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

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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 1874 by gezelter, Wed May 15 15:09:35 2013 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, 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		*/
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();
137	<	return total;
138	<	}
188	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189
190	<	RealType Thermo::getTemperature() {
190	>	if (!snap->hasTemperature) {
191	>
192	>	RealType temperature = ( 2.0 * this->getKinetic() )
193	>	/ (info_->getNdf()* PhysicalConstants::kb );
194	>
195	>	snap->setTemperature(temperature);
196	>	}
197
198	<	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
143	<	return temperature;
198	>	return snap->getTemperature();
199		}
200
201	<	RealType Thermo::getVolume() {
202	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148	<	return curSnapshot->getVolume();
149	<	}
201	>	RealType Thermo::getElectronicTemperature() {
202	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203
204	<	RealType Thermo::getPressure() {
204	>	if (!snap->hasElectronicTemperature) {
205	>
206	>	SimInfo::MoleculeIterator miter;
207	>	vector<Atom*>::iterator iiter;
208	>	Molecule* mol;
209	>	Atom* atom;
210	>	RealType cvel;
211	>	RealType cmass;
212	>	RealType kinetic(0.0);
213	>	RealType eTemp;
214	>
215	>	for (mol = info_->beginMolecule(miter); mol != NULL;
216	>	mol = info_->nextMolecule(miter)) {
217	>
218	>	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
219	>	atom = mol->nextFluctuatingCharge(iiter)) {
220	>
221	>	cmass = atom->getChargeMass();
222	>	cvel = atom->getFlucQVel();
223	>
224	>	kinetic += cmass * cvel * cvel;
225	>
226	>	}
227	>	}
228	>
229	>	#ifdef IS_MPI
230	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
231	>	MPI::SUM);
232	>	#endif
233
234	<	// Relies on the calculation of the full molecular pressure tensor
234	>	kinetic *= 0.5;
235	>	eTemp =  (2.0 * kinetic) /
236	>	(info_->getNFluctuatingCharges() * PhysicalConstants::kb );
237	>
238	>	snap->setElectronicTemperature(eTemp);
239	>	}
240
241	+	return snap->getElectronicTemperature();
242	+	}
243
156	–	Mat3x3d tensor;
157	–	RealType pressure;
244
245	<	tensor = getPressureTensor();
246	<
247	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162	<
163	<	return pressure;
245	>	RealType Thermo::getVolume() {
246	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247	>	return snap->getVolume();
248		}
249
250	<	RealType Thermo::getPressure(int direction) {
250	>	RealType Thermo::getPressure() {
251	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252
253	<	// Relies on the calculation of the full molecular pressure tensor
254	<
255	<
256	<	Mat3x3d tensor;
257	<	RealType pressure;
258	<
259	<	tensor = getPressureTensor();
260	<
261	<	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
262	<
263	<	return pressure;
253	>	if (!snap->hasPressure) {
254	>	// Relies on the calculation of the full molecular pressure tensor
255	>
256	>	Mat3x3d tensor;
257	>	RealType pressure;
258	>
259	>	tensor = getPressureTensor();
260	>
261	>	pressure = PhysicalConstants::pressureConvert *
262	>	(tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
263	>
264	>	snap->setPressure(pressure);
265	>	}
266	>
267	>	return snap->getPressure();
268		}
269
270		Mat3x3d Thermo::getPressureTensor() {
271		// returns pressure tensor in units amu*fs^-2*Ang^-1
272		// routine derived via viral theorem description in:
273		// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
274	<	Mat3x3d pressureTensor;
186	<	Mat3x3d p_local(0.0);
187	<	Mat3x3d p_global(0.0);
274	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275
276	<	SimInfo::MoleculeIterator i;
190	<	std::vector<StuntDouble*>::iterator j;
191	<	Molecule* mol;
192	<	StuntDouble* integrableObject;
193	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195	<	integrableObject = mol->nextIntegrableObject(j)) {
276	>	if (!snap->hasPressureTensor) {
277
278	<	RealType mass = integrableObject->getMass();
279	<	Vector3d vcom = integrableObject->getVel();
280	<	p_local += mass * outProduct(vcom, vcom);
278	>	Mat3x3d pressureTensor;
279	>	Mat3x3d p_tens(0.0);
280	>	RealType mass;
281	>	Vector3d vcom;
282	>
283	>	SimInfo::MoleculeIterator i;
284	>	vector<StuntDouble*>::iterator j;
285	>	Molecule* mol;
286	>	StuntDouble* sd;
287	>	for (mol = info_->beginMolecule(i); mol != NULL;
288	>	mol = info_->nextMolecule(i)) {
289	>
290	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
291	>	sd = mol->nextIntegrableObject(j)) {
292	>
293	>	mass = sd->getMass();
294	>	vcom = sd->getVel();
295	>	p_tens += mass * outProduct(vcom, vcom);
296	>	}
297		}
298	+
299	+	#ifdef IS_MPI
300	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, p_tens.getArrayPointer(), 9,
301	+	MPI::REALTYPE, MPI::SUM);
302	+	#endif
303	+
304	+	RealType volume = this->getVolume();
305	+	Mat3x3d stressTensor = snap->getStressTensor();
306	+
307	+	pressureTensor =  (p_tens +
308	+	PhysicalConstants::energyConvert * stressTensor)/volume;
309	+
310	+	snap->setPressureTensor(pressureTensor);
311		}
312	<
312	>	return snap->getPressureTensor();
313	>	}
314	>
315	>
316	>
317	>
318	>	Vector3d Thermo::getSystemDipole() {
319	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
320	>
321	>	if (!snap->hasSystemDipole) {
322	>	SimInfo::MoleculeIterator miter;
323	>	vector<Atom*>::iterator aiter;
324	>	Molecule* mol;
325	>	Atom* atom;
326	>	RealType charge;
327	>	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::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
383	>	MPI::SUM);
384	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
385	>	MPI::SUM);
386
387	<	RealType volume = this->getVolume();
388	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
389	<	Mat3x3d tau = curSnapshot->statData.getTau();
387	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
388	>	MPI::SUM);
389	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
390	>	MPI::SUM);
391
392	<	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
393	<
394	<	return pressureTensor;
395	<	}
392	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
393	>	MPI::REALTYPE, MPI::SUM);
394	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
395	>	MPI::REALTYPE, MPI::SUM);
396
397	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
398	+	3, MPI::REALTYPE, MPI::SUM);
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	<	void Thermo::saveStat(){
418	>	return snap->getSystemDipole();
419	>	}
420	>
421	>	// Returns the Heat Flux Vector for the system
422	>	Vector3d Thermo::getHeatFlux(){
423		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
424	<	Stats& stat = currSnapshot->statData;
425	<
426	<	stat[Stats::KINETIC_ENERGY] = getKinetic();
427	<	stat[Stats::POTENTIAL_ENERGY] = getPotential();
428	<	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
429	<	stat[Stats::TEMPERATURE] = getTemperature();
430	<	stat[Stats::PRESSURE] = getPressure();
431	<	stat[Stats::VOLUME] = getVolume();
424	>	SimInfo::MoleculeIterator miter;
425	>	vector<StuntDouble*>::iterator iiter;
426	>	Molecule* mol;
427	>	StuntDouble* sd;
428	>	RigidBody::AtomIterator ai;
429	>	Atom* atom;
430	>	Vector3d vel;
431	>	Vector3d angMom;
432	>	Mat3x3d I;
433	>	int i;
434	>	int j;
435	>	int k;
436	>	RealType mass;
437
438	<	Mat3x3d tensor =getPressureTensor();
439	<	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
440	<	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
441	<	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
442	<	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
443	<	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
236	<	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);
438	>	Vector3d x_a;
439	>	RealType kinetic;
440	>	RealType potential;
441	>	RealType eatom;
442	>	// Convective portion of the heat flux
443	>	Vector3d heatFluxJc = V3Zero;
444
445	+	/* Calculate convective portion of the heat flux */
446	+	for (mol = info_->beginMolecule(miter); mol != NULL;
447	+	mol = info_->nextMolecule(miter)) {
448	+
449	+	for (sd = mol->beginIntegrableObject(iiter);
450	+	sd != NULL;
451	+	sd = mol->nextIntegrableObject(iiter)) {
452	+
453	+	mass = sd->getMass();
454	+	vel = sd->getVel();
455
456	<	Globals* simParams = info_->getSimParams();
456	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
457	>
458	>	if (sd->isDirectional()) {
459	>	angMom = sd->getJ();
460	>	I = sd->getI();
461
462	+	if (sd->isLinear()) {
463	+	i = sd->linearAxis();
464	+	j = (i + 1) % 3;
465	+	k = (i + 2) % 3;
466	+	kinetic += angMom[j] * angMom[j] / I(j, j)
467	+	+ angMom[k] * angMom[k] / I(k, k);
468	+	} else {
469	+	kinetic += angMom[0]*angMom[0]/I(0, 0)
470	+	+ angMom[1]*angMom[1]/I(1, 1)
471	+	+ angMom[2]*angMom[2]/I(2, 2);
472	+	}
473	+	}
474	+
475	+	potential = 0.0;
476	+
477	+	if (sd->isRigidBody()) {
478	+	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
479	+	for (atom = rb->beginAtom(ai); atom != NULL;
480	+	atom = rb->nextAtom(ai)) {
481	+	potential +=  atom->getParticlePot();
482	+	}
483	+	} else {
484	+	potential = sd->getParticlePot();
485	+	}
486	+
487	+	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
488	+	// The potential may not be a 1/2 factor
489	+	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
490	+	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
491	+	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
492	+	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
493	+	}
494	+	}
495	+
496	+	/* The J_v vector is reduced in the forceManager so everyone has
497	+	*  the global Jv. Jc is computed over the local atoms and must be
498	+	*  reduced among all processors.
499	+	*/
500	+	#ifdef IS_MPI
501	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
502	+	MPI::SUM);
503	+	#endif
504	+
505	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
506	+
507	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
508	+	PhysicalConstants::energyConvert;
509	+
510	+	// Correct for the fact the flux is 1/V (Jc + Jv)
511	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
512	+	}
513	+
514	+
515	+	Vector3d Thermo::getComVel(){
516	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
517	+
518	+	if (!snap->hasCOMvel) {
519	+
520	+	SimInfo::MoleculeIterator i;
521	+	Molecule* mol;
522	+
523	+	Vector3d comVel(0.0);
524	+	RealType totalMass(0.0);
525	+
526	+	for (mol = info_->beginMolecule(i); mol != NULL;
527	+	mol = info_->nextMolecule(i)) {
528	+	RealType mass = mol->getMass();
529	+	totalMass += mass;
530	+	comVel += mass * mol->getComVel();
531	+	}
532	+
533	+	#ifdef IS_MPI
534	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
535	+	MPI::SUM);
536	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
537	+	MPI::REALTYPE, MPI::SUM);
538	+	#endif
539	+
540	+	comVel /= totalMass;
541	+	snap->setCOMvel(comVel);
542	+	}
543	+	return snap->getCOMvel();
544	+	}
545	+
546	+	Vector3d Thermo::getCom(){
547	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
548	+
549	+	if (!snap->hasCOM) {
550	+
551	+	SimInfo::MoleculeIterator i;
552	+	Molecule* mol;
553	+
554	+	Vector3d com(0.0);
555	+	RealType totalMass(0.0);
556	+
557	+	for (mol = info_->beginMolecule(i); mol != NULL;
558	+	mol = info_->nextMolecule(i)) {
559	+	RealType mass = mol->getMass();
560	+	totalMass += mass;
561	+	com += mass * mol->getCom();
562	+	}
563	+
564	+	#ifdef IS_MPI
565	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
566	+	MPI::SUM);
567	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
568	+	MPI::REALTYPE, MPI::SUM);
569	+	#endif
570	+
571	+	com /= totalMass;
572	+	snap->setCOM(com);
573	+	}
574	+	return snap->getCOM();
575	+	}
576	+
577	+	/**
578	+	* Returns center of mass and center of mass velocity in one
579	+	* function call.
580	+	*/
581	+	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
582	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
583	+
584	+	if (!(snap->hasCOM && snap->hasCOMvel)) {
585	+
586	+	SimInfo::MoleculeIterator i;
587	+	Molecule* mol;
588	+
589	+	RealType totalMass(0.0);
590	+
591	+	com = 0.0;
592	+	comVel = 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	+	com += mass * mol->getCom();
599	+	comVel += mass * mol->getComVel();
600	+	}
601	+
602	+	#ifdef IS_MPI
603	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
604	+	MPI::SUM);
605	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
606	+	MPI::REALTYPE, MPI::SUM);
607	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
608	+	MPI::REALTYPE, MPI::SUM);
609	+	#endif
610	+
611	+	com /= totalMass;
612	+	comVel /= totalMass;
613	+	snap->setCOM(com);
614	+	snap->setCOMvel(comVel);
615	+	}
616	+	com = snap->getCOM();
617	+	comVel = snap->getCOMvel();
618	+	return;
619	+	}
620	+
621	+	/**
622	+	* \brief Return inertia tensor for entire system and angular momentum
623	+	*  Vector.
624	+	*
625	+	*
626	+	*
627	+	*    [  Ixx -Ixy  -Ixz ]
628	+	* I =| -Iyx  Iyy  -Iyz |
629	+	*    [ -Izx -Iyz   Izz ]
630	+	*/
631	+	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
632	+	Vector3d &angularMomentum){
633	+
634	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
635	+
636	+	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
637	+
638	+	RealType xx = 0.0;
639	+	RealType yy = 0.0;
640	+	RealType zz = 0.0;
641	+	RealType xy = 0.0;
642	+	RealType xz = 0.0;
643	+	RealType yz = 0.0;
644	+	Vector3d com(0.0);
645	+	Vector3d comVel(0.0);
646	+
647	+	getComAll(com, comVel);
648	+
649	+	SimInfo::MoleculeIterator i;
650	+	Molecule* mol;
651	+
652	+	Vector3d thisq(0.0);
653	+	Vector3d thisv(0.0);
654	+
655	+	RealType thisMass = 0.0;
656	+
657	+	for (mol = info_->beginMolecule(i); mol != NULL;
658	+	mol = info_->nextMolecule(i)) {
659	+
660	+	thisq = mol->getCom()-com;
661	+	thisv = mol->getComVel()-comVel;
662	+	thisMass = mol->getMass();
663	+	// Compute moment of intertia coefficients.
664	+	xx += thisq[0]*thisq[0]*thisMass;
665	+	yy += thisq[1]*thisq[1]*thisMass;
666	+	zz += thisq[2]*thisq[2]*thisMass;
667	+
668	+	// compute products of intertia
669	+	xy += thisq[0]*thisq[1]*thisMass;
670	+	xz += thisq[0]*thisq[2]*thisMass;
671	+	yz += thisq[1]*thisq[2]*thisMass;
672	+
673	+	angularMomentum += cross( thisq, thisv ) * thisMass;
674	+	}
675	+
676	+	inertiaTensor(0,0) = yy + zz;
677	+	inertiaTensor(0,1) = -xy;
678	+	inertiaTensor(0,2) = -xz;
679	+	inertiaTensor(1,0) = -xy;
680	+	inertiaTensor(1,1) = xx + zz;
681	+	inertiaTensor(1,2) = -yz;
682	+	inertiaTensor(2,0) = -xz;
683	+	inertiaTensor(2,1) = -yz;
684	+	inertiaTensor(2,2) = xx + yy;
685	+
686	+	#ifdef IS_MPI
687	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
688	+	9, MPI::REALTYPE, MPI::SUM);
689	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
690	+	angularMomentum.getArrayPointer(), 3,
691	+	MPI::REALTYPE, MPI::SUM);
692	+	#endif
693	+
694	+	snap->setCOMw(angularMomentum);
695	+	snap->setInertiaTensor(inertiaTensor);
696	+	}
697	+
698	+	angularMomentum = snap->getCOMw();
699	+	inertiaTensor = snap->getInertiaTensor();
700	+
701	+	return;
702	+	}
703	+
704	+
705	+	Mat3x3d Thermo::getBoundingBox(){
706	+
707	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
708	+
709	+	if (!(snap->hasBoundingBox)) {
710	+
711	+	SimInfo::MoleculeIterator i;
712	+	Molecule::RigidBodyIterator ri;
713	+	Molecule::AtomIterator ai;
714	+	Molecule* mol;
715	+	RigidBody* rb;
716	+	Atom* atom;
717	+	Vector3d pos, bMax, bMin;
718	+	int index = 0;
719	+
720	+	for (mol = info_->beginMolecule(i); mol != NULL;
721	+	mol = info_->nextMolecule(i)) {
722	+
723	+	//change the positions of atoms which belong to the rigidbodies
724	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
725	+	rb = mol->nextRigidBody(ri)) {
726	+	rb->updateAtoms();
727	+	}
728	+
729	+	for(atom = mol->beginAtom(ai); atom != NULL;
730	+	atom = mol->nextAtom(ai)) {
731	+
732	+	pos = atom->getPos();
733	+
734	+	if (index == 0) {
735	+	bMax = pos;
736	+	bMin = pos;
737	+	} else {
738	+	for (int i = 0; i < 3; i++) {
739	+	bMax[i] = max(bMax[i], pos[i]);
740	+	bMin[i] = min(bMin[i], pos[i]);
741	+	}
742	+	}
743	+	index++;
744	+	}
745	+	}
746	+
747	+	#ifdef IS_MPI
748	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMax[0], 3, MPI::REALTYPE,
749	+	MPI::MAX);
750	+
751	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMin[0], 3, MPI::REALTYPE,
752	+	MPI::MIN);
753	+	#endif
754	+	Mat3x3d bBox = Mat3x3d(0.0);
755	+	for (int i = 0; i < 3; i++) {
756	+	bBox(i,i) = bMax[i] - bMin[i];
757	+	}
758	+	snap->setBoundingBox(bBox);
759	+	}
760	+
761	+	return snap->getBoundingBox();
762	+	}
763	+
764	+
765	+	// Returns the angular momentum of the system
766	+	Vector3d Thermo::getAngularMomentum(){
767	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
768	+
769	+	if (!snap->hasCOMw) {
770	+
771	+	Vector3d com(0.0);
772	+	Vector3d comVel(0.0);
773	+	Vector3d angularMomentum(0.0);
774	+
775	+	getComAll(com, comVel);
776	+
777	+	SimInfo::MoleculeIterator i;
778	+	Molecule* mol;
779	+
780	+	Vector3d thisr(0.0);
781	+	Vector3d thisp(0.0);
782	+
783	+	RealType thisMass;
784	+
785	+	for (mol = info_->beginMolecule(i); mol != NULL;
786	+	mol = info_->nextMolecule(i)) {
787	+	thisMass = mol->getMass();
788	+	thisr = mol->getCom() - com;
789	+	thisp = (mol->getComVel() - comVel) * thisMass;
790	+
791	+	angularMomentum += cross( thisr, thisp );
792	+	}
793	+
794	+	#ifdef IS_MPI
795	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
796	+	angularMomentum.getArrayPointer(), 3,
797	+	MPI::REALTYPE, MPI::SUM);
798	+	#endif
799	+
800	+	snap->setCOMw(angularMomentum);
801	+	}
802	+
803	+	return snap->getCOMw();
804	+	}
805	+
806	+
807	+	/**
808	+	* Returns the Volume of the system based on a ellipsoid with
809	+	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
810	+	* where R_i are related to the principle inertia moments
811	+	*  R_i = sqrt(C*I_i/N), this reduces to
812	+	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
813	+	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
814	+	*/
815	+	RealType Thermo::getGyrationalVolume(){
816	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
817	+
818	+	if (!snap->hasGyrationalVolume) {
819	+
820	+	Mat3x3d intTensor;
821	+	RealType det;
822	+	Vector3d dummyAngMom;
823	+	RealType sysconstants;
824	+	RealType geomCnst;
825	+	RealType volume;
826	+
827	+	geomCnst = 3.0/2.0;
828	+	/* Get the inertial tensor and angular momentum for free*/
829	+	getInertiaTensor(intTensor, dummyAngMom);
830	+
831	+	det = intTensor.determinant();
832	+	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
833	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
834	+
835	+	snap->setGyrationalVolume(volume);
836	+	}
837	+	return snap->getGyrationalVolume();
838	+	}
839	+
840	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
841	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
842	+
843	+	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
844	+
845	+	Mat3x3d intTensor;
846	+	Vector3d dummyAngMom;
847	+	RealType sysconstants;
848	+	RealType geomCnst;
849	+
850	+	geomCnst = 3.0/2.0;
851	+	/* Get the inertia tensor and angular momentum for free*/
852	+	this->getInertiaTensor(intTensor, dummyAngMom);
853	+
854	+	detI = intTensor.determinant();
855	+	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
856	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
857	+	snap->setGyrationalVolume(volume);
858	+	} else {
859	+	volume = snap->getGyrationalVolume();
860	+	detI = snap->getInertiaTensor().determinant();
861	+	}
862	+	return;
863	+	}
864	+
865	+	RealType Thermo::getTaggedAtomPairDistance(){
866	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
867	+	Globals* simParams = info_->getSimParams();
868	+
869		if (simParams->haveTaggedAtomPair() &&
870		simParams->havePrintTaggedPairDistance()) {
871		if ( simParams->getPrintTaggedPairDistance()) {
872
873	<	std::pair<int, int> tap = simParams->getTaggedAtomPair();
873	>	pair<int, int> tap = simParams->getTaggedAtomPair();
874		Vector3d pos1, pos2, rab;
875	<
875	>
876		#ifdef IS_MPI
877	+	int mol1 = info_->getGlobalMolMembership(tap.first);
878	+	int mol2 = info_->getGlobalMolMembership(tap.second);
879
253	–	mol1 = info_.globalMolMembership_[tap.first];
254	–	mol2 = info_.globalMolMembership_[tap.second];
255	–
880		int proc1 = info_->getMolToProc(mol1);
881		int proc2 = info_->getMolToProc(mol2);
882
883	+	RealType data[3];
884		if (proc1 == worldRank) {
260	–	RealType data[3];
885		StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
886		pos1 = sd1->getPos();
887		data[0] = pos1.x();
888		data[1] = pos1.y();
889		data[2] = pos1.z();
890	<	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
890	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
891		} else {
892	<	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
892	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
893		pos1 = Vector3d(data);
894		}
895	<
895	>
896		if (proc2 == worldRank) {
273	–	RealType data[3];
897		StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
898		pos2 = sd2->getPos();
899		data[0] = pos2.x();
900		data[1] = pos2.y();
901	<	data[2] = pos2.z();
902	<	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
901	>	data[2] = pos2.z();
902	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
903		} else {
904	<	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
904	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
905		pos2 = Vector3d(data);
906		}
907		#else
#	Line 289 | Line 912 | namespace oopse {
912		#endif
913		rab = pos2 - pos1;
914		currSnapshot->wrapVector(rab);
915	<	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
915	>	return rab.length();
916		}
917	+	return 0.0;
918		}
919	+	return 0.0;
920	+	}
921	+
922	+	RealType Thermo::getHullVolume(){
923	+	#ifdef HAVE_QHULL
924	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
925	+	if (!snap->hasHullVolume) {
926	+	Hull* surfaceMesh_;
927
928	<	/**@todo need refactorying*/
929	<	//Conserved Quantity is set by integrator and time is set by setTime
928	>	Globals* simParams = info_->getSimParams();
929	>	const std::string ht = simParams->getHULL_Method();
930	>
931	>	if (ht == "Convex") {
932	>	surfaceMesh_ = new ConvexHull();
933	>	} else if (ht == "AlphaShape") {
934	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
935	>	} else {
936	>	return 0.0;
937	>	}
938	>
939	>	// Build a vector of stunt doubles to determine if they are
940	>	// surface atoms
941	>	std::vector<StuntDouble*> localSites_;
942	>	Molecule* mol;
943	>	StuntDouble* sd;
944	>	SimInfo::MoleculeIterator i;
945	>	Molecule::IntegrableObjectIterator  j;
946	>
947	>	for (mol = info_->beginMolecule(i); mol != NULL;
948	>	mol = info_->nextMolecule(i)) {
949	>	for (sd = mol->beginIntegrableObject(j);
950	>	sd != NULL;
951	>	sd = mol->nextIntegrableObject(j)) {
952	>	localSites_.push_back(sd);
953	>	}
954	>	}
955	>
956	>	// Compute surface Mesh
957	>	surfaceMesh_->computeHull(localSites_);
958	>	snap->setHullVolume(surfaceMesh_->getVolume());
959	>
960	>	delete surfaceMesh_;
961	>	}
962
963	+	return snap->getHullVolume();
964	+	#else
965	+	return 0.0;
966	+	#endif
967		}
968
969	<	} //end namespace oopse
969	>
970	>	}

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 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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