271	–	painCave.severity = OOPSE_ERROR;
272	–	simError();
273	–	return;
274	–	}
275	–
276	–	nobj = info->integrableObjects.size();
277	–
278	–	temperature   = info->target_temp;
279	–
280	–	kebar = kb * temperature * (double)info->ndfRaw /
281	–	( 2.0 * (double)info->ndf );
282	–
283	–	for(vr = 0; vr < nobj; vr++){
284	–
285	–	// uses equipartition theory to solve for vbar in angstrom/fs
286	–
287	–	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
288	–	vbar = sqrt( av2 );
289	–
290	–	// picks random velocities from a gaussian distribution
291	–	// centered on vbar
292	–
293	–	for (j=0; j<3; j++)
294	–	aVel[j] = vbar * gaussStream->getGaussian();
295	–
296	–	info->integrableObjects[vr]->setVel( aVel );
297	–
298	–	if(info->integrableObjects[vr]->isDirectional()){
299	–
300	–	info->integrableObjects[vr]->getI( I );
301	–
302	–	if (info->integrableObjects[vr]->isLinear()) {
303	–
304	–	l= info->integrableObjects[vr]->linearAxis();
305	–	m = (l+1)%3;
306	–	n = (l+2)%3;
307	–
308	–	aJ[l] = 0.0;
309	–	vbar = sqrt( 2.0 * kebar * I[m][m] );
310	–	aJ[m] = vbar * gaussStream->getGaussian();
311	–	vbar = sqrt( 2.0 * kebar * I[n][n] );
312	–	aJ[n] = vbar * gaussStream->getGaussian();
313	–
314	–	} else {
315	–	for (j = 0 ; j < 3; j++) {
316	–	vbar = sqrt( 2.0 * kebar * I[j][j] );
317	–	aJ[j] = vbar * gaussStream->getGaussian();
318	–	}
319	–	} // else isLinear
320	–
321	–	info->integrableObjects[vr]->setJ( aJ );
301
302	<	}//isDirectional
303	<
325	<	}
326	<
327	<	// Get the Center of Mass drift velocity.
328	<
329	<	getCOMVel(vdrift);
330	<
331	<	//  Corrects for the center of mass drift.
332	<	// sums all the momentum and divides by total mass.
333	<
334	<	for(vd = 0; vd < nobj; vd++){
302	>	/**@todo need refactorying*/
303	>	//Conserved Quantity is set by integrator and time is set by setTime
304
336	–	info->integrableObjects[vd]->getVel(aVel);
337	–
338	–	for (j=0; j < 3; j++)
339	–	aVel[j] -= vdrift[j];
340	–
341	–	info->integrableObjects[vd]->setVel( aVel );
305		}
306
307	<	}
345	<
346	<	void Thermo::getCOMVel(double vdrift[3]){
347	<
348	<	double mtot, mtot_local;
349	<	double aVel[3], amass;
350	<	double vdrift_local[3];
351	<	int vd, j;
352	<	int nobj;
353	<
354	<	nobj   = info->integrableObjects.size();
355	<
356	<	mtot_local = 0.0;
357	<	vdrift_local[0] = 0.0;
358	<	vdrift_local[1] = 0.0;
359	<	vdrift_local[2] = 0.0;
360	<
361	<	for(vd = 0; vd < nobj; vd++){
362	<
363	<	amass = info->integrableObjects[vd]->getMass();
364	<	info->integrableObjects[vd]->getVel( aVel );
365	<
366	<	for(j = 0; j < 3; j++)
367	<	vdrift_local[j] += aVel[j] * amass;
368	<
369	<	mtot_local += amass;
370	<	}
371	<
372	<	#ifdef IS_MPI
373	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
374	<	MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
375	<	#else
376	<	mtot = mtot_local;
377	<	for(vd = 0; vd < 3; vd++) {
378	<	vdrift[vd] = vdrift_local[vd];
379	<	}
380	<	#endif
381	<
382	<	for (vd = 0; vd < 3; vd++) {
383	<	vdrift[vd] = vdrift[vd] / mtot;
384	<	}
385	<
386	<	}
387	<
388	<	void Thermo::getCOM(double COM[3]){
389	<
390	<	double mtot, mtot_local;
391	<	double aPos[3], amass;
392	<	double COM_local[3];
393	<	int i, j;
394	<	int nobj;
395	<
396	<	mtot_local = 0.0;
397	<	COM_local[0] = 0.0;
398	<	COM_local[1] = 0.0;
399	<	COM_local[2] = 0.0;
400	<
401	<	nobj = info->integrableObjects.size();
402	<	for(i = 0; i < nobj; i++){
403	<
404	<	amass = info->integrableObjects[i]->getMass();
405	<	info->integrableObjects[i]->getPos( aPos );
406	<
407	<	for(j = 0; j < 3; j++)
408	<	COM_local[j] += aPos[j] * amass;
409	<
410	<	mtot_local += amass;
411	<	}
412	<
413	<	#ifdef IS_MPI
414	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
415	<	MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
416	<	#else
417	<	mtot = mtot_local;
418	<	for(i = 0; i < 3; i++) {
419	<	COM[i] = COM_local[i];
420	<	}
421	<	#endif
422	<
423	<	for (i = 0; i < 3; i++) {
424	<	COM[i] = COM[i] / mtot;
425	<	}
426	<	}
427	<
428	<	void Thermo::removeCOMdrift() {
429	<	double vdrift[3], aVel[3];
430	<	int vd, j, nobj;
431	<
432	<	nobj = info->integrableObjects.size();
433	<
434	<	// Get the Center of Mass drift velocity.
435	<
436	<	getCOMVel(vdrift);
437	<
438	<	//  Corrects for the center of mass drift.
439	<	// sums all the momentum and divides by total mass.
440	<
441	<	for(vd = 0; vd < nobj; vd++){
442	<
443	<	info->integrableObjects[vd]->getVel(aVel);
444	<
445	<	for (j=0; j < 3; j++)
446	<	aVel[j] -= vdrift[j];
447	<
448	<	info->integrableObjects[vd]->setVel( aVel );
449	<	}
450	<	}
307	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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