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

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trunk/src/brains/Thermo.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <math.h>
#	Line 49 | Line 50
50		#include "brains/Thermo.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "utils/simError.h"
53	<	#include "utils/OOPSEConstant.hpp"
53	>	#include "utils/PhysicalConstants.hpp"
54	>	#include "types/MultipoleAdapter.hpp"
55
56	<	namespace oopse {
56	>	namespace OpenMD {
57
58	<	double Thermo::getKinetic() {
58	>	RealType Thermo::getKinetic() {
59		SimInfo::MoleculeIterator miter;
60		std::vector<StuntDouble*>::iterator iiter;
61		Molecule* mol;
#	Line 64 | Line 66 | namespace oopse {
66		int i;
67		int j;
68		int k;
69	<	double kinetic = 0.0;
70	<	double kinetic_global = 0.0;
69	>	RealType mass;
70	>	RealType kinetic = 0.0;
71	>	RealType kinetic_global = 0.0;
72
73		for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
74		for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
75		integrableObject = mol->nextIntegrableObject(iiter)) {
76	<
77	<	double mass = integrableObject->getMass();
78	<	Vector3d vel = integrableObject->getVel();
79	<
76	>
77	>	mass = integrableObject->getMass();
78	>	vel = integrableObject->getVel();
79	>
80		kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
81	<
81	>
82		if (integrableObject->isDirectional()) {
83		angMom = integrableObject->getJ();
84		I = integrableObject->getI();
#	Line 96 | Line 99 | namespace oopse {
99
100		#ifdef IS_MPI
101
102	<	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM,
102	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
103		MPI_COMM_WORLD);
104		kinetic = kinetic_global;
105
106		#endif //is_mpi
107
108	<	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
108	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
109
110		return kinetic;
111		}
112
113	<	double Thermo::getPotential() {
114	<	double potential = 0.0;
113	>	RealType Thermo::getPotential() {
114	>	RealType potential = 0.0;
115		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
116	<	double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
114	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
116	>	RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
117
118		// Get total potential for entire system from MPI.
119
120		#ifdef IS_MPI
121
122	<	MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
122	>	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
123		MPI_COMM_WORLD);
124	+	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
125
126		#else
127
128	<	potential = potential_local;
128	>	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
129
130		#endif // is_mpi
131
132		return potential;
133		}
134
135	<	double Thermo::getTotalE() {
136	<	double total;
135	>	RealType Thermo::getTotalE() {
136	>	RealType total;
137
138		total = this->getKinetic() + this->getPotential();
139		return total;
140		}
141
142	<	double Thermo::getTemperature() {
142	>	RealType Thermo::getTemperature() {
143
144	<	double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
144	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
145		return temperature;
146		}
147
148	<	double Thermo::getVolume() {
148	>	RealType Thermo::getElectronicTemperature() {
149	>	SimInfo::MoleculeIterator miter;
150	>	std::vector<Atom*>::iterator iiter;
151	>	Molecule* mol;
152	>	Atom* atom;
153	>	RealType cvel;
154	>	RealType cmass;
155	>	RealType kinetic = 0.0;
156	>	RealType kinetic_global = 0.0;
157	>
158	>	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
159	>	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
160	>	atom = mol->nextFluctuatingCharge(iiter)) {
161	>	cmass = atom->getChargeMass();
162	>	cvel = atom->getFlucQVel();
163	>
164	>	kinetic += cmass * cvel * cvel;
165	>
166	>	}
167	>	}
168	>
169	>	#ifdef IS_MPI
170	>
171	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
172	>	MPI_COMM_WORLD);
173	>	kinetic = kinetic_global;
174	>
175	>	#endif //is_mpi
176	>
177	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
178	>	return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );
179	>	}
180	>
181	>
182	>
183	>
184	>	RealType Thermo::getVolume() {
185		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
186		return curSnapshot->getVolume();
187		}
188
189	<	double Thermo::getPressure() {
189	>	RealType Thermo::getPressure() {
190
191		// Relies on the calculation of the full molecular pressure tensor
192
193
194		Mat3x3d tensor;
195	<	double pressure;
195	>	RealType pressure;
196
197		tensor = getPressureTensor();
198
199	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
199	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
200
201		return pressure;
202		}
203
204	+	RealType Thermo::getPressure(int direction) {
205	+
206	+	// Relies on the calculation of the full molecular pressure tensor
207	+
208	+
209	+	Mat3x3d tensor;
210	+	RealType pressure;
211	+
212	+	tensor = getPressureTensor();
213	+
214	+	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
215	+
216	+	return pressure;
217	+	}
218	+
219		Mat3x3d Thermo::getPressureTensor() {
220		// returns pressure tensor in units amu*fs^-2*Ang^-1
221		// routine derived via viral theorem description in:
#	Line 178 | Line 232 | namespace oopse {
232		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
233		integrableObject = mol->nextIntegrableObject(j)) {
234
235	<	double mass = integrableObject->getMass();
235	>	RealType mass = integrableObject->getMass();
236		Vector3d vcom = integrableObject->getVel();
237		p_local += mass * outProduct(vcom, vcom);
238		}
239		}
240
241		#ifdef IS_MPI
242	<	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
242	>	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
243		#else
244		p_global = p_local;
245		#endif // is_mpi
246
247	<	double volume = this->getVolume();
247	>	RealType volume = this->getVolume();
248		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
249	<	Mat3x3d tau = curSnapshot->statData.getTau();
249	>	Mat3x3d stressTensor = curSnapshot->getStressTensor();
250
251	<	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
252	<
251	>	pressureTensor =  (p_global +
252	>	PhysicalConstants::energyConvert * stressTensor)/volume;
253	>
254		return pressureTensor;
255		}
256
257	+
258		void Thermo::saveStat(){
259		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
260		Stats& stat = currSnapshot->statData;
#	Line 210 | Line 266 | namespace oopse {
266		stat[Stats::PRESSURE] = getPressure();
267		stat[Stats::VOLUME] = getVolume();
268
269	+	Mat3x3d tensor =getPressureTensor();
270	+	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
271	+	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
272	+	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
273	+	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
274	+	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
275	+	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
276	+	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
277	+	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
278	+	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
279	+
280	+	// grab the simulation box dipole moment if specified
281	+	if (info_->getCalcBoxDipole()){
282	+	Vector3d totalDipole = getBoxDipole();
283	+	stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
284	+	stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
285	+	stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
286	+	}
287	+
288	+	Globals* simParams = info_->getSimParams();
289	+	// grab the heat flux if desired
290	+	if (simParams->havePrintHeatFlux()) {
291	+	if (simParams->getPrintHeatFlux()){
292	+	Vector3d heatFlux = getHeatFlux();
293	+	stat[Stats::HEATFLUX_X] = heatFlux(0);
294	+	stat[Stats::HEATFLUX_Y] = heatFlux(1);
295	+	stat[Stats::HEATFLUX_Z] = heatFlux(2);
296	+	}
297	+	}
298	+
299	+	if (simParams->haveTaggedAtomPair() &&
300	+	simParams->havePrintTaggedPairDistance()) {
301	+	if ( simParams->getPrintTaggedPairDistance()) {
302	+
303	+	std::pair<int, int> tap = simParams->getTaggedAtomPair();
304	+	Vector3d pos1, pos2, rab;
305	+
306	+	#ifdef IS_MPI
307	+	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
308	+
309	+	int mol1 = info_->getGlobalMolMembership(tap.first);
310	+	int mol2 = info_->getGlobalMolMembership(tap.second);
311	+	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
312	+
313	+	int proc1 = info_->getMolToProc(mol1);
314	+	int proc2 = info_->getMolToProc(mol2);
315	+
316	+	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
317	+
318	+	RealType data[3];
319	+	if (proc1 == worldRank) {
320	+	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
321	+	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
322	+	pos1 = sd1->getPos();
323	+	data[0] = pos1.x();
324	+	data[1] = pos1.y();
325	+	data[2] = pos1.z();
326	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
327	+	} else {
328	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
329	+	pos1 = Vector3d(data);
330	+	}
331	+
332	+
333	+	if (proc2 == worldRank) {
334	+	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
335	+	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
336	+	pos2 = sd2->getPos();
337	+	data[0] = pos2.x();
338	+	data[1] = pos2.y();
339	+	data[2] = pos2.z();
340	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
341	+	} else {
342	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
343	+	pos2 = Vector3d(data);
344	+	}
345	+	#else
346	+	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
347	+	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
348	+	pos1 = at1->getPos();
349	+	pos2 = at2->getPos();
350	+	#endif
351	+	rab = pos2 - pos1;
352	+	currSnapshot->wrapVector(rab);
353	+	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
354	+	}
355	+	}
356	+
357		/**@todo need refactorying*/
358		//Conserved Quantity is set by integrator and time is set by setTime
359
360		}
361
362	<	} //end namespace oopse
362	>
363	>	Vector3d Thermo::getBoxDipole() {
364	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
365	>	SimInfo::MoleculeIterator miter;
366	>	std::vector<Atom*>::iterator aiter;
367	>	Molecule* mol;
368	>	Atom* atom;
369	>	RealType charge;
370	>	RealType moment(0.0);
371	>	Vector3d ri(0.0);
372	>	Vector3d dipoleVector(0.0);
373	>	Vector3d nPos(0.0);
374	>	Vector3d pPos(0.0);
375	>	RealType nChg(0.0);
376	>	RealType pChg(0.0);
377	>	int nCount = 0;
378	>	int pCount = 0;
379	>
380	>	RealType chargeToC = 1.60217733e-19;
381	>	RealType angstromToM = 1.0e-10;
382	>	RealType debyeToCm = 3.33564095198e-30;
383	>
384	>	for (mol = info_->beginMolecule(miter); mol != NULL;
385	>	mol = info_->nextMolecule(miter)) {
386	>
387	>	for (atom = mol->beginAtom(aiter); atom != NULL;
388	>	atom = mol->nextAtom(aiter)) {
389	>
390	>	if (atom->isCharge() ) {
391	>	charge = 0.0;
392	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
393	>	if (data != NULL) {
394	>
395	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
396	>	charge *= chargeToC;
397	>
398	>	ri = atom->getPos();
399	>	currSnapshot->wrapVector(ri);
400	>	ri *= angstromToM;
401	>
402	>	if (charge < 0.0) {
403	>	nPos += ri;
404	>	nChg -= charge;
405	>	nCount++;
406	>	} else if (charge > 0.0) {
407	>	pPos += ri;
408	>	pChg += charge;
409	>	pCount++;
410	>	}
411	>	}
412	>	}
413	>
414	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
415	>	if (ma.isDipole() ) {
416	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
417	>	moment = ma.getDipoleMoment();
418	>	moment *= debyeToCm;
419	>	dipoleVector += u_i * moment;
420	>	}
421	>	}
422	>	}
423	>
424	>
425	>	#ifdef IS_MPI
426	>	RealType pChg_global, nChg_global;
427	>	int pCount_global, nCount_global;
428	>	Vector3d pPos_global, nPos_global, dipVec_global;
429	>
430	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
431	>	MPI_COMM_WORLD);
432	>	pChg = pChg_global;
433	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
434	>	MPI_COMM_WORLD);
435	>	nChg = nChg_global;
436	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
437	>	MPI_COMM_WORLD);
438	>	pCount = pCount_global;
439	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
440	>	MPI_COMM_WORLD);
441	>	nCount = nCount_global;
442	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
443	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
444	>	pPos = pPos_global;
445	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
446	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
447	>	nPos = nPos_global;
448	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
449	>	dipVec_global.getArrayPointer(), 3,
450	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
451	>	dipoleVector = dipVec_global;
452	>	#endif //is_mpi
453	>
454	>	// first load the accumulated dipole moment (if dipoles were present)
455	>	Vector3d boxDipole = dipoleVector;
456	>	// now include the dipole moment due to charges
457	>	// use the lesser of the positive and negative charge totals
458	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
459	>
460	>	// find the average positions
461	>	if (pCount > 0 && nCount > 0 ) {
462	>	pPos /= pCount;
463	>	nPos /= nCount;
464	>	}
465	>
466	>	// dipole is from the negative to the positive (physics notation)
467	>	boxDipole += (pPos - nPos) * chg_value;
468	>
469	>	return boxDipole;
470	>	}
471	>
472	>	// Returns the Heat Flux Vector for the system
473	>	Vector3d Thermo::getHeatFlux(){
474	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
475	>	SimInfo::MoleculeIterator miter;
476	>	std::vector<StuntDouble*>::iterator iiter;
477	>	Molecule* mol;
478	>	StuntDouble* integrableObject;
479	>	RigidBody::AtomIterator ai;
480	>	Atom* atom;
481	>	Vector3d vel;
482	>	Vector3d angMom;
483	>	Mat3x3d I;
484	>	int i;
485	>	int j;
486	>	int k;
487	>	RealType mass;
488	>
489	>	Vector3d x_a;
490	>	RealType kinetic;
491	>	RealType potential;
492	>	RealType eatom;
493	>	RealType AvgE_a_ = 0;
494	>	// Convective portion of the heat flux
495	>	Vector3d heatFluxJc = V3Zero;
496	>
497	>	/* Calculate convective portion of the heat flux */
498	>	for (mol = info_->beginMolecule(miter); mol != NULL;
499	>	mol = info_->nextMolecule(miter)) {
500	>
501	>	for (integrableObject = mol->beginIntegrableObject(iiter);
502	>	integrableObject != NULL;
503	>	integrableObject = mol->nextIntegrableObject(iiter)) {
504	>
505	>	mass = integrableObject->getMass();
506	>	vel = integrableObject->getVel();
507	>
508	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
509	>
510	>	if (integrableObject->isDirectional()) {
511	>	angMom = integrableObject->getJ();
512	>	I = integrableObject->getI();
513	>
514	>	if (integrableObject->isLinear()) {
515	>	i = integrableObject->linearAxis();
516	>	j = (i + 1) % 3;
517	>	k = (i + 2) % 3;
518	>	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
519	>	} else {
520	>	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
521	>	+ angMom[2]*angMom[2]/I(2, 2);
522	>	}
523	>	}
524	>
525	>	potential = 0.0;
526	>
527	>	if (integrableObject->isRigidBody()) {
528	>	RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject);
529	>	for (atom = rb->beginAtom(ai); atom != NULL;
530	>	atom = rb->nextAtom(ai)) {
531	>	potential +=  atom->getParticlePot();
532	>	}
533	>	} else {
534	>	potential = integrableObject->getParticlePot();
535	>	cerr << "ppot = "  << potential << "\n";
536	>	}
537	>
538	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
539	>	// The potential may not be a 1/2 factor
540	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
541	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
542	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
543	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
544	>	}
545	>	}
546	>
547	>	std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl;
548	>
549	>	/* The J_v vector is reduced in fortan so everyone has the global
550	>	*  Jv. Jc is computed over the local atoms and must be reduced
551	>	*  among all processors.
552	>	*/
553	>	#ifdef IS_MPI
554	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
555	>	MPI::SUM);
556	>	#endif
557	>
558	>	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
559	>
560	>	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
561	>	PhysicalConstants::energyConvert;
562	>
563	>	std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl;
564	>	std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl;
565	>
566	>	// Correct for the fact the flux is 1/V (Jc + Jv)
567	>	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
568	>	}
569	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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