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trunk/src/brains/Thermo.cpp (file contents), Revision 1291 by gezelter, Thu Sep 11 19:40:59 2008 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <math.h>
#	Line 49 | Line 50
50		#include "brains/Thermo.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "utils/simError.h"
53	<	#include "utils/OOPSEConstant.hpp"
53	>	#include "utils/PhysicalConstants.hpp"
54	>	#include "types/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	<	namespace oopse {
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 / OOPSEConstant::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();
189	<	return total;
188	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189	>
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	>	return snap->getTemperature();
199		}
200
201	<	RealType Thermo::getTemperature() {
201	>	RealType Thermo::getElectronicTemperature() {
202	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203	>
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	<	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
230	<	return temperature;
229	>	#ifdef IS_MPI
230	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
231	>	MPI::SUM);
232	>	#endif
233	>
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
244	+
245		RealType Thermo::getVolume() {
246	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
247	<	return curSnapshot->getVolume();
246	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247	>	return snap->getVolume();
248		}
249
250		RealType Thermo::getPressure() {
251	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252
253	<	// Relies on the calculation of the full molecular pressure tensor
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	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275
276	<	Mat3x3d tensor;
157	<	RealType pressure;
276	>	if (!snap->hasPressureTensor) {
277
278	<	tensor = getPressureTensor();
279	<
280	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
281	<
282	<	return pressure;
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	>	return snap->getPressureTensor();
313		}
314
166	–	RealType Thermo::getPressure(int direction) {
315
168	–	// Relies on the calculation of the full molecular pressure tensor
316
170	–
171	–	Mat3x3d tensor;
172	–	RealType pressure;
317
318	<	tensor = getPressureTensor();
318	>	Vector3d Thermo::getSystemDipole() {
319	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
320
321	<	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
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	>	if (atom->isDipole()) {
376	>	dipoleVector += atom->getDipole() * debyeToCm;
377	>	}
378	>	}
379	>	}
380	>
381	>
382	>	#ifdef IS_MPI
383	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
384	>	MPI::SUM);
385	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
386	>	MPI::SUM);
387
388	<	return pressure;
389	<	}
388	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
389	>	MPI::SUM);
390	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
391	>	MPI::SUM);
392
393	<	Mat3x3d Thermo::getPressureTensor() {
394	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
395	<	// routine derived via viral theorem description in:
396	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
185	<	Mat3x3d pressureTensor;
186	<	Mat3x3d p_local(0.0);
187	<	Mat3x3d p_global(0.0);
393	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
394	>	MPI::REALTYPE, MPI::SUM);
395	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
396	>	MPI::REALTYPE, MPI::SUM);
397
398	<	SimInfo::MoleculeIterator i;
399	<	std::vector<StuntDouble*>::iterator j;
400	<	Molecule* mol;
401	<	StuntDouble* integrableObject;
402	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
403	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
404	<	integrableObject = mol->nextIntegrableObject(j)) {
405	<
406	<	RealType mass = integrableObject->getMass();
407	<	Vector3d vcom = integrableObject->getVel();
408	<	p_local += mass * outProduct(vcom, vcom);
398	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
399	>	3, MPI::REALTYPE, MPI::SUM);
400	>	#endif
401	>
402	>	// first load the accumulated dipole moment (if dipoles were present)
403	>	Vector3d boxDipole = dipoleVector;
404	>	// now include the dipole moment due to charges
405	>	// use the lesser of the positive and negative charge totals
406	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
407	>
408	>	// find the average positions
409	>	if (pCount > 0 && nCount > 0 ) {
410	>	pPos /= pCount;
411	>	nPos /= nCount;
412		}
413	+
414	+	// dipole is from the negative to the positive (physics notation)
415	+	boxDipole += (pPos - nPos) * chg_value;
416	+	snap->setSystemDipole(boxDipole);
417		}
202	–
203	–	#ifdef IS_MPI
204	–	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205	–	#else
206	–	p_global = p_local;
207	–	#endif // is_mpi
418
419	<	RealType volume = this->getVolume();
210	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211	<	Mat3x3d tau = curSnapshot->statData.getTau();
212	<
213	<	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
214	<
215	<	return pressureTensor;
419	>	return snap->getSystemDipole();
420		}
421
422	<
423	<	void Thermo::saveStat(){
422	>	// Returns the Heat Flux Vector for the system
423	>	Vector3d Thermo::getHeatFlux(){
424		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
425	<	Stats& stat = currSnapshot->statData;
426	<
427	<	stat[Stats::KINETIC_ENERGY] = getKinetic();
428	<	stat[Stats::POTENTIAL_ENERGY] = getPotential();
429	<	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
430	<	stat[Stats::TEMPERATURE] = getTemperature();
431	<	stat[Stats::PRESSURE] = getPressure();
432	<	stat[Stats::VOLUME] = getVolume();
425	>	SimInfo::MoleculeIterator miter;
426	>	vector<StuntDouble*>::iterator iiter;
427	>	Molecule* mol;
428	>	StuntDouble* sd;
429	>	RigidBody::AtomIterator ai;
430	>	Atom* atom;
431	>	Vector3d vel;
432	>	Vector3d angMom;
433	>	Mat3x3d I;
434	>	int i;
435	>	int j;
436	>	int k;
437	>	RealType mass;
438
439	<	Mat3x3d tensor =getPressureTensor();
440	<	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
441	<	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
442	<	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
443	<	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
444	<	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
445	<	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
237	<	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
238	<	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
239	<	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
439	>	Vector3d x_a;
440	>	RealType kinetic;
441	>	RealType potential;
442	>	RealType eatom;
443	>	RealType AvgE_a_ = 0;
444	>	// Convective portion of the heat flux
445	>	Vector3d heatFluxJc = V3Zero;
446
447	+	/* Calculate convective portion of the heat flux */
448	+	for (mol = info_->beginMolecule(miter); mol != NULL;
449	+	mol = info_->nextMolecule(miter)) {
450	+
451	+	for (sd = mol->beginIntegrableObject(iiter);
452	+	sd != NULL;
453	+	sd = mol->nextIntegrableObject(iiter)) {
454	+
455	+	mass = sd->getMass();
456	+	vel = sd->getVel();
457
458	<	Globals* simParams = info_->getSimParams();
458	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
459	>
460	>	if (sd->isDirectional()) {
461	>	angMom = sd->getJ();
462	>	I = sd->getI();
463
464	+	if (sd->isLinear()) {
465	+	i = sd->linearAxis();
466	+	j = (i + 1) % 3;
467	+	k = (i + 2) % 3;
468	+	kinetic += angMom[j] * angMom[j] / I(j, j)
469	+	+ angMom[k] * angMom[k] / I(k, k);
470	+	} else {
471	+	kinetic += angMom[0]*angMom[0]/I(0, 0)
472	+	+ angMom[1]*angMom[1]/I(1, 1)
473	+	+ angMom[2]*angMom[2]/I(2, 2);
474	+	}
475	+	}
476	+
477	+	potential = 0.0;
478	+
479	+	if (sd->isRigidBody()) {
480	+	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
481	+	for (atom = rb->beginAtom(ai); atom != NULL;
482	+	atom = rb->nextAtom(ai)) {
483	+	potential +=  atom->getParticlePot();
484	+	}
485	+	} else {
486	+	potential = sd->getParticlePot();
487	+	}
488	+
489	+	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
490	+	// The potential may not be a 1/2 factor
491	+	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
492	+	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
493	+	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
494	+	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
495	+	}
496	+	}
497	+
498	+	/* The J_v vector is reduced in the forceManager so everyone has
499	+	*  the global Jv. Jc is computed over the local atoms and must be
500	+	*  reduced among all processors.
501	+	*/
502	+	#ifdef IS_MPI
503	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
504	+	MPI::SUM);
505	+	#endif
506	+
507	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
508	+
509	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
510	+	PhysicalConstants::energyConvert;
511	+
512	+	// Correct for the fact the flux is 1/V (Jc + Jv)
513	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
514	+	}
515	+
516	+
517	+	Vector3d Thermo::getComVel(){
518	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
519	+
520	+	if (!snap->hasCOMvel) {
521	+
522	+	SimInfo::MoleculeIterator i;
523	+	Molecule* mol;
524	+
525	+	Vector3d comVel(0.0);
526	+	RealType totalMass(0.0);
527	+
528	+	for (mol = info_->beginMolecule(i); mol != NULL;
529	+	mol = info_->nextMolecule(i)) {
530	+	RealType mass = mol->getMass();
531	+	totalMass += mass;
532	+	comVel += mass * mol->getComVel();
533	+	}
534	+
535	+	#ifdef IS_MPI
536	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
537	+	MPI::SUM);
538	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
539	+	MPI::REALTYPE, MPI::SUM);
540	+	#endif
541	+
542	+	comVel /= totalMass;
543	+	snap->setCOMvel(comVel);
544	+	}
545	+	return snap->getCOMvel();
546	+	}
547	+
548	+	Vector3d Thermo::getCom(){
549	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
550	+
551	+	if (!snap->hasCOM) {
552	+
553	+	SimInfo::MoleculeIterator i;
554	+	Molecule* mol;
555	+
556	+	Vector3d com(0.0);
557	+	RealType totalMass(0.0);
558	+
559	+	for (mol = info_->beginMolecule(i); mol != NULL;
560	+	mol = info_->nextMolecule(i)) {
561	+	RealType mass = mol->getMass();
562	+	totalMass += mass;
563	+	com += mass * mol->getCom();
564	+	}
565	+
566	+	#ifdef IS_MPI
567	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
568	+	MPI::SUM);
569	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
570	+	MPI::REALTYPE, MPI::SUM);
571	+	#endif
572	+
573	+	com /= totalMass;
574	+	snap->setCOM(com);
575	+	}
576	+	return snap->getCOM();
577	+	}
578	+
579	+	/**
580	+	* Returns center of mass and center of mass velocity in one
581	+	* function call.
582	+	*/
583	+	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
584	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
585	+
586	+	if (!(snap->hasCOM && snap->hasCOMvel)) {
587	+
588	+	SimInfo::MoleculeIterator i;
589	+	Molecule* mol;
590	+
591	+	RealType totalMass(0.0);
592	+
593	+	com = 0.0;
594	+	comVel = 0.0;
595	+
596	+	for (mol = info_->beginMolecule(i); mol != NULL;
597	+	mol = info_->nextMolecule(i)) {
598	+	RealType mass = mol->getMass();
599	+	totalMass += mass;
600	+	com += mass * mol->getCom();
601	+	comVel += mass * mol->getComVel();
602	+	}
603	+
604	+	#ifdef IS_MPI
605	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
606	+	MPI::SUM);
607	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
608	+	MPI::REALTYPE, MPI::SUM);
609	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
610	+	MPI::REALTYPE, MPI::SUM);
611	+	#endif
612	+
613	+	com /= totalMass;
614	+	comVel /= totalMass;
615	+	snap->setCOM(com);
616	+	snap->setCOMvel(comVel);
617	+	}
618	+	com = snap->getCOM();
619	+	comVel = snap->getCOMvel();
620	+	return;
621	+	}
622	+
623	+	/**
624	+	* Return intertia tensor for entire system and angular momentum
625	+	* Vector.
626	+	*
627	+	*
628	+	*
629	+	*    [  Ixx -Ixy  -Ixz ]
630	+	* I =| -Iyx  Iyy  -Iyz |
631	+	*    [ -Izx -Iyz   Izz ]
632	+	*/
633	+	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
634	+	Vector3d &angularMomentum){
635	+
636	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
637	+
638	+	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
639	+
640	+	RealType xx = 0.0;
641	+	RealType yy = 0.0;
642	+	RealType zz = 0.0;
643	+	RealType xy = 0.0;
644	+	RealType xz = 0.0;
645	+	RealType yz = 0.0;
646	+	Vector3d com(0.0);
647	+	Vector3d comVel(0.0);
648	+
649	+	getComAll(com, comVel);
650	+
651	+	SimInfo::MoleculeIterator i;
652	+	Molecule* mol;
653	+
654	+	Vector3d thisq(0.0);
655	+	Vector3d thisv(0.0);
656	+
657	+	RealType thisMass = 0.0;
658	+
659	+	for (mol = info_->beginMolecule(i); mol != NULL;
660	+	mol = info_->nextMolecule(i)) {
661	+
662	+	thisq = mol->getCom()-com;
663	+	thisv = mol->getComVel()-comVel;
664	+	thisMass = mol->getMass();
665	+	// Compute moment of intertia coefficients.
666	+	xx += thisq[0]*thisq[0]*thisMass;
667	+	yy += thisq[1]*thisq[1]*thisMass;
668	+	zz += thisq[2]*thisq[2]*thisMass;
669	+
670	+	// compute products of intertia
671	+	xy += thisq[0]*thisq[1]*thisMass;
672	+	xz += thisq[0]*thisq[2]*thisMass;
673	+	yz += thisq[1]*thisq[2]*thisMass;
674	+
675	+	angularMomentum += cross( thisq, thisv ) * thisMass;
676	+	}
677	+
678	+	inertiaTensor(0,0) = yy + zz;
679	+	inertiaTensor(0,1) = -xy;
680	+	inertiaTensor(0,2) = -xz;
681	+	inertiaTensor(1,0) = -xy;
682	+	inertiaTensor(1,1) = xx + zz;
683	+	inertiaTensor(1,2) = -yz;
684	+	inertiaTensor(2,0) = -xz;
685	+	inertiaTensor(2,1) = -yz;
686	+	inertiaTensor(2,2) = xx + yy;
687	+
688	+	#ifdef IS_MPI
689	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
690	+	9, MPI::REALTYPE, MPI::SUM);
691	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
692	+	angularMomentum.getArrayPointer(), 3,
693	+	MPI::REALTYPE, MPI::SUM);
694	+	#endif
695	+
696	+	snap->setCOMw(angularMomentum);
697	+	snap->setInertiaTensor(inertiaTensor);
698	+	}
699	+
700	+	angularMomentum = snap->getCOMw();
701	+	inertiaTensor = snap->getInertiaTensor();
702	+
703	+	return;
704	+	}
705	+
706	+	// Returns the angular momentum of the system
707	+	Vector3d Thermo::getAngularMomentum(){
708	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
709	+
710	+	if (!snap->hasCOMw) {
711	+
712	+	Vector3d com(0.0);
713	+	Vector3d comVel(0.0);
714	+	Vector3d angularMomentum(0.0);
715	+
716	+	getComAll(com, comVel);
717	+
718	+	SimInfo::MoleculeIterator i;
719	+	Molecule* mol;
720	+
721	+	Vector3d thisr(0.0);
722	+	Vector3d thisp(0.0);
723	+
724	+	RealType thisMass;
725	+
726	+	for (mol = info_->beginMolecule(i); mol != NULL;
727	+	mol = info_->nextMolecule(i)) {
728	+	thisMass = mol->getMass();
729	+	thisr = mol->getCom() - com;
730	+	thisp = (mol->getComVel() - comVel) * thisMass;
731	+
732	+	angularMomentum += cross( thisr, thisp );
733	+	}
734	+
735	+	#ifdef IS_MPI
736	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
737	+	angularMomentum.getArrayPointer(), 3,
738	+	MPI::REALTYPE, MPI::SUM);
739	+	#endif
740	+
741	+	snap->setCOMw(angularMomentum);
742	+	}
743	+
744	+	return snap->getCOMw();
745	+	}
746	+
747	+
748	+	/**
749	+	* Returns the Volume of the system based on a ellipsoid with
750	+	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
751	+	* where R_i are related to the principle inertia moments
752	+	*  R_i = sqrt(C*I_i/N), this reduces to
753	+	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
754	+	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
755	+	*/
756	+	RealType Thermo::getGyrationalVolume(){
757	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
758	+
759	+	if (!snap->hasGyrationalVolume) {
760	+
761	+	Mat3x3d intTensor;
762	+	RealType det;
763	+	Vector3d dummyAngMom;
764	+	RealType sysconstants;
765	+	RealType geomCnst;
766	+	RealType volume;
767	+
768	+	geomCnst = 3.0/2.0;
769	+	/* Get the inertial tensor and angular momentum for free*/
770	+	getInertiaTensor(intTensor, dummyAngMom);
771	+
772	+	det = intTensor.determinant();
773	+	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
774	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
775	+
776	+	snap->setGyrationalVolume(volume);
777	+	}
778	+	return snap->getGyrationalVolume();
779	+	}
780	+
781	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
782	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
783	+
784	+	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
785	+
786	+	Mat3x3d intTensor;
787	+	Vector3d dummyAngMom;
788	+	RealType sysconstants;
789	+	RealType geomCnst;
790	+
791	+	geomCnst = 3.0/2.0;
792	+	/* Get the inertia tensor and angular momentum for free*/
793	+	this->getInertiaTensor(intTensor, dummyAngMom);
794	+
795	+	detI = intTensor.determinant();
796	+	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
797	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
798	+	snap->setGyrationalVolume(volume);
799	+	} else {
800	+	volume = snap->getGyrationalVolume();
801	+	detI = snap->getInertiaTensor().determinant();
802	+	}
803	+	return;
804	+	}
805	+
806	+	RealType Thermo::getTaggedAtomPairDistance(){
807	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
808	+	Globals* simParams = info_->getSimParams();
809	+
810		if (simParams->haveTaggedAtomPair() &&
811		simParams->havePrintTaggedPairDistance()) {
812		if ( simParams->getPrintTaggedPairDistance()) {
813
814	<	std::pair<int, int> tap = simParams->getTaggedAtomPair();
814	>	pair<int, int> tap = simParams->getTaggedAtomPair();
815		Vector3d pos1, pos2, rab;
816	<
816	>
817		#ifdef IS_MPI
818	+	int mol1 = info_->getGlobalMolMembership(tap.first);
819	+	int mol2 = info_->getGlobalMolMembership(tap.second);
820
253	–	mol1 = info_.globalMolMembership_[tap.first];
254	–	mol2 = info_.globalMolMembership_[tap.second];
255	–
821		int proc1 = info_->getMolToProc(mol1);
822		int proc2 = info_->getMolToProc(mol2);
823
824	+	RealType data[3];
825		if (proc1 == worldRank) {
260	–	RealType data[3];
826		StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
827		pos1 = sd1->getPos();
828		data[0] = pos1.x();
#	Line 268 | Line 833 | namespace oopse {
833		MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
834		pos1 = Vector3d(data);
835		}
836	<
836	>
837		if (proc2 == worldRank) {
273	–	RealType data[3];
838		StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
839		pos2 = sd2->getPos();
840		data[0] = pos2.x();
#	Line 289 | Line 853 | namespace oopse {
853		#endif
854		rab = pos2 - pos1;
855		currSnapshot->wrapVector(rab);
856	<	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
856	>	return rab.length();
857		}
858	+	return 0.0;
859		}
860	<
296	<	/**@todo need refactorying*/
297	<	//Conserved Quantity is set by integrator and time is set by setTime
298	<
860	>	return 0.0;
861		}
862
863	<	} //end namespace oopse
863	>	RealType Thermo::getHullVolume(){
864	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
865	>
866	>	#ifdef HAVE_QHULL
867	>	if (!snap->hasHullVolume) {
868	>	Hull* surfaceMesh_;
869	>
870	>	Globals* simParams = info_->getSimParams();
871	>	const std::string ht = simParams->getHULL_Method();
872	>
873	>	if (ht == "Convex") {
874	>	surfaceMesh_ = new ConvexHull();
875	>	} else if (ht == "AlphaShape") {
876	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
877	>	} else {
878	>	return 0.0;
879	>	}
880	>
881	>	// Build a vector of stunt doubles to determine if they are
882	>	// surface atoms
883	>	std::vector<StuntDouble*> localSites_;
884	>	Molecule* mol;
885	>	StuntDouble* sd;
886	>	SimInfo::MoleculeIterator i;
887	>	Molecule::IntegrableObjectIterator  j;
888	>
889	>	for (mol = info_->beginMolecule(i); mol != NULL;
890	>	mol = info_->nextMolecule(i)) {
891	>	for (sd = mol->beginIntegrableObject(j);
892	>	sd != NULL;
893	>	sd = mol->nextIntegrableObject(j)) {
894	>	localSites_.push_back(sd);
895	>	}
896	>	}
897	>
898	>	// Compute surface Mesh
899	>	surfaceMesh_->computeHull(localSites_);
900	>	snap->setHullVolume(surfaceMesh_->getVolume());
901	>	}
902	>	return snap->getHullVolume();
903	>	#else
904	>	return 0.0;
905	>	#endif
906	>	}
907	>	}

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 1291 by gezelter, Thu Sep 11 19:40:59 2008 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

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