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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 2022 by gezelter, Fri Sep 26 22:22:28 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	>	}
471
472	+	if ( ma.isQuadrupole() ) {
473	+	qpole += atom->getQuadrupole() * debyeToCm * angstromToM;
474	+	}
475	+	}
476	+	}
477	+
478	+	#ifdef IS_MPI
479	+	MPI_Allreduce(MPI_IN_PLACE, qpole.getArrayPointer(),
480	+	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
481	+	#endif
482	+
483	+	snap->setSystemQuadrupole(qpole);
484	+	}
485	+
486	+	return snap->getSystemQuadrupole();
487	+	}
488	+
489	+	// Returns the Heat Flux Vector for the system
490	+	Vector3d Thermo::getHeatFlux(){
491	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
492	+	SimInfo::MoleculeIterator miter;
493	+	vector<StuntDouble*>::iterator iiter;
494	+	Molecule* mol;
495	+	StuntDouble* sd;
496	+	RigidBody::AtomIterator ai;
497	+	Atom* atom;
498	+	Vector3d vel;
499	+	Vector3d angMom;
500	+	Mat3x3d I;
501	+	int i;
502	+	int j;
503	+	int k;
504	+	RealType mass;
505	+
506	+	Vector3d x_a;
507	+	RealType kinetic;
508	+	RealType potential;
509	+	RealType eatom;
510	+	// Convective portion of the heat flux
511	+	Vector3d heatFluxJc = V3Zero;
512	+
513	+	/* Calculate convective portion of the heat flux */
514	+	for (mol = info_->beginMolecule(miter); mol != NULL;
515	+	mol = info_->nextMolecule(miter)) {
516	+
517	+	for (sd = mol->beginIntegrableObject(iiter);
518	+	sd != NULL;
519	+	sd = mol->nextIntegrableObject(iiter)) {
520	+
521	+	mass = sd->getMass();
522	+	vel = sd->getVel();
523	+
524	+	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
525	+
526	+	if (sd->isDirectional()) {
527	+	angMom = sd->getJ();
528	+	I = sd->getI();
529	+
530	+	if (sd->isLinear()) {
531	+	i = sd->linearAxis();
532	+	j = (i + 1) % 3;
533	+	k = (i + 2) % 3;
534	+	kinetic += angMom[j] * angMom[j] / I(j, j)
535	+	+ angMom[k] * angMom[k] / I(k, k);
536	+	} else {
537	+	kinetic += angMom[0]*angMom[0]/I(0, 0)
538	+	+ angMom[1]*angMom[1]/I(1, 1)
539	+	+ angMom[2]*angMom[2]/I(2, 2);
540	+	}
541	+	}
542	+
543	+	potential = 0.0;
544	+
545	+	if (sd->isRigidBody()) {
546	+	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
547	+	for (atom = rb->beginAtom(ai); atom != NULL;
548	+	atom = rb->nextAtom(ai)) {
549	+	potential +=  atom->getParticlePot();
550	+	}
551	+	} else {
552	+	potential = sd->getParticlePot();
553	+	}
554	+
555	+	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
556	+	// The potential may not be a 1/2 factor
557	+	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
558	+	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
559	+	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
560	+	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
561	+	}
562	+	}
563	+
564	+	/* The J_v vector is reduced in the forceManager so everyone has
565	+	*  the global Jv. Jc is computed over the local atoms and must be
566	+	*  reduced among all processors.
567	+	*/
568	+	#ifdef IS_MPI
569	+	MPI_Allreduce(MPI_IN_PLACE, &heatFluxJc[0], 3, MPI_REALTYPE,
570	+	MPI_SUM, MPI_COMM_WORLD);
571	+	#endif
572	+
573	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
574	+
575	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
576	+	PhysicalConstants::energyConvert;
577	+
578	+	// Correct for the fact the flux is 1/V (Jc + Jv)
579	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
580	+	}
581	+
582	+
583	+	Vector3d Thermo::getComVel(){
584	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
585	+
586	+	if (!snap->hasCOMvel) {
587	+
588	+	SimInfo::MoleculeIterator i;
589	+	Molecule* mol;
590	+
591	+	Vector3d comVel(0.0);
592	+	RealType totalMass(0.0);
593	+
594	+	for (mol = info_->beginMolecule(i); mol != NULL;
595	+	mol = info_->nextMolecule(i)) {
596	+	RealType mass = mol->getMass();
597	+	totalMass += mass;
598	+	comVel += mass * mol->getComVel();
599	+	}
600	+
601	+	#ifdef IS_MPI
602	+	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
603	+	MPI_SUM, MPI_COMM_WORLD);
604	+	MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
605	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
606	+	#endif
607	+
608	+	comVel /= totalMass;
609	+	snap->setCOMvel(comVel);
610	+	}
611	+	return snap->getCOMvel();
612	+	}
613	+
614	+	Vector3d Thermo::getCom(){
615	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
616	+
617	+	if (!snap->hasCOM) {
618	+
619	+	SimInfo::MoleculeIterator i;
620	+	Molecule* mol;
621	+
622	+	Vector3d com(0.0);
623	+	RealType totalMass(0.0);
624	+
625	+	for (mol = info_->beginMolecule(i); mol != NULL;
626	+	mol = info_->nextMolecule(i)) {
627	+	RealType mass = mol->getMass();
628	+	totalMass += mass;
629	+	com += mass * mol->getCom();
630	+	}
631	+
632	+	#ifdef IS_MPI
633	+	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
634	+	MPI_SUM, MPI_COMM_WORLD);
635	+	MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
636	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
637	+	#endif
638	+
639	+	com /= totalMass;
640	+	snap->setCOM(com);
641	+	}
642	+	return snap->getCOM();
643	+	}
644	+
645	+	/**
646	+	* Returns center of mass and center of mass velocity in one
647	+	* function call.
648	+	*/
649	+	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
650	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
651	+
652	+	if (!(snap->hasCOM && snap->hasCOMvel)) {
653	+
654	+	SimInfo::MoleculeIterator i;
655	+	Molecule* mol;
656	+
657	+	RealType totalMass(0.0);
658	+
659	+	com = 0.0;
660	+	comVel = 0.0;
661	+
662	+	for (mol = info_->beginMolecule(i); mol != NULL;
663	+	mol = info_->nextMolecule(i)) {
664	+	RealType mass = mol->getMass();
665	+	totalMass += mass;
666	+	com += mass * mol->getCom();
667	+	comVel += mass * mol->getComVel();
668	+	}
669	+
670	+	#ifdef IS_MPI
671	+	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
672	+	MPI_SUM, MPI_COMM_WORLD);
673	+	MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
674	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
675	+	MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
676	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
677	+	#endif
678	+
679	+	com /= totalMass;
680	+	comVel /= totalMass;
681	+	snap->setCOM(com);
682	+	snap->setCOMvel(comVel);
683	+	}
684	+	com = snap->getCOM();
685	+	comVel = snap->getCOMvel();
686	+	return;
687	+	}
688	+
689	+	/**
690	+	* \brief Return inertia tensor for entire system and angular momentum
691	+	*  Vector.
692	+	*
693	+	*
694	+	*
695	+	*    [  Ixx -Ixy  -Ixz ]
696	+	* I =| -Iyx  Iyy  -Iyz |
697	+	*    [ -Izx -Iyz   Izz ]
698	+	*/
699	+	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
700	+	Vector3d &angularMomentum){
701	+
702	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
703	+
704	+	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
705	+
706	+	RealType xx = 0.0;
707	+	RealType yy = 0.0;
708	+	RealType zz = 0.0;
709	+	RealType xy = 0.0;
710	+	RealType xz = 0.0;
711	+	RealType yz = 0.0;
712	+	Vector3d com(0.0);
713	+	Vector3d comVel(0.0);
714	+
715	+	getComAll(com, comVel);
716	+
717	+	SimInfo::MoleculeIterator i;
718	+	Molecule* mol;
719	+
720	+	Vector3d thisq(0.0);
721	+	Vector3d thisv(0.0);
722	+
723	+	RealType thisMass = 0.0;
724	+
725	+	for (mol = info_->beginMolecule(i); mol != NULL;
726	+	mol = info_->nextMolecule(i)) {
727	+
728	+	thisq = mol->getCom()-com;
729	+	thisv = mol->getComVel()-comVel;
730	+	thisMass = mol->getMass();
731	+	// Compute moment of intertia coefficients.
732	+	xx += thisq[0]*thisq[0]*thisMass;
733	+	yy += thisq[1]*thisq[1]*thisMass;
734	+	zz += thisq[2]*thisq[2]*thisMass;
735	+
736	+	// compute products of intertia
737	+	xy += thisq[0]*thisq[1]*thisMass;
738	+	xz += thisq[0]*thisq[2]*thisMass;
739	+	yz += thisq[1]*thisq[2]*thisMass;
740	+
741	+	angularMomentum += cross( thisq, thisv ) * thisMass;
742	+	}
743	+
744	+	inertiaTensor(0,0) = yy + zz;
745	+	inertiaTensor(0,1) = -xy;
746	+	inertiaTensor(0,2) = -xz;
747	+	inertiaTensor(1,0) = -xy;
748	+	inertiaTensor(1,1) = xx + zz;
749	+	inertiaTensor(1,2) = -yz;
750	+	inertiaTensor(2,0) = -xz;
751	+	inertiaTensor(2,1) = -yz;
752	+	inertiaTensor(2,2) = xx + yy;
753	+
754	+	#ifdef IS_MPI
755	+	MPI_Allreduce(MPI_IN_PLACE, inertiaTensor.getArrayPointer(),
756	+	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
757	+	MPI_Allreduce(MPI_IN_PLACE,
758	+	angularMomentum.getArrayPointer(), 3,
759	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
760	+	#endif
761	+
762	+	snap->setCOMw(angularMomentum);
763	+	snap->setInertiaTensor(inertiaTensor);
764	+	}
765	+
766	+	angularMomentum = snap->getCOMw();
767	+	inertiaTensor = snap->getInertiaTensor();
768	+
769	+	return;
770	+	}
771	+
772	+
773	+	Mat3x3d Thermo::getBoundingBox(){
774	+
775	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
776	+
777	+	if (!(snap->hasBoundingBox)) {
778	+
779	+	SimInfo::MoleculeIterator i;
780	+	Molecule::RigidBodyIterator ri;
781	+	Molecule::AtomIterator ai;
782	+	Molecule* mol;
783	+	RigidBody* rb;
784	+	Atom* atom;
785	+	Vector3d pos, bMax, bMin;
786	+	int index = 0;
787	+
788	+	for (mol = info_->beginMolecule(i); mol != NULL;
789	+	mol = info_->nextMolecule(i)) {
790	+
791	+	//change the positions of atoms which belong to the rigidbodies
792	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
793	+	rb = mol->nextRigidBody(ri)) {
794	+	rb->updateAtoms();
795	+	}
796	+
797	+	for(atom = mol->beginAtom(ai); atom != NULL;
798	+	atom = mol->nextAtom(ai)) {
799	+
800	+	pos = atom->getPos();
801	+
802	+	if (index == 0) {
803	+	bMax = pos;
804	+	bMin = pos;
805	+	} else {
806	+	for (int i = 0; i < 3; i++) {
807	+	bMax[i] = max(bMax[i], pos[i]);
808	+	bMin[i] = min(bMin[i], pos[i]);
809	+	}
810	+	}
811	+	index++;
812	+	}
813	+	}
814	+
815	+	#ifdef IS_MPI
816	+	MPI_Allreduce(MPI_IN_PLACE, &bMax[0], 3, MPI_REALTYPE,
817	+	MPI_MAX, MPI_COMM_WORLD);
818	+
819	+	MPI_Allreduce(MPI_IN_PLACE, &bMin[0], 3, MPI_REALTYPE,
820	+	MPI_MIN, MPI_COMM_WORLD);
821	+	#endif
822	+	Mat3x3d bBox = Mat3x3d(0.0);
823	+	for (int i = 0; i < 3; i++) {
824	+	bBox(i,i) = bMax[i] - bMin[i];
825	+	}
826	+	snap->setBoundingBox(bBox);
827	+	}
828	+
829	+	return snap->getBoundingBox();
830	+	}
831	+
832	+
833	+	// Returns the angular momentum of the system
834	+	Vector3d Thermo::getAngularMomentum(){
835	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
836	+
837	+	if (!snap->hasCOMw) {
838	+
839	+	Vector3d com(0.0);
840	+	Vector3d comVel(0.0);
841	+	Vector3d angularMomentum(0.0);
842	+
843	+	getComAll(com, comVel);
844	+
845	+	SimInfo::MoleculeIterator i;
846	+	Molecule* mol;
847	+
848	+	Vector3d thisr(0.0);
849	+	Vector3d thisp(0.0);
850	+
851	+	RealType thisMass;
852	+
853	+	for (mol = info_->beginMolecule(i); mol != NULL;
854	+	mol = info_->nextMolecule(i)) {
855	+	thisMass = mol->getMass();
856	+	thisr = mol->getCom() - com;
857	+	thisp = (mol->getComVel() - comVel) * thisMass;
858	+
859	+	angularMomentum += cross( thisr, thisp );
860	+	}
861	+
862	+	#ifdef IS_MPI
863	+	MPI_Allreduce(MPI_IN_PLACE,
864	+	angularMomentum.getArrayPointer(), 3,
865	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
866	+	#endif
867	+
868	+	snap->setCOMw(angularMomentum);
869	+	}
870	+
871	+	return snap->getCOMw();
872	+	}
873	+
874	+
875	+	/**
876	+	* Returns the Volume of the system based on a ellipsoid with
877	+	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
878	+	* where R_i are related to the principle inertia moments
879	+	*  R_i = sqrt(C*I_i/N), this reduces to
880	+	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
881	+	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
882	+	*/
883	+	RealType Thermo::getGyrationalVolume(){
884	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
885	+
886	+	if (!snap->hasGyrationalVolume) {
887	+
888	+	Mat3x3d intTensor;
889	+	RealType det;
890	+	Vector3d dummyAngMom;
891	+	RealType sysconstants;
892	+	RealType geomCnst;
893	+	RealType volume;
894	+
895	+	geomCnst = 3.0/2.0;
896	+	/* Get the inertial tensor and angular momentum for free*/
897	+	getInertiaTensor(intTensor, dummyAngMom);
898	+
899	+	det = intTensor.determinant();
900	+	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
901	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
902	+
903	+	snap->setGyrationalVolume(volume);
904	+	}
905	+	return snap->getGyrationalVolume();
906	+	}
907	+
908	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
909	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
910	+
911	+	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
912	+
913	+	Mat3x3d intTensor;
914	+	Vector3d dummyAngMom;
915	+	RealType sysconstants;
916	+	RealType geomCnst;
917	+
918	+	geomCnst = 3.0/2.0;
919	+	/* Get the inertia tensor and angular momentum for free*/
920	+	this->getInertiaTensor(intTensor, dummyAngMom);
921	+
922	+	detI = intTensor.determinant();
923	+	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
924	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
925	+	snap->setGyrationalVolume(volume);
926	+	} else {
927	+	volume = snap->getGyrationalVolume();
928	+	detI = snap->getInertiaTensor().determinant();
929	+	}
930	+	return;
931	+	}
932	+
933	+	RealType Thermo::getTaggedAtomPairDistance(){
934	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
935	+	Globals* simParams = info_->getSimParams();
936	+
937		if (simParams->haveTaggedAtomPair() &&
938		simParams->havePrintTaggedPairDistance()) {
939		if ( simParams->getPrintTaggedPairDistance()) {
940
941	<	std::pair<int, int> tap = simParams->getTaggedAtomPair();
941	>	pair<int, int> tap = simParams->getTaggedAtomPair();
942		Vector3d pos1, pos2, rab;
943	<
943	>
944		#ifdef IS_MPI
252	–	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
253	–
945		int mol1 = info_->getGlobalMolMembership(tap.first);
946		int mol2 = info_->getGlobalMolMembership(tap.second);
256	–	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
947
948		int proc1 = info_->getMolToProc(mol1);
949		int proc2 = info_->getMolToProc(mol2);
950
261	–	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
262	–
951		RealType data[3];
952		if (proc1 == worldRank) {
953		StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
266	–	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
954		pos1 = sd1->getPos();
955		data[0] = pos1.x();
956		data[1] = pos1.y();
#	Line 274 | Line 961 | namespace OpenMD {
961		pos1 = Vector3d(data);
962		}
963
277	–
964		if (proc2 == worldRank) {
965		StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
280	–	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
966		pos2 = sd2->getPos();
967		data[0] = pos2.x();
968		data[1] = pos2.y();
969	<	data[2] = pos2.z();
969	>	data[2] = pos2.z();
970		MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
971		} else {
972		MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
#	Line 295 | Line 980 | namespace OpenMD {
980		#endif
981		rab = pos2 - pos1;
982		currSnapshot->wrapVector(rab);
983	<	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
983	>	return rab.length();
984		}
985	+	return 0.0;
986		}
987	+	return 0.0;
988	+	}
989	+
990	+	RealType Thermo::getHullVolume(){
991	+	#ifdef HAVE_QHULL
992	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
993	+	if (!snap->hasHullVolume) {
994	+	Hull* surfaceMesh_;
995
996	<	/**@todo need refactorying*/
997	<	//Conserved Quantity is set by integrator and time is set by setTime
996	>	Globals* simParams = info_->getSimParams();
997	>	const std::string ht = simParams->getHULL_Method();
998	>
999	>	if (ht == "Convex") {
1000	>	surfaceMesh_ = new ConvexHull();
1001	>	} else if (ht == "AlphaShape") {
1002	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
1003	>	} else {
1004	>	return 0.0;
1005	>	}
1006	>
1007	>	// Build a vector of stunt doubles to determine if they are
1008	>	// surface atoms
1009	>	std::vector<StuntDouble*> localSites_;
1010	>	Molecule* mol;
1011	>	StuntDouble* sd;
1012	>	SimInfo::MoleculeIterator i;
1013	>	Molecule::IntegrableObjectIterator  j;
1014	>
1015	>	for (mol = info_->beginMolecule(i); mol != NULL;
1016	>	mol = info_->nextMolecule(i)) {
1017	>	for (sd = mol->beginIntegrableObject(j);
1018	>	sd != NULL;
1019	>	sd = mol->nextIntegrableObject(j)) {
1020	>	localSites_.push_back(sd);
1021	>	}
1022	>	}
1023	>
1024	>	// Compute surface Mesh
1025	>	surfaceMesh_->computeHull(localSites_);
1026	>	snap->setHullVolume(surfaceMesh_->getVolume());
1027	>
1028	>	delete surfaceMesh_;
1029	>	}
1030
1031	+	return snap->getHullVolume();
1032	+	#else
1033	+	return 0.0;
1034	+	#endif
1035		}
1036
1037	<	} //end namespace OpenMD
1037	>
1038	>	}

Comparing trunk/src/brains/Thermo.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 2014 UTC

#	Line 0 | Line 1
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