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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 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

#	Line 35 | Line 35
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
41	–
42	–	#include <math.h>
43	–	#include <iostream>
42
43		#ifdef IS_MPI
44		#include <mpi.h>
45		#endif //is_mpi
46	+
47	+	#include <math.h>
48	+	#include <iostream>
49
50		#include "brains/Thermo.hpp"
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
93	>	MPI_SUM, MPI_COMM_WORLD);
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
144	+	MPI_SUM, MPI_COMM_WORLD);
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
133	–	RealType Thermo::getTotalE() {
134	–	RealType total;
135	–
136	–	total = this->getKinetic() + this->getPotential();
137	–	return total;
138	–	}
139	–
186		RealType Thermo::getTemperature() {
141	–
142	–	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143	–	return temperature;
144	–	}
187
188	<	RealType Thermo::getVolume() {
147	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148	<	return curSnapshot->getVolume();
149	<	}
188	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189
190	<	RealType Thermo::getPressure() {
190	>	if (!snap->hasTemperature) {
191
192	<	// Relies on the calculation of the full molecular pressure tensor
192	>	RealType temperature = ( 2.0 * this->getKinetic() )
193	>	/ (info_->getNdf()* PhysicalConstants::kb );
194
195	+	snap->setTemperature(temperature);
196	+	}
197	+
198	+	return snap->getTemperature();
199	+	}
200
201	<	Mat3x3d tensor;
202	<	RealType pressure;
201	>	RealType Thermo::getElectronicTemperature() {
202	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203
204	<	tensor = getPressureTensor();
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
231	>	MPI_SUM, MPI_COMM_WORLD);
232	>	#endif
233
234	<	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
234	>	kinetic *= 0.5;
235	>	eTemp =  (2.0 * kinetic) /
236	>	(info_->getNFluctuatingCharges() * PhysicalConstants::kb );
237	>
238	>	snap->setElectronicTemperature(eTemp);
239	>	}
240
241	<	return pressure;
241	>	return snap->getElectronicTemperature();
242		}
243
166	–	RealType Thermo::getPressure(int direction) {
244
245	<	// Relies on the calculation of the full molecular pressure tensor
245	>	RealType Thermo::getVolume() {
246	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247	>	return snap->getVolume();
248	>	}
249
250	<
251	<	Mat3x3d tensor;
172	<	RealType pressure;
250	>	RealType Thermo::getPressure() {
251	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252
253	<	tensor = getPressureTensor();
254	<
255	<	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
256	<
257	<	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_Allreduce(MPI_IN_PLACE, p_tens.getArrayPointer(), 9,
301	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
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	>	Vector3d ri(0.0);
328	>	Vector3d dipoleVector(0.0);
329	>	Vector3d nPos(0.0);
330	>	Vector3d pPos(0.0);
331	>	RealType nChg(0.0);
332	>	RealType pChg(0.0);
333	>	int nCount = 0;
334	>	int pCount = 0;
335	>
336	>	RealType chargeToC = 1.60217733e-19;
337	>	RealType angstromToM = 1.0e-10;
338	>	RealType debyeToCm = 3.33564095198e-30;
339	>
340	>	for (mol = info_->beginMolecule(miter); mol != NULL;
341	>	mol = info_->nextMolecule(miter)) {
342	>
343	>	for (atom = mol->beginAtom(aiter); atom != NULL;
344	>	atom = mol->nextAtom(aiter)) {
345	>
346	>	charge = 0.0;
347	>
348	>	FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
349	>	if ( fca.isFixedCharge() ) {
350	>	charge = fca.getCharge();
351	>	}
352	>
353	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
354	>	if ( fqa.isFluctuatingCharge() ) {
355	>	charge += atom->getFlucQPos();
356	>	}
357	>
358	>	charge *= chargeToC;
359	>
360	>	ri = atom->getPos();
361	>	snap->wrapVector(ri);
362	>	ri *= angstromToM;
363	>
364	>	if (charge < 0.0) {
365	>	nPos += ri;
366	>	nChg -= charge;
367	>	nCount++;
368	>	} else if (charge > 0.0) {
369	>	pPos += ri;
370	>	pChg += charge;
371	>	pCount++;
372	>	}
373	>
374	>	if (atom->isDipole()) {
375	>	dipoleVector += atom->getDipole() * debyeToCm;
376	>	}
377	>	}
378	>	}
379	>
380	>
381		#ifdef IS_MPI
382	<	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
383	<	#else
384	<	p_global = p_local;
385	<	#endif // is_mpi
382	>	MPI_Allreduce(MPI_IN_PLACE, &pChg, 1, MPI_REALTYPE,
383	>	MPI_SUM, MPI_COMM_WORLD);
384	>	MPI_Allreduce(MPI_IN_PLACE, &nChg, 1, MPI_REALTYPE,
385	>	MPI_SUM, MPI_COMM_WORLD);
386	>
387	>	MPI_Allreduce(MPI_IN_PLACE, &pCount, 1, MPI_INTEGER,
388	>	MPI_SUM, MPI_COMM_WORLD);
389	>	MPI_Allreduce(MPI_IN_PLACE, &nCount, 1, MPI_INTEGER,
390	>	MPI_SUM, MPI_COMM_WORLD);
391	>
392	>	MPI_Allreduce(MPI_IN_PLACE, pPos.getArrayPointer(), 3,
393	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
394	>	MPI_Allreduce(MPI_IN_PLACE, nPos.getArrayPointer(), 3,
395	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
396
397	<	RealType volume = this->getVolume();
398	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
399	<	Mat3x3d tau = curSnapshot->statData.getTau();
397	>	MPI_Allreduce(MPI_IN_PLACE, dipoleVector.getArrayPointer(),
398	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
399	>	#endif
400	>
401	>	// first load the accumulated dipole moment (if dipoles were present)
402	>	Vector3d boxDipole = dipoleVector;
403	>	// now include the dipole moment due to charges
404	>	// use the lesser of the positive and negative charge totals
405	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
406	>
407	>	// find the average positions
408	>	if (pCount > 0 && nCount > 0 ) {
409	>	pPos /= pCount;
410	>	nPos /= nCount;
411	>	}
412	>
413	>	// dipole is from the negative to the positive (physics notation)
414	>	boxDipole += (pPos - nPos) * chg_value;
415	>	snap->setSystemDipole(boxDipole);
416	>	}
417
418	<	pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
214	<
215	<	return pressureTensor;
418	>	return snap->getSystemDipole();
419		}
420
421
422	<	void Thermo::saveStat(){
423	<	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();
422	>	Mat3x3d Thermo::getSystemQuadrupole() {
423	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
424
425	<	Mat3x3d tensor =getPressureTensor();
426	<	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
427	<	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
428	<	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
429	<	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
430	<	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
431	<	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
432	<	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
433	<	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
434	<	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
425	>	if (!snap->hasSystemQuadrupole) {
426	>	SimInfo::MoleculeIterator miter;
427	>	vector<Atom*>::iterator aiter;
428	>	Molecule* mol;
429	>	Atom* atom;
430	>	RealType charge;
431	>	Vector3d ri(0.0);
432	>	Vector3d dipole(0.0);
433	>	Mat3x3d qpole(0.0);
434	>
435	>	RealType chargeToC = 1.60217733e-19;
436	>	RealType angstromToM = 1.0e-10;
437	>	RealType debyeToCm = 3.33564095198e-30;
438	>
439	>	for (mol = info_->beginMolecule(miter); mol != NULL;
440	>	mol = info_->nextMolecule(miter)) {
441	>
442	>	for (atom = mol->beginAtom(aiter); atom != NULL;
443	>	atom = mol->nextAtom(aiter)) {
444
445	+	ri = atom->getPos();
446	+	snap->wrapVector(ri);
447	+	ri *= angstromToM;
448	+
449	+	charge = 0.0;
450	+
451	+	FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
452	+	if ( fca.isFixedCharge() ) {
453	+	charge = fca.getCharge();
454	+	}
455	+
456	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
457	+	if ( fqa.isFluctuatingCharge() ) {
458	+	charge += atom->getFlucQPos();
459	+	}
460	+
461	+	charge *= chargeToC;
462	+
463	+	qpole += 0.5 * charge * outProduct(ri, ri);
464
465	<	Globals* simParams = info_->getSimParams();
465	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
466	>
467	>	if ( ma.isDipole() ) {
468	>	dipole = atom->getDipole() * debyeToCm;
469	>	qpole += 0.5 * outProduct( dipole, ri );
470	>	qpole += 0.5 * outProduct( ri, dipole );
471	>	}
472	>
473	>	if ( ma.isQuadrupole() ) {
474	>	qpole += atom->getQuadrupole() * debyeToCm * angstromToM;
475	>	}
476	>	}
477	>	}
478	>
479	>	#ifdef IS_MPI
480	>	MPI_Allreduce(MPI_IN_PLACE, qpole.getArrayPointer(),
481	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
482	>	#endif
483	>
484	>	snap->setSystemQuadrupole(qpole);
485	>	}
486	>
487	>	return snap->getSystemQuadrupole();
488	>	}
489
490	+	// Returns the Heat Flux Vector for the system
491	+	Vector3d Thermo::getHeatFlux(){
492	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
493	+	SimInfo::MoleculeIterator miter;
494	+	vector<StuntDouble*>::iterator iiter;
495	+	Molecule* mol;
496	+	StuntDouble* sd;
497	+	RigidBody::AtomIterator ai;
498	+	Atom* atom;
499	+	Vector3d vel;
500	+	Vector3d angMom;
501	+	Mat3x3d I;
502	+	int i;
503	+	int j;
504	+	int k;
505	+	RealType mass;
506	+
507	+	Vector3d x_a;
508	+	RealType kinetic;
509	+	RealType potential;
510	+	RealType eatom;
511	+	// Convective portion of the heat flux
512	+	Vector3d heatFluxJc = V3Zero;
513	+
514	+	/* Calculate convective portion of the heat flux */
515	+	for (mol = info_->beginMolecule(miter); mol != NULL;
516	+	mol = info_->nextMolecule(miter)) {
517	+
518	+	for (sd = mol->beginIntegrableObject(iiter);
519	+	sd != NULL;
520	+	sd = mol->nextIntegrableObject(iiter)) {
521	+
522	+	mass = sd->getMass();
523	+	vel = sd->getVel();
524	+
525	+	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
526	+
527	+	if (sd->isDirectional()) {
528	+	angMom = sd->getJ();
529	+	I = sd->getI();
530	+
531	+	if (sd->isLinear()) {
532	+	i = sd->linearAxis();
533	+	j = (i + 1) % 3;
534	+	k = (i + 2) % 3;
535	+	kinetic += angMom[j] * angMom[j] / I(j, j)
536	+	+ angMom[k] * angMom[k] / I(k, k);
537	+	} else {
538	+	kinetic += angMom[0]*angMom[0]/I(0, 0)
539	+	+ angMom[1]*angMom[1]/I(1, 1)
540	+	+ angMom[2]*angMom[2]/I(2, 2);
541	+	}
542	+	}
543	+
544	+	potential = 0.0;
545	+
546	+	if (sd->isRigidBody()) {
547	+	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
548	+	for (atom = rb->beginAtom(ai); atom != NULL;
549	+	atom = rb->nextAtom(ai)) {
550	+	potential +=  atom->getParticlePot();
551	+	}
552	+	} else {
553	+	potential = sd->getParticlePot();
554	+	}
555	+
556	+	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
557	+	// The potential may not be a 1/2 factor
558	+	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
559	+	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
560	+	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
561	+	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
562	+	}
563	+	}
564	+
565	+	/* The J_v vector is reduced in the forceManager so everyone has
566	+	*  the global Jv. Jc is computed over the local atoms and must be
567	+	*  reduced among all processors.
568	+	*/
569	+	#ifdef IS_MPI
570	+	MPI_Allreduce(MPI_IN_PLACE, &heatFluxJc[0], 3, MPI_REALTYPE,
571	+	MPI_SUM, MPI_COMM_WORLD);
572	+	#endif
573	+
574	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
575	+
576	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
577	+	PhysicalConstants::energyConvert;
578	+
579	+	// Correct for the fact the flux is 1/V (Jc + Jv)
580	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
581	+	}
582	+
583	+
584	+	Vector3d Thermo::getComVel(){
585	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
586	+
587	+	if (!snap->hasCOMvel) {
588	+
589	+	SimInfo::MoleculeIterator i;
590	+	Molecule* mol;
591	+
592	+	Vector3d comVel(0.0);
593	+	RealType totalMass(0.0);
594	+
595	+	for (mol = info_->beginMolecule(i); mol != NULL;
596	+	mol = info_->nextMolecule(i)) {
597	+	RealType mass = mol->getMass();
598	+	totalMass += mass;
599	+	comVel += mass * mol->getComVel();
600	+	}
601	+
602	+	#ifdef IS_MPI
603	+	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
604	+	MPI_SUM, MPI_COMM_WORLD);
605	+	MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
606	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
607	+	#endif
608	+
609	+	comVel /= totalMass;
610	+	snap->setCOMvel(comVel);
611	+	}
612	+	return snap->getCOMvel();
613	+	}
614	+
615	+	Vector3d Thermo::getCom(){
616	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
617	+
618	+	if (!snap->hasCOM) {
619	+
620	+	SimInfo::MoleculeIterator i;
621	+	Molecule* mol;
622	+
623	+	Vector3d com(0.0);
624	+	RealType totalMass(0.0);
625	+
626	+	for (mol = info_->beginMolecule(i); mol != NULL;
627	+	mol = info_->nextMolecule(i)) {
628	+	RealType mass = mol->getMass();
629	+	totalMass += mass;
630	+	com += mass * mol->getCom();
631	+	}
632	+
633	+	#ifdef IS_MPI
634	+	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
635	+	MPI_SUM, MPI_COMM_WORLD);
636	+	MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
637	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
638	+	#endif
639	+
640	+	com /= totalMass;
641	+	snap->setCOM(com);
642	+	}
643	+	return snap->getCOM();
644	+	}
645	+
646	+	/**
647	+	* Returns center of mass and center of mass velocity in one
648	+	* function call.
649	+	*/
650	+	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
651	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
652	+
653	+	if (!(snap->hasCOM && snap->hasCOMvel)) {
654	+
655	+	SimInfo::MoleculeIterator i;
656	+	Molecule* mol;
657	+
658	+	RealType totalMass(0.0);
659	+
660	+	com = 0.0;
661	+	comVel = 0.0;
662	+
663	+	for (mol = info_->beginMolecule(i); mol != NULL;
664	+	mol = info_->nextMolecule(i)) {
665	+	RealType mass = mol->getMass();
666	+	totalMass += mass;
667	+	com += mass * mol->getCom();
668	+	comVel += mass * mol->getComVel();
669	+	}
670	+
671	+	#ifdef IS_MPI
672	+	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
673	+	MPI_SUM, MPI_COMM_WORLD);
674	+	MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
675	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
676	+	MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
677	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
678	+	#endif
679	+
680	+	com /= totalMass;
681	+	comVel /= totalMass;
682	+	snap->setCOM(com);
683	+	snap->setCOMvel(comVel);
684	+	}
685	+	com = snap->getCOM();
686	+	comVel = snap->getCOMvel();
687	+	return;
688	+	}
689	+
690	+	/**
691	+	* \brief Return inertia tensor for entire system and angular momentum
692	+	*  Vector.
693	+	*
694	+	*
695	+	*
696	+	*    [  Ixx -Ixy  -Ixz ]
697	+	* I =| -Iyx  Iyy  -Iyz |
698	+	*    [ -Izx -Iyz   Izz ]
699	+	*/
700	+	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
701	+	Vector3d &angularMomentum){
702	+
703	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
704	+
705	+	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
706	+
707	+	RealType xx = 0.0;
708	+	RealType yy = 0.0;
709	+	RealType zz = 0.0;
710	+	RealType xy = 0.0;
711	+	RealType xz = 0.0;
712	+	RealType yz = 0.0;
713	+	Vector3d com(0.0);
714	+	Vector3d comVel(0.0);
715	+
716	+	getComAll(com, comVel);
717	+
718	+	SimInfo::MoleculeIterator i;
719	+	Molecule* mol;
720	+
721	+	Vector3d thisq(0.0);
722	+	Vector3d thisv(0.0);
723	+
724	+	RealType thisMass = 0.0;
725	+
726	+	for (mol = info_->beginMolecule(i); mol != NULL;
727	+	mol = info_->nextMolecule(i)) {
728	+
729	+	thisq = mol->getCom()-com;
730	+	thisv = mol->getComVel()-comVel;
731	+	thisMass = mol->getMass();
732	+	// Compute moment of intertia coefficients.
733	+	xx += thisq[0]*thisq[0]*thisMass;
734	+	yy += thisq[1]*thisq[1]*thisMass;
735	+	zz += thisq[2]*thisq[2]*thisMass;
736	+
737	+	// compute products of intertia
738	+	xy += thisq[0]*thisq[1]*thisMass;
739	+	xz += thisq[0]*thisq[2]*thisMass;
740	+	yz += thisq[1]*thisq[2]*thisMass;
741	+
742	+	angularMomentum += cross( thisq, thisv ) * thisMass;
743	+	}
744	+
745	+	inertiaTensor(0,0) = yy + zz;
746	+	inertiaTensor(0,1) = -xy;
747	+	inertiaTensor(0,2) = -xz;
748	+	inertiaTensor(1,0) = -xy;
749	+	inertiaTensor(1,1) = xx + zz;
750	+	inertiaTensor(1,2) = -yz;
751	+	inertiaTensor(2,0) = -xz;
752	+	inertiaTensor(2,1) = -yz;
753	+	inertiaTensor(2,2) = xx + yy;
754	+
755	+	#ifdef IS_MPI
756	+	MPI_Allreduce(MPI_IN_PLACE, inertiaTensor.getArrayPointer(),
757	+	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
758	+	MPI_Allreduce(MPI_IN_PLACE,
759	+	angularMomentum.getArrayPointer(), 3,
760	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
761	+	#endif
762	+
763	+	snap->setCOMw(angularMomentum);
764	+	snap->setInertiaTensor(inertiaTensor);
765	+	}
766	+
767	+	angularMomentum = snap->getCOMw();
768	+	inertiaTensor = snap->getInertiaTensor();
769	+
770	+	return;
771	+	}
772	+
773	+
774	+	Mat3x3d Thermo::getBoundingBox(){
775	+
776	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
777	+
778	+	if (!(snap->hasBoundingBox)) {
779	+
780	+	SimInfo::MoleculeIterator i;
781	+	Molecule::RigidBodyIterator ri;
782	+	Molecule::AtomIterator ai;
783	+	Molecule* mol;
784	+	RigidBody* rb;
785	+	Atom* atom;
786	+	Vector3d pos, bMax, bMin;
787	+	int index = 0;
788	+
789	+	for (mol = info_->beginMolecule(i); mol != NULL;
790	+	mol = info_->nextMolecule(i)) {
791	+
792	+	//change the positions of atoms which belong to the rigidbodies
793	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
794	+	rb = mol->nextRigidBody(ri)) {
795	+	rb->updateAtoms();
796	+	}
797	+
798	+	for(atom = mol->beginAtom(ai); atom != NULL;
799	+	atom = mol->nextAtom(ai)) {
800	+
801	+	pos = atom->getPos();
802	+
803	+	if (index == 0) {
804	+	bMax = pos;
805	+	bMin = pos;
806	+	} else {
807	+	for (int i = 0; i < 3; i++) {
808	+	bMax[i] = max(bMax[i], pos[i]);
809	+	bMin[i] = min(bMin[i], pos[i]);
810	+	}
811	+	}
812	+	index++;
813	+	}
814	+	}
815	+
816	+	#ifdef IS_MPI
817	+	MPI_Allreduce(MPI_IN_PLACE, &bMax[0], 3, MPI_REALTYPE,
818	+	MPI_MAX, MPI_COMM_WORLD);
819	+
820	+	MPI_Allreduce(MPI_IN_PLACE, &bMin[0], 3, MPI_REALTYPE,
821	+	MPI_MIN, MPI_COMM_WORLD);
822	+	#endif
823	+	Mat3x3d bBox = Mat3x3d(0.0);
824	+	for (int i = 0; i < 3; i++) {
825	+	bBox(i,i) = bMax[i] - bMin[i];
826	+	}
827	+	snap->setBoundingBox(bBox);
828	+	}
829	+
830	+	return snap->getBoundingBox();
831	+	}
832	+
833	+
834	+	// Returns the angular momentum of the system
835	+	Vector3d Thermo::getAngularMomentum(){
836	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
837	+
838	+	if (!snap->hasCOMw) {
839	+
840	+	Vector3d com(0.0);
841	+	Vector3d comVel(0.0);
842	+	Vector3d angularMomentum(0.0);
843	+
844	+	getComAll(com, comVel);
845	+
846	+	SimInfo::MoleculeIterator i;
847	+	Molecule* mol;
848	+
849	+	Vector3d thisr(0.0);
850	+	Vector3d thisp(0.0);
851	+
852	+	RealType thisMass;
853	+
854	+	for (mol = info_->beginMolecule(i); mol != NULL;
855	+	mol = info_->nextMolecule(i)) {
856	+	thisMass = mol->getMass();
857	+	thisr = mol->getCom() - com;
858	+	thisp = (mol->getComVel() - comVel) * thisMass;
859	+
860	+	angularMomentum += cross( thisr, thisp );
861	+	}
862	+
863	+	#ifdef IS_MPI
864	+	MPI_Allreduce(MPI_IN_PLACE,
865	+	angularMomentum.getArrayPointer(), 3,
866	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
867	+	#endif
868	+
869	+	snap->setCOMw(angularMomentum);
870	+	}
871	+
872	+	return snap->getCOMw();
873	+	}
874	+
875	+
876	+	/**
877	+	* Returns the Volume of the system based on a ellipsoid with
878	+	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
879	+	* where R_i are related to the principle inertia moments
880	+	*  R_i = sqrt(C*I_i/N), this reduces to
881	+	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
882	+	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
883	+	*/
884	+	RealType Thermo::getGyrationalVolume(){
885	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
886	+
887	+	if (!snap->hasGyrationalVolume) {
888	+
889	+	Mat3x3d intTensor;
890	+	RealType det;
891	+	Vector3d dummyAngMom;
892	+	RealType sysconstants;
893	+	RealType geomCnst;
894	+	RealType volume;
895	+
896	+	geomCnst = 3.0/2.0;
897	+	/* Get the inertial tensor and angular momentum for free*/
898	+	getInertiaTensor(intTensor, dummyAngMom);
899	+
900	+	det = intTensor.determinant();
901	+	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
902	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
903	+
904	+	snap->setGyrationalVolume(volume);
905	+	}
906	+	return snap->getGyrationalVolume();
907	+	}
908	+
909	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
910	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
911	+
912	+	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
913	+
914	+	Mat3x3d intTensor;
915	+	Vector3d dummyAngMom;
916	+	RealType sysconstants;
917	+	RealType geomCnst;
918	+
919	+	geomCnst = 3.0/2.0;
920	+	/* Get the inertia tensor and angular momentum for free*/
921	+	this->getInertiaTensor(intTensor, dummyAngMom);
922	+
923	+	detI = intTensor.determinant();
924	+	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
925	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
926	+	snap->setGyrationalVolume(volume);
927	+	} else {
928	+	volume = snap->getGyrationalVolume();
929	+	detI = snap->getInertiaTensor().determinant();
930	+	}
931	+	return;
932	+	}
933	+
934	+	RealType Thermo::getTaggedAtomPairDistance(){
935	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
936	+	Globals* simParams = info_->getSimParams();
937	+
938		if (simParams->haveTaggedAtomPair() &&
939		simParams->havePrintTaggedPairDistance()) {
940		if ( simParams->getPrintTaggedPairDistance()) {
941
942	<	std::pair<int, int> tap = simParams->getTaggedAtomPair();
942	>	pair<int, int> tap = simParams->getTaggedAtomPair();
943		Vector3d pos1, pos2, rab;
944	<
944	>
945		#ifdef IS_MPI
252	–	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
253	–
946		int mol1 = info_->getGlobalMolMembership(tap.first);
947		int mol2 = info_->getGlobalMolMembership(tap.second);
256	–	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
948
949		int proc1 = info_->getMolToProc(mol1);
950		int proc2 = info_->getMolToProc(mol2);
951
261	–	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
262	–
952		RealType data[3];
953		if (proc1 == worldRank) {
954		StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
266	–	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
955		pos1 = sd1->getPos();
956		data[0] = pos1.x();
957		data[1] = pos1.y();
#	Line 274 | Line 962 | namespace OpenMD {
962		pos1 = Vector3d(data);
963		}
964
277	–
965		if (proc2 == worldRank) {
966		StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
280	–	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
967		pos2 = sd2->getPos();
968		data[0] = pos2.x();
969		data[1] = pos2.y();
970	<	data[2] = pos2.z();
970	>	data[2] = pos2.z();
971		MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
972		} else {
973		MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
#	Line 295 | Line 981 | namespace OpenMD {
981		#endif
982		rab = pos2 - pos1;
983		currSnapshot->wrapVector(rab);
984	<	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
984	>	return rab.length();
985		}
986	+	return 0.0;
987		}
988	+	return 0.0;
989	+	}
990	+
991	+	RealType Thermo::getHullVolume(){
992	+	#ifdef HAVE_QHULL
993	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
994	+	if (!snap->hasHullVolume) {
995	+	Hull* surfaceMesh_;
996
997	<	/**@todo need refactorying*/
998	<	//Conserved Quantity is set by integrator and time is set by setTime
997	>	Globals* simParams = info_->getSimParams();
998	>	const std::string ht = simParams->getHULL_Method();
999	>
1000	>	if (ht == "Convex") {
1001	>	surfaceMesh_ = new ConvexHull();
1002	>	} else if (ht == "AlphaShape") {
1003	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
1004	>	} else {
1005	>	return 0.0;
1006	>	}
1007	>
1008	>	// Build a vector of stunt doubles to determine if they are
1009	>	// surface atoms
1010	>	std::vector<StuntDouble*> localSites_;
1011	>	Molecule* mol;
1012	>	StuntDouble* sd;
1013	>	SimInfo::MoleculeIterator i;
1014	>	Molecule::IntegrableObjectIterator  j;
1015	>
1016	>	for (mol = info_->beginMolecule(i); mol != NULL;
1017	>	mol = info_->nextMolecule(i)) {
1018	>	for (sd = mol->beginIntegrableObject(j);
1019	>	sd != NULL;
1020	>	sd = mol->nextIntegrableObject(j)) {
1021	>	localSites_.push_back(sd);
1022	>	}
1023	>	}
1024	>
1025	>	// Compute surface Mesh
1026	>	surfaceMesh_->computeHull(localSites_);
1027	>	snap->setHullVolume(surfaceMesh_->getVolume());
1028	>
1029	>	delete surfaceMesh_;
1030	>	}
1031
1032	+	return snap->getHullVolume();
1033	+	#else
1034	+	return 0.0;
1035	+	#endif
1036		}
1037
1038	<	} //end namespace OpenMD
1038	>
1039	>	}

Comparing trunk/src/brains/Thermo.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

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