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root/OpenMD/trunk/src/brains/Thermo.cpp

Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1792 by gezelter, Fri Aug 31 17:29:35 2012 UTC

#	Line 36 | Line 36
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).
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 50 | Line 51
51		#include "primitives/Molecule.hpp"
52		#include "utils/simError.h"
53		#include "utils/PhysicalConstants.hpp"
54	+	#include "types/FixedChargeAdapter.hpp"
55	+	#include "types/FluctuatingChargeAdapter.hpp"
56	+	#include "types/MultipoleAdapter.hpp"
57	+	#ifdef HAVE_QHULL
58	+	#include "math/ConvexHull.hpp"
59	+	#include "math/AlphaHull.hpp"
60	+	#endif
61
62	+	using namespace std;
63		namespace OpenMD {
64
65	<	RealType Thermo::getKinetic() {
66	<	SimInfo::MoleculeIterator miter;
67	<	std::vector<StuntDouble*>::iterator iiter;
68	<	Molecule* mol;
69	<	StuntDouble* integrableObject;
70	<	Vector3d vel;
71	<	Vector3d angMom;
72	<	Mat3x3d I;
73	<	int i;
74	<	int j;
75	<	int k;
76	<	RealType mass;
77	<	RealType kinetic = 0.0;
78	<	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)) {
65	>	RealType Thermo::getTranslationalKinetic() {
66	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
67	>
68	>	if (!snap->hasTranslationalKineticEnergy) {
69	>	SimInfo::MoleculeIterator miter;
70	>	vector<StuntDouble*>::iterator iiter;
71	>	Molecule* mol;
72	>	StuntDouble* sd;
73	>	Vector3d vel;
74	>	RealType mass;
75	>	RealType kinetic(0.0);
76	>
77	>	for (mol = info_->beginMolecule(miter); mol != NULL;
78	>	mol = info_->nextMolecule(miter)) {
79
80	<	mass = integrableObject->getMass();
81	<	vel = integrableObject->getVel();
82	<
83	<	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
84	<
85	<	if (integrableObject->isDirectional()) {
86	<	angMom = integrableObject->getJ();
87	<	I = integrableObject->getI();
80	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
81	>	sd = mol->nextIntegrableObject(iiter)) {
82	>
83	>	mass = sd->getMass();
84	>	vel = sd->getVel();
85	>
86	>	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
87	>
88	>	}
89	>	}
90	>
91	>	#ifdef IS_MPI
92	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
93	>	MPI::SUM);
94	>	#endif
95	>
96	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
97	>
98	>
99	>	snap->setTranslationalKineticEnergy(kinetic);
100	>	}
101	>	return snap->getTranslationalKineticEnergy();
102	>	}
103
104	<	if (integrableObject->isLinear()) {
105	<	i = integrableObject->linearAxis();
106	<	j = (i + 1) % 3;
107	<	k = (i + 2) % 3;
108	<	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
109	<	} else {
110	<	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
111	<	+ angMom[2]*angMom[2]/I(2, 2);
112	<	}
113	<	}
104	>	RealType Thermo::getRotationalKinetic() {
105	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
106	>
107	>	if (!snap->hasRotationalKineticEnergy) {
108	>	SimInfo::MoleculeIterator miter;
109	>	vector<StuntDouble*>::iterator iiter;
110	>	Molecule* mol;
111	>	StuntDouble* sd;
112	>	Vector3d angMom;
113	>	Mat3x3d I;
114	>	int i, j, k;
115	>	RealType kinetic(0.0);
116	>
117	>	for (mol = info_->beginMolecule(miter); mol != NULL;
118	>	mol = info_->nextMolecule(miter)) {
119	>
120	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
121	>	sd = mol->nextIntegrableObject(iiter)) {
122	>
123	>	if (sd->isDirectional()) {
124	>	angMom = sd->getJ();
125	>	I = sd->getI();
126
127	+	if (sd->isLinear()) {
128	+	i = sd->linearAxis();
129	+	j = (i + 1) % 3;
130	+	k = (i + 2) % 3;
131	+	kinetic += angMom[j] * angMom[j] / I(j, j)
132	+	+ angMom[k] * angMom[k] / I(k, k);
133	+	} else {
134	+	kinetic += angMom[0]*angMom[0]/I(0, 0)
135	+	+ angMom[1]*angMom[1]/I(1, 1)
136	+	+ angMom[2]*angMom[2]/I(2, 2);
137	+	}
138	+	}
139	+	}
140		}
141	<	}
97	<
141	>
142		#ifdef IS_MPI
143	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
144	+	MPI::SUM);
145	+	#endif
146	+
147	+	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
148	+
149	+	snap->setRotationalKineticEnergy(kinetic);
150	+	}
151	+	return snap->getRotationalKineticEnergy();
152	+	}
153
154	<	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	<	MPI_COMM_WORLD);
102	<	kinetic = kinetic_global;
154	>
155
156	<	#endif //is_mpi
156	>	RealType Thermo::getKinetic() {
157	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
158
159	<	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
160	<
161	<	return kinetic;
159	>	if (!snap->hasKineticEnergy) {
160	>	RealType ke = getTranslationalKinetic() + getRotationalKinetic();
161	>	snap->setKineticEnergy(ke);
162	>	}
163	>	return snap->getKineticEnergy();
164		}
165
166		RealType Thermo::getPotential() {
112	–	RealType potential = 0.0;
113	–	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	–	RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
167
168	<	// Get total potential for entire system from MPI.
168	>	// ForceManager computes the potential and stores it in the
169	>	// Snapshot.  All we have to do is report it.
170
171	<	#ifdef IS_MPI
171	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
172	>	return snap->getPotentialEnergy();
173	>	}
174
175	<	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	<	MPI_COMM_WORLD);
122	<	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
175	>	RealType Thermo::getTotalEnergy() {
176
177	<	#else
177	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
178
179	<	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
179	>	if (!snap->hasTotalEnergy) {
180	>	snap->setTotalEnergy(this->getKinetic() + this->getPotential());
181	>	}
182
183	<	#endif // is_mpi
129	<
130	<	return potential;
183	>	return snap->getTotalEnergy();
184		}
185
186	<	RealType Thermo::getTotalE() {
134	<	RealType total;
186	>	RealType Thermo::getTemperature() {
187
188	<	total = this->getKinetic() + this->getPotential();
137	<	return total;
138	<	}
188	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189
190	<	RealType Thermo::getTemperature() {
190	>	if (!snap->hasTemperature) {
191	>
192	>	RealType temperature = ( 2.0 * this->getKinetic() )
193	>	/ (info_->getNdf()* PhysicalConstants::kb );
194	>
195	>	snap->setTemperature(temperature);
196	>	}
197
198	<	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143	<	return temperature;
198	>	return snap->getTemperature();
199		}
200
201	<	RealType Thermo::getVolume() {
202	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148	<	return curSnapshot->getVolume();
149	<	}
201	>	RealType Thermo::getElectronicTemperature() {
202	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203
204	<	RealType Thermo::getPressure() {
204	>	if (!snap->hasElectronicTemperature) {
205	>
206	>	SimInfo::MoleculeIterator miter;
207	>	vector<Atom*>::iterator iiter;
208	>	Molecule* mol;
209	>	Atom* atom;
210	>	RealType cvel;
211	>	RealType cmass;
212	>	RealType kinetic(0.0);
213	>	RealType eTemp;
214	>
215	>	for (mol = info_->beginMolecule(miter); mol != NULL;
216	>	mol = info_->nextMolecule(miter)) {
217	>
218	>	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
219	>	atom = mol->nextFluctuatingCharge(iiter)) {
220	>
221	>	cmass = atom->getChargeMass();
222	>	cvel = atom->getFlucQVel();
223	>
224	>	kinetic += cmass * cvel * cvel;
225	>
226	>	}
227	>	}
228	>
229	>	#ifdef IS_MPI
230	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
231	>	MPI::SUM);
232	>	#endif
233
234	<	// Relies on the calculation of the full molecular pressure tensor
234	>	kinetic *= 0.5;
235	>	eTemp =  (2.0 * kinetic) /
236	>	(info_->getNFluctuatingCharges() * PhysicalConstants::kb );
237	>
238	>	snap->setElectronicTemperature(eTemp);
239	>	}
240
241	+	return snap->getElectronicTemperature();
242	+	}
243
156	–	Mat3x3d tensor;
157	–	RealType pressure;
244
245	<	tensor = getPressureTensor();
246	<
247	<	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162	<
163	<	return pressure;
245	>	RealType Thermo::getVolume() {
246	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247	>	return snap->getVolume();
248		}
249
250	<	RealType Thermo::getPressure(int direction) {
250	>	RealType Thermo::getPressure() {
251	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252
253	<	// Relies on the calculation of the full molecular pressure tensor
254	<
255	<
256	<	Mat3x3d tensor;
257	<	RealType pressure;
258	<
259	<	tensor = getPressureTensor();
260	<
261	<	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
262	<
263	<	return pressure;
253	>	if (!snap->hasPressure) {
254	>	// Relies on the calculation of the full molecular pressure tensor
255	>
256	>	Mat3x3d tensor;
257	>	RealType pressure;
258	>
259	>	tensor = getPressureTensor();
260	>
261	>	pressure = PhysicalConstants::pressureConvert *
262	>	(tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
263	>
264	>	snap->setPressure(pressure);
265	>	}
266	>
267	>	return snap->getPressure();
268		}
269
270		Mat3x3d Thermo::getPressureTensor() {
271		// returns pressure tensor in units amu*fs^-2*Ang^-1
272		// routine derived via viral theorem description in:
273		// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
274	<	Mat3x3d pressureTensor;
186	<	Mat3x3d p_local(0.0);
187	<	Mat3x3d p_global(0.0);
274	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275
276	<	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)) {
276	>	if (!snap->hasPressureTensor) {
277
278	<	RealType mass = integrableObject->getMass();
279	<	Vector3d vcom = integrableObject->getVel();
280	<	p_local += mass * outProduct(vcom, vcom);
278	>	Mat3x3d pressureTensor;
279	>	Mat3x3d p_tens(0.0);
280	>	RealType mass;
281	>	Vector3d vcom;
282	>
283	>	SimInfo::MoleculeIterator i;
284	>	vector<StuntDouble*>::iterator j;
285	>	Molecule* mol;
286	>	StuntDouble* sd;
287	>	for (mol = info_->beginMolecule(i); mol != NULL;
288	>	mol = info_->nextMolecule(i)) {
289	>
290	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
291	>	sd = mol->nextIntegrableObject(j)) {
292	>
293	>	mass = sd->getMass();
294	>	vcom = sd->getVel();
295	>	p_tens += mass * outProduct(vcom, vcom);
296	>	}
297		}
298	+
299	+	#ifdef IS_MPI
300	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, p_tens.getArrayPointer(), 9,
301	+	MPI::REALTYPE, MPI::SUM);
302	+	#endif
303	+
304	+	RealType volume = this->getVolume();
305	+	Mat3x3d stressTensor = snap->getStressTensor();
306	+
307	+	pressureTensor =  (p_tens +
308	+	PhysicalConstants::energyConvert * stressTensor)/volume;
309	+
310	+	snap->setPressureTensor(pressureTensor);
311		}
312	<
312	>	return snap->getPressureTensor();
313	>	}
314	>
315	>
316	>
317	>
318	>	Vector3d Thermo::getSystemDipole() {
319	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
320	>
321	>	if (!snap->hasSystemDipole) {
322	>	SimInfo::MoleculeIterator miter;
323	>	vector<Atom*>::iterator aiter;
324	>	Molecule* mol;
325	>	Atom* atom;
326	>	RealType charge;
327	>	RealType moment(0.0);
328	>	Vector3d ri(0.0);
329	>	Vector3d dipoleVector(0.0);
330	>	Vector3d nPos(0.0);
331	>	Vector3d pPos(0.0);
332	>	RealType nChg(0.0);
333	>	RealType pChg(0.0);
334	>	int nCount = 0;
335	>	int pCount = 0;
336	>
337	>	RealType chargeToC = 1.60217733e-19;
338	>	RealType angstromToM = 1.0e-10;
339	>	RealType debyeToCm = 3.33564095198e-30;
340	>
341	>	for (mol = info_->beginMolecule(miter); mol != NULL;
342	>	mol = info_->nextMolecule(miter)) {
343	>
344	>	for (atom = mol->beginAtom(aiter); atom != NULL;
345	>	atom = mol->nextAtom(aiter)) {
346	>
347	>	charge = 0.0;
348	>
349	>	FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
350	>	if ( fca.isFixedCharge() ) {
351	>	charge = fca.getCharge();
352	>	}
353	>
354	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
355	>	if ( fqa.isFluctuatingCharge() ) {
356	>	charge += atom->getFlucQPos();
357	>	}
358	>
359	>	charge *= chargeToC;
360	>
361	>	ri = atom->getPos();
362	>	snap->wrapVector(ri);
363	>	ri *= angstromToM;
364	>
365	>	if (charge < 0.0) {
366	>	nPos += ri;
367	>	nChg -= charge;
368	>	nCount++;
369	>	} else if (charge > 0.0) {
370	>	pPos += ri;
371	>	pChg += charge;
372	>	pCount++;
373	>	}
374	>
375	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
376	>	if (ma.isDipole() ) {
377	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
378	>	moment = ma.getDipoleMoment();
379	>	moment *= debyeToCm;
380	>	dipoleVector += u_i * moment;
381	>	}
382	>	}
383	>	}
384	>
385	>
386		#ifdef IS_MPI
387	<	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
388	<	#else
389	<	p_global = p_local;
390	<	#endif // is_mpi
387	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
388	>	MPI::SUM);
389	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
390	>	MPI::SUM);
391
392	<	RealType volume = this->getVolume();
393	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
394	<	Mat3x3d tau = curSnapshot->statData.getTau();
392	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
393	>	MPI::SUM);
394	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
395	>	MPI::SUM);
396
397	<	pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
398	<
399	<	return pressureTensor;
400	<	}
397	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
398	>	MPI::REALTYPE, MPI::SUM);
399	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
400	>	MPI::REALTYPE, MPI::SUM);
401
402	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
403	+	3, MPI::REALTYPE, MPI::SUM);
404	+	#endif
405	+
406	+	// first load the accumulated dipole moment (if dipoles were present)
407	+	Vector3d boxDipole = dipoleVector;
408	+	// now include the dipole moment due to charges
409	+	// use the lesser of the positive and negative charge totals
410	+	RealType chg_value = nChg <= pChg ? nChg : pChg;
411	+
412	+	// find the average positions
413	+	if (pCount > 0 && nCount > 0 ) {
414	+	pPos /= pCount;
415	+	nPos /= nCount;
416	+	}
417	+
418	+	// dipole is from the negative to the positive (physics notation)
419	+	boxDipole += (pPos - nPos) * chg_value;
420	+	snap->setSystemDipole(boxDipole);
421	+	}
422
423	<	void Thermo::saveStat(){
424	<	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();
423	>	return snap->getSystemDipole();
424	>	}
425
426	<	Mat3x3d tensor =getPressureTensor();
427	<	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
428	<	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
429	<	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
430	<	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
431	<	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
432	<	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
433	<	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
434	<	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
435	<	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
426	>	// Returns the Heat Flux Vector for the system
427	>	Vector3d Thermo::getHeatFlux(){
428	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
429	>	SimInfo::MoleculeIterator miter;
430	>	vector<StuntDouble*>::iterator iiter;
431	>	Molecule* mol;
432	>	StuntDouble* sd;
433	>	RigidBody::AtomIterator ai;
434	>	Atom* atom;
435	>	Vector3d vel;
436	>	Vector3d angMom;
437	>	Mat3x3d I;
438	>	int i;
439	>	int j;
440	>	int k;
441	>	RealType mass;
442
443	+	Vector3d x_a;
444	+	RealType kinetic;
445	+	RealType potential;
446	+	RealType eatom;
447	+	// Convective portion of the heat flux
448	+	Vector3d heatFluxJc = V3Zero;
449
450	<	Globals* simParams = info_->getSimParams();
450	>	/* Calculate convective portion of the heat flux */
451	>	for (mol = info_->beginMolecule(miter); mol != NULL;
452	>	mol = info_->nextMolecule(miter)) {
453	>
454	>	for (sd = mol->beginIntegrableObject(iiter);
455	>	sd != NULL;
456	>	sd = mol->nextIntegrableObject(iiter)) {
457	>
458	>	mass = sd->getMass();
459	>	vel = sd->getVel();
460
461	+	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
462	+
463	+	if (sd->isDirectional()) {
464	+	angMom = sd->getJ();
465	+	I = sd->getI();
466	+
467	+	if (sd->isLinear()) {
468	+	i = sd->linearAxis();
469	+	j = (i + 1) % 3;
470	+	k = (i + 2) % 3;
471	+	kinetic += angMom[j] * angMom[j] / I(j, j)
472	+	+ angMom[k] * angMom[k] / I(k, k);
473	+	} else {
474	+	kinetic += angMom[0]*angMom[0]/I(0, 0)
475	+	+ angMom[1]*angMom[1]/I(1, 1)
476	+	+ angMom[2]*angMom[2]/I(2, 2);
477	+	}
478	+	}
479	+
480	+	potential = 0.0;
481	+
482	+	if (sd->isRigidBody()) {
483	+	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
484	+	for (atom = rb->beginAtom(ai); atom != NULL;
485	+	atom = rb->nextAtom(ai)) {
486	+	potential +=  atom->getParticlePot();
487	+	}
488	+	} else {
489	+	potential = sd->getParticlePot();
490	+	}
491	+
492	+	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
493	+	// The potential may not be a 1/2 factor
494	+	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
495	+	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
496	+	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
497	+	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
498	+	}
499	+	}
500	+
501	+	/* The J_v vector is reduced in the forceManager so everyone has
502	+	*  the global Jv. Jc is computed over the local atoms and must be
503	+	*  reduced among all processors.
504	+	*/
505	+	#ifdef IS_MPI
506	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
507	+	MPI::SUM);
508	+	#endif
509	+
510	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
511	+
512	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
513	+	PhysicalConstants::energyConvert;
514	+
515	+	// Correct for the fact the flux is 1/V (Jc + Jv)
516	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
517	+	}
518	+
519	+
520	+	Vector3d Thermo::getComVel(){
521	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
522	+
523	+	if (!snap->hasCOMvel) {
524	+
525	+	SimInfo::MoleculeIterator i;
526	+	Molecule* mol;
527	+
528	+	Vector3d comVel(0.0);
529	+	RealType totalMass(0.0);
530	+
531	+	for (mol = info_->beginMolecule(i); mol != NULL;
532	+	mol = info_->nextMolecule(i)) {
533	+	RealType mass = mol->getMass();
534	+	totalMass += mass;
535	+	comVel += mass * mol->getComVel();
536	+	}
537	+
538	+	#ifdef IS_MPI
539	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
540	+	MPI::SUM);
541	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
542	+	MPI::REALTYPE, MPI::SUM);
543	+	#endif
544	+
545	+	comVel /= totalMass;
546	+	snap->setCOMvel(comVel);
547	+	}
548	+	return snap->getCOMvel();
549	+	}
550	+
551	+	Vector3d Thermo::getCom(){
552	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
553	+
554	+	if (!snap->hasCOM) {
555	+
556	+	SimInfo::MoleculeIterator i;
557	+	Molecule* mol;
558	+
559	+	Vector3d com(0.0);
560	+	RealType totalMass(0.0);
561	+
562	+	for (mol = info_->beginMolecule(i); mol != NULL;
563	+	mol = info_->nextMolecule(i)) {
564	+	RealType mass = mol->getMass();
565	+	totalMass += mass;
566	+	com += mass * mol->getCom();
567	+	}
568	+
569	+	#ifdef IS_MPI
570	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
571	+	MPI::SUM);
572	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
573	+	MPI::REALTYPE, MPI::SUM);
574	+	#endif
575	+
576	+	com /= totalMass;
577	+	snap->setCOM(com);
578	+	}
579	+	return snap->getCOM();
580	+	}
581	+
582	+	/**
583	+	* Returns center of mass and center of mass velocity in one
584	+	* function call.
585	+	*/
586	+	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
587	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
588	+
589	+	if (!(snap->hasCOM && snap->hasCOMvel)) {
590	+
591	+	SimInfo::MoleculeIterator i;
592	+	Molecule* mol;
593	+
594	+	RealType totalMass(0.0);
595	+
596	+	com = 0.0;
597	+	comVel = 0.0;
598	+
599	+	for (mol = info_->beginMolecule(i); mol != NULL;
600	+	mol = info_->nextMolecule(i)) {
601	+	RealType mass = mol->getMass();
602	+	totalMass += mass;
603	+	com += mass * mol->getCom();
604	+	comVel += mass * mol->getComVel();
605	+	}
606	+
607	+	#ifdef IS_MPI
608	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
609	+	MPI::SUM);
610	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
611	+	MPI::REALTYPE, MPI::SUM);
612	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
613	+	MPI::REALTYPE, MPI::SUM);
614	+	#endif
615	+
616	+	com /= totalMass;
617	+	comVel /= totalMass;
618	+	snap->setCOM(com);
619	+	snap->setCOMvel(comVel);
620	+	}
621	+	com = snap->getCOM();
622	+	comVel = snap->getCOMvel();
623	+	return;
624	+	}
625	+
626	+	/**
627	+	* Return intertia tensor for entire system and angular momentum
628	+	* Vector.
629	+	*
630	+	*
631	+	*
632	+	*    [  Ixx -Ixy  -Ixz ]
633	+	* I =| -Iyx  Iyy  -Iyz |
634	+	*    [ -Izx -Iyz   Izz ]
635	+	*/
636	+	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
637	+	Vector3d &angularMomentum){
638	+
639	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
640	+
641	+	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
642	+
643	+	RealType xx = 0.0;
644	+	RealType yy = 0.0;
645	+	RealType zz = 0.0;
646	+	RealType xy = 0.0;
647	+	RealType xz = 0.0;
648	+	RealType yz = 0.0;
649	+	Vector3d com(0.0);
650	+	Vector3d comVel(0.0);
651	+
652	+	getComAll(com, comVel);
653	+
654	+	SimInfo::MoleculeIterator i;
655	+	Molecule* mol;
656	+
657	+	Vector3d thisq(0.0);
658	+	Vector3d thisv(0.0);
659	+
660	+	RealType thisMass = 0.0;
661	+
662	+	for (mol = info_->beginMolecule(i); mol != NULL;
663	+	mol = info_->nextMolecule(i)) {
664	+
665	+	thisq = mol->getCom()-com;
666	+	thisv = mol->getComVel()-comVel;
667	+	thisMass = mol->getMass();
668	+	// Compute moment of intertia coefficients.
669	+	xx += thisq[0]*thisq[0]*thisMass;
670	+	yy += thisq[1]*thisq[1]*thisMass;
671	+	zz += thisq[2]*thisq[2]*thisMass;
672	+
673	+	// compute products of intertia
674	+	xy += thisq[0]*thisq[1]*thisMass;
675	+	xz += thisq[0]*thisq[2]*thisMass;
676	+	yz += thisq[1]*thisq[2]*thisMass;
677	+
678	+	angularMomentum += cross( thisq, thisv ) * thisMass;
679	+	}
680	+
681	+	inertiaTensor(0,0) = yy + zz;
682	+	inertiaTensor(0,1) = -xy;
683	+	inertiaTensor(0,2) = -xz;
684	+	inertiaTensor(1,0) = -xy;
685	+	inertiaTensor(1,1) = xx + zz;
686	+	inertiaTensor(1,2) = -yz;
687	+	inertiaTensor(2,0) = -xz;
688	+	inertiaTensor(2,1) = -yz;
689	+	inertiaTensor(2,2) = xx + yy;
690	+
691	+	#ifdef IS_MPI
692	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
693	+	9, MPI::REALTYPE, MPI::SUM);
694	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
695	+	angularMomentum.getArrayPointer(), 3,
696	+	MPI::REALTYPE, MPI::SUM);
697	+	#endif
698	+
699	+	snap->setCOMw(angularMomentum);
700	+	snap->setInertiaTensor(inertiaTensor);
701	+	}
702	+
703	+	angularMomentum = snap->getCOMw();
704	+	inertiaTensor = snap->getInertiaTensor();
705	+
706	+	return;
707	+	}
708	+
709	+	// Returns the angular momentum of the system
710	+	Vector3d Thermo::getAngularMomentum(){
711	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
712	+
713	+	if (!snap->hasCOMw) {
714	+
715	+	Vector3d com(0.0);
716	+	Vector3d comVel(0.0);
717	+	Vector3d angularMomentum(0.0);
718	+
719	+	getComAll(com, comVel);
720	+
721	+	SimInfo::MoleculeIterator i;
722	+	Molecule* mol;
723	+
724	+	Vector3d thisr(0.0);
725	+	Vector3d thisp(0.0);
726	+
727	+	RealType thisMass;
728	+
729	+	for (mol = info_->beginMolecule(i); mol != NULL;
730	+	mol = info_->nextMolecule(i)) {
731	+	thisMass = mol->getMass();
732	+	thisr = mol->getCom() - com;
733	+	thisp = (mol->getComVel() - comVel) * thisMass;
734	+
735	+	angularMomentum += cross( thisr, thisp );
736	+	}
737	+
738	+	#ifdef IS_MPI
739	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
740	+	angularMomentum.getArrayPointer(), 3,
741	+	MPI::REALTYPE, MPI::SUM);
742	+	#endif
743	+
744	+	snap->setCOMw(angularMomentum);
745	+	}
746	+
747	+	return snap->getCOMw();
748	+	}
749	+
750	+
751	+	/**
752	+	* Returns the Volume of the system based on a ellipsoid with
753	+	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
754	+	* where R_i are related to the principle inertia moments
755	+	*  R_i = sqrt(C*I_i/N), this reduces to
756	+	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
757	+	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
758	+	*/
759	+	RealType Thermo::getGyrationalVolume(){
760	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
761	+
762	+	if (!snap->hasGyrationalVolume) {
763	+
764	+	Mat3x3d intTensor;
765	+	RealType det;
766	+	Vector3d dummyAngMom;
767	+	RealType sysconstants;
768	+	RealType geomCnst;
769	+	RealType volume;
770	+
771	+	geomCnst = 3.0/2.0;
772	+	/* Get the inertial tensor and angular momentum for free*/
773	+	getInertiaTensor(intTensor, dummyAngMom);
774	+
775	+	det = intTensor.determinant();
776	+	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
777	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
778	+
779	+	snap->setGyrationalVolume(volume);
780	+	}
781	+	return snap->getGyrationalVolume();
782	+	}
783	+
784	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
785	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
786	+
787	+	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
788	+
789	+	Mat3x3d intTensor;
790	+	Vector3d dummyAngMom;
791	+	RealType sysconstants;
792	+	RealType geomCnst;
793	+
794	+	geomCnst = 3.0/2.0;
795	+	/* Get the inertia tensor and angular momentum for free*/
796	+	this->getInertiaTensor(intTensor, dummyAngMom);
797	+
798	+	detI = intTensor.determinant();
799	+	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
800	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
801	+	snap->setGyrationalVolume(volume);
802	+	} else {
803	+	volume = snap->getGyrationalVolume();
804	+	detI = snap->getInertiaTensor().determinant();
805	+	}
806	+	return;
807	+	}
808	+
809	+	RealType Thermo::getTaggedAtomPairDistance(){
810	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
811	+	Globals* simParams = info_->getSimParams();
812	+
813		if (simParams->haveTaggedAtomPair() &&
814		simParams->havePrintTaggedPairDistance()) {
815		if ( simParams->getPrintTaggedPairDistance()) {
816
817	<	std::pair<int, int> tap = simParams->getTaggedAtomPair();
817	>	pair<int, int> tap = simParams->getTaggedAtomPair();
818		Vector3d pos1, pos2, rab;
819	<
819	>
820		#ifdef IS_MPI
252	–	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
253	–
821		int mol1 = info_->getGlobalMolMembership(tap.first);
822		int mol2 = info_->getGlobalMolMembership(tap.second);
256	–	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
823
824		int proc1 = info_->getMolToProc(mol1);
825		int proc2 = info_->getMolToProc(mol2);
826
261	–	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
262	–
827		RealType data[3];
828		if (proc1 == worldRank) {
829		StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
266	–	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
830		pos1 = sd1->getPos();
831		data[0] = pos1.x();
832		data[1] = pos1.y();
#	Line 274 | Line 837 | namespace OpenMD {
837		pos1 = Vector3d(data);
838		}
839
277	–
840		if (proc2 == worldRank) {
841		StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
280	–	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
842		pos2 = sd2->getPos();
843		data[0] = pos2.x();
844		data[1] = pos2.y();
#	Line 295 | Line 856 | namespace OpenMD {
856		#endif
857		rab = pos2 - pos1;
858		currSnapshot->wrapVector(rab);
859	<	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
859	>	return rab.length();
860		}
861	+	return 0.0;
862		}
863	<
302	<	/**@todo need refactorying*/
303	<	//Conserved Quantity is set by integrator and time is set by setTime
304	<
863	>	return 0.0;
864		}
865
866	<	} //end namespace OpenMD
866	>	RealType Thermo::getHullVolume(){
867	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
868	>
869	>	#ifdef HAVE_QHULL
870	>	if (!snap->hasHullVolume) {
871	>	Hull* surfaceMesh_;
872	>
873	>	Globals* simParams = info_->getSimParams();
874	>	const std::string ht = simParams->getHULL_Method();
875	>
876	>	if (ht == "Convex") {
877	>	surfaceMesh_ = new ConvexHull();
878	>	} else if (ht == "AlphaShape") {
879	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
880	>	} else {
881	>	return 0.0;
882	>	}
883	>
884	>	// Build a vector of stunt doubles to determine if they are
885	>	// surface atoms
886	>	std::vector<StuntDouble*> localSites_;
887	>	Molecule* mol;
888	>	StuntDouble* sd;
889	>	SimInfo::MoleculeIterator i;
890	>	Molecule::IntegrableObjectIterator  j;
891	>
892	>	for (mol = info_->beginMolecule(i); mol != NULL;
893	>	mol = info_->nextMolecule(i)) {
894	>	for (sd = mol->beginIntegrableObject(j);
895	>	sd != NULL;
896	>	sd = mol->nextIntegrableObject(j)) {
897	>	localSites_.push_back(sd);
898	>	}
899	>	}
900	>
901	>	// Compute surface Mesh
902	>	surfaceMesh_->computeHull(localSites_);
903	>	snap->setHullVolume(surfaceMesh_->getVolume());
904	>	}
905	>	return snap->getHullVolume();
906	>	#else
907	>	return 0.0;
908	>	#endif
909	>	}
910	>	}

Comparing trunk/src/brains/Thermo.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1792 by gezelter, Fri Aug 31 17:29:35 2012 UTC

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