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

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trunk/src/brains/Thermo.cpp (file contents), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 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	>	#include "math/ConvexHull.hpp"
58	>	#include "math/AlphaHull.hpp"
59
60	<	namespace oopse {
60	>	using namespace std;
61	>	namespace OpenMD {
62
63	<	RealType Thermo::getKinetic() {
64	<	SimInfo::MoleculeIterator miter;
65	<	std::vector<StuntDouble*>::iterator iiter;
66	<	Molecule* mol;
67	<	StuntDouble* integrableObject;
68	<	Vector3d vel;
69	<	Vector3d angMom;
70	<	Mat3x3d I;
71	<	int i;
72	<	int j;
73	<	int k;
74	<	RealType mass;
75	<	RealType kinetic = 0.0;
76	<	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)) {
63	>	RealType Thermo::getTranslationalKinetic() {
64	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
65	>
66	>	if (!snap->hasTranslationalKineticEnergy) {
67	>	SimInfo::MoleculeIterator miter;
68	>	vector<StuntDouble*>::iterator iiter;
69	>	Molecule* mol;
70	>	StuntDouble* sd;
71	>	Vector3d vel;
72	>	RealType mass;
73	>	RealType kinetic(0.0);
74	>
75	>	for (mol = info_->beginMolecule(miter); mol != NULL;
76	>	mol = info_->nextMolecule(miter)) {
77
78	<	mass = integrableObject->getMass();
79	<	vel = integrableObject->getVel();
80	<
81	<	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
82	<
83	<	if (integrableObject->isDirectional()) {
84	<	angMom = integrableObject->getJ();
85	<	I = integrableObject->getI();
78	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
79	>	sd = mol->nextIntegrableObject(iiter)) {
80	>
81	>	mass = sd->getMass();
82	>	vel = sd->getVel();
83	>
84	>	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
85	>
86	>	}
87	>	}
88	>
89	>	#ifdef IS_MPI
90	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
91	>	MPI::SUM);
92	>	#endif
93	>
94	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
95	>
96	>
97	>	snap->setTranslationalKineticEnergy(kinetic);
98	>	}
99	>	return snap->getTranslationalKineticEnergy();
100	>	}
101
102	<	if (integrableObject->isLinear()) {
103	<	i = integrableObject->linearAxis();
104	<	j = (i + 1) % 3;
105	<	k = (i + 2) % 3;
106	<	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
107	<	} else {
108	<	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
109	<	+ angMom[2]*angMom[2]/I(2, 2);
110	<	}
111	<	}
102	>	RealType Thermo::getRotationalKinetic() {
103	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
104	>
105	>	if (!snap->hasRotationalKineticEnergy) {
106	>	SimInfo::MoleculeIterator miter;
107	>	vector<StuntDouble*>::iterator iiter;
108	>	Molecule* mol;
109	>	StuntDouble* sd;
110	>	Vector3d angMom;
111	>	Mat3x3d I;
112	>	int i, j, k;
113	>	RealType kinetic(0.0);
114	>
115	>	for (mol = info_->beginMolecule(miter); mol != NULL;
116	>	mol = info_->nextMolecule(miter)) {
117	>
118	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
119	>	sd = mol->nextIntegrableObject(iiter)) {
120	>
121	>	if (sd->isDirectional()) {
122	>	angMom = sd->getJ();
123	>	I = sd->getI();
124
125	+	if (sd->isLinear()) {
126	+	i = sd->linearAxis();
127	+	j = (i + 1) % 3;
128	+	k = (i + 2) % 3;
129	+	kinetic += angMom[j] * angMom[j] / I(j, j)
130	+	+ angMom[k] * angMom[k] / I(k, k);
131	+	} else {
132	+	kinetic += angMom[0]*angMom[0]/I(0, 0)
133	+	+ angMom[1]*angMom[1]/I(1, 1)
134	+	+ angMom[2]*angMom[2]/I(2, 2);
135	+	}
136	+	}
137	+	}
138		}
139	<	}
97	<
139	>
140		#ifdef IS_MPI
141	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
142	+	MPI::SUM);
143	+	#endif
144	+
145	+	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
146	+
147	+	snap->setRotationalKineticEnergy(kinetic);
148	+	}
149	+	return snap->getRotationalKineticEnergy();
150	+	}
151
152	<	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	<	MPI_COMM_WORLD);
102	<	kinetic = kinetic_global;
152	>
153
154	<	#endif //is_mpi
154	>	RealType Thermo::getKinetic() {
155	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
156
157	<	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
158	<
159	<	return kinetic;
157	>	if (!snap->hasKineticEnergy) {
158	>	RealType ke = getTranslationalKinetic() + getRotationalKinetic();
159	>	snap->setKineticEnergy(ke);
160	>	}
161	>	return snap->getKineticEnergy();
162		}
163
164		RealType Thermo::getPotential() {
112	–	RealType potential = 0.0;
113	–	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	–	RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
165
166	<	// Get total potential for entire system from MPI.
166	>	// ForceManager computes the potential and stores it in the
167	>	// Snapshot.  All we have to do is report it.
168
169	<	#ifdef IS_MPI
169	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
170	>	return snap->getPotentialEnergy();
171	>	}
172
173	<	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	<	MPI_COMM_WORLD);
122	<	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
173	>	RealType Thermo::getTotalEnergy() {
174
175	<	#else
175	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
176
177	<	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
177	>	if (!snap->hasTotalEnergy) {
178	>	snap->setTotalEnergy(this->getKinetic() + this->getPotential());
179	>	}
180
181	<	#endif // is_mpi
129	<
130	<	return potential;
181	>	return snap->getTotalEnergy();
182		}
183
184	<	RealType Thermo::getTotalE() {
134	<	RealType total;
184	>	RealType Thermo::getTemperature() {
185
186	<	total = this->getKinetic() + this->getPotential();
187	<	return total;
186	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
187	>
188	>	if (!snap->hasTemperature) {
189	>
190	>	RealType temperature = ( 2.0 * this->getKinetic() )
191	>	/ (info_->getNdf()* PhysicalConstants::kb );
192	>
193	>	snap->setTemperature(temperature);
194	>	}
195	>
196	>	return snap->getTemperature();
197		}
198
199	<	RealType Thermo::getTemperature() {
199	>	RealType Thermo::getElectronicTemperature() {
200	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
201	>
202	>	if (!snap->hasElectronicTemperature) {
203	>
204	>	SimInfo::MoleculeIterator miter;
205	>	vector<Atom*>::iterator iiter;
206	>	Molecule* mol;
207	>	Atom* atom;
208	>	RealType cvel;
209	>	RealType cmass;
210	>	RealType kinetic(0.0);
211	>	RealType eTemp;
212	>
213	>	for (mol = info_->beginMolecule(miter); mol != NULL;
214	>	mol = info_->nextMolecule(miter)) {
215	>
216	>	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
217	>	atom = mol->nextFluctuatingCharge(iiter)) {
218	>
219	>	cmass = atom->getChargeMass();
220	>	cvel = atom->getFlucQVel();
221	>
222	>	kinetic += cmass * cvel * cvel;
223	>
224	>	}
225	>	}
226
227	<	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
228	<	return temperature;
227	>	#ifdef IS_MPI
228	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
229	>	MPI::SUM);
230	>	#endif
231	>
232	>	kinetic *= 0.5;
233	>	eTemp =  (2.0 * kinetic) /
234	>	(info_->getNFluctuatingCharges() * PhysicalConstants::kb );
235	>
236	>	snap->setElectronicTemperature(eTemp);
237	>	}
238	>
239	>	return snap->getElectronicTemperature();
240		}
241
242	+
243		RealType Thermo::getVolume() {
244	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
245	<	return curSnapshot->getVolume();
244	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
245	>	return snap->getVolume();
246		}
247
248		RealType Thermo::getPressure() {
249	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
250
251	<	// Relies on the calculation of the full molecular pressure tensor
251	>	if (!snap->hasPressure) {
252	>	// Relies on the calculation of the full molecular pressure tensor
253	>
254	>	Mat3x3d tensor;
255	>	RealType pressure;
256	>
257	>	tensor = getPressureTensor();
258	>
259	>	pressure = PhysicalConstants::pressureConvert *
260	>	(tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
261	>
262	>	snap->setPressure(pressure);
263	>	}
264	>
265	>	return snap->getPressure();
266	>	}
267
268	+	Mat3x3d Thermo::getPressureTensor() {
269	+	// returns pressure tensor in units amu*fs^-2*Ang^-1
270	+	// routine derived via viral theorem description in:
271	+	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
272	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
273
274	<	Mat3x3d tensor;
157	<	RealType pressure;
274	>	if (!snap->hasPressureTensor) {
275
276	<	tensor = getPressureTensor();
277	<
278	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
279	<
280	<	return pressure;
276	>	Mat3x3d pressureTensor;
277	>	Mat3x3d p_tens(0.0);
278	>	RealType mass;
279	>	Vector3d vcom;
280	>
281	>	SimInfo::MoleculeIterator i;
282	>	vector<StuntDouble*>::iterator j;
283	>	Molecule* mol;
284	>	StuntDouble* sd;
285	>	for (mol = info_->beginMolecule(i); mol != NULL;
286	>	mol = info_->nextMolecule(i)) {
287	>
288	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
289	>	sd = mol->nextIntegrableObject(j)) {
290	>
291	>	mass = sd->getMass();
292	>	vcom = sd->getVel();
293	>	p_tens += mass * outProduct(vcom, vcom);
294	>	}
295	>	}
296	>
297	>	#ifdef IS_MPI
298	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, p_tens.getArrayPointer(), 9,
299	>	MPI::REALTYPE, MPI::SUM);
300	>	#endif
301	>
302	>	RealType volume = this->getVolume();
303	>	Mat3x3d stressTensor = snap->getStressTensor();
304	>
305	>	pressureTensor =  (p_tens +
306	>	PhysicalConstants::energyConvert * stressTensor)/volume;
307	>
308	>	snap->setPressureTensor(pressureTensor);
309	>	}
310	>	return snap->getPressureTensor();
311		}
312
166	–	RealType Thermo::getPressure(int direction) {
313
168	–	// Relies on the calculation of the full molecular pressure tensor
314
170	–
171	–	Mat3x3d tensor;
172	–	RealType pressure;
315
316	<	tensor = getPressureTensor();
316	>	Vector3d Thermo::getSystemDipole() {
317	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
318
319	<	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
319	>	if (!snap->hasSystemDipole) {
320	>	SimInfo::MoleculeIterator miter;
321	>	vector<Atom*>::iterator aiter;
322	>	Molecule* mol;
323	>	Atom* atom;
324	>	RealType charge;
325	>	RealType moment(0.0);
326	>	Vector3d ri(0.0);
327	>	Vector3d dipoleVector(0.0);
328	>	Vector3d nPos(0.0);
329	>	Vector3d pPos(0.0);
330	>	RealType nChg(0.0);
331	>	RealType pChg(0.0);
332	>	int nCount = 0;
333	>	int pCount = 0;
334	>
335	>	RealType chargeToC = 1.60217733e-19;
336	>	RealType angstromToM = 1.0e-10;
337	>	RealType debyeToCm = 3.33564095198e-30;
338	>
339	>	for (mol = info_->beginMolecule(miter); mol != NULL;
340	>	mol = info_->nextMolecule(miter)) {
341	>
342	>	for (atom = mol->beginAtom(aiter); atom != NULL;
343	>	atom = mol->nextAtom(aiter)) {
344	>
345	>	charge = 0.0;
346	>
347	>	FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
348	>	if ( fca.isFixedCharge() ) {
349	>	charge = fca.getCharge();
350	>	}
351	>
352	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
353	>	if ( fqa.isFluctuatingCharge() ) {
354	>	charge += atom->getFlucQPos();
355	>	}
356	>
357	>	charge *= chargeToC;
358	>
359	>	ri = atom->getPos();
360	>	snap->wrapVector(ri);
361	>	ri *= angstromToM;
362	>
363	>	if (charge < 0.0) {
364	>	nPos += ri;
365	>	nChg -= charge;
366	>	nCount++;
367	>	} else if (charge > 0.0) {
368	>	pPos += ri;
369	>	pChg += charge;
370	>	pCount++;
371	>	}
372	>
373	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
374	>	if (ma.isDipole() ) {
375	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
376	>	moment = ma.getDipoleMoment();
377	>	moment *= debyeToCm;
378	>	dipoleVector += u_i * moment;
379	>	}
380	>	}
381	>	}
382	>
383	>
384	>	#ifdef IS_MPI
385	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
386	>	MPI::SUM);
387	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
388	>	MPI::SUM);
389
390	<	return pressure;
391	<	}
390	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
391	>	MPI::SUM);
392	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
393	>	MPI::SUM);
394
395	<	Mat3x3d Thermo::getPressureTensor() {
396	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
397	<	// routine derived via viral theorem description in:
398	<	// 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);
395	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
396	>	MPI::REALTYPE, MPI::SUM);
397	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
398	>	MPI::REALTYPE, MPI::SUM);
399
400	<	SimInfo::MoleculeIterator i;
401	<	std::vector<StuntDouble*>::iterator j;
402	<	Molecule* mol;
403	<	StuntDouble* integrableObject;
404	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
405	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
406	<	integrableObject = mol->nextIntegrableObject(j)) {
407	<
408	<	RealType mass = integrableObject->getMass();
409	<	Vector3d vcom = integrableObject->getVel();
410	<	p_local += mass * outProduct(vcom, vcom);
400	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
401	>	3, MPI::REALTYPE, MPI::SUM);
402	>	#endif
403	>
404	>	// first load the accumulated dipole moment (if dipoles were present)
405	>	Vector3d boxDipole = dipoleVector;
406	>	// now include the dipole moment due to charges
407	>	// use the lesser of the positive and negative charge totals
408	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
409	>
410	>	// find the average positions
411	>	if (pCount > 0 && nCount > 0 ) {
412	>	pPos /= pCount;
413	>	nPos /= nCount;
414		}
415	+
416	+	// dipole is from the negative to the positive (physics notation)
417	+	boxDipole += (pPos - nPos) * chg_value;
418	+	snap->setSystemDipole(boxDipole);
419		}
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
420
421	<	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;
421	>	return snap->getSystemDipole();
422		}
423
424	<
425	<	void Thermo::saveStat(){
426	<	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
427	<	Stats& stat = currSnapshot->statData;
428	<
429	<	stat[Stats::KINETIC_ENERGY] = getKinetic();
430	<	stat[Stats::POTENTIAL_ENERGY] = getPotential();
431	<	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
432	<	stat[Stats::TEMPERATURE] = getTemperature();
433	<	stat[Stats::PRESSURE] = getPressure();
434	<	stat[Stats::VOLUME] = getVolume();
435	<
436	<	Mat3x3d tensor =getPressureTensor();
437	<	stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);
438	<	stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);
439	<	stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);
440	<
441	<
442	<	/**@todo need refactorying*/
443	<	//Conserved Quantity is set by integrator and time is set by setTime
424	>	// Returns the Heat Flux Vector for the system
425	>	Vector3d Thermo::getHeatFlux(){
426	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
427	>	SimInfo::MoleculeIterator miter;
428	>	vector<StuntDouble*>::iterator iiter;
429	>	Molecule* mol;
430	>	StuntDouble* sd;
431	>	RigidBody::AtomIterator ai;
432	>	Atom* atom;
433	>	Vector3d vel;
434	>	Vector3d angMom;
435	>	Mat3x3d I;
436	>	int i;
437	>	int j;
438	>	int k;
439	>	RealType mass;
440	>
441	>	Vector3d x_a;
442	>	RealType kinetic;
443	>	RealType potential;
444	>	RealType eatom;
445	>	RealType AvgE_a_ = 0;
446	>	// Convective portion of the heat flux
447	>	Vector3d heatFluxJc = V3Zero;
448	>
449	>	/* Calculate convective portion of the heat flux */
450	>	for (mol = info_->beginMolecule(miter); mol != NULL;
451	>	mol = info_->nextMolecule(miter)) {
452	>
453	>	for (sd = mol->beginIntegrableObject(iiter);
454	>	sd != NULL;
455	>	sd = mol->nextIntegrableObject(iiter)) {
456	>
457	>	mass = sd->getMass();
458	>	vel = sd->getVel();
459	>
460	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
461	>
462	>	if (sd->isDirectional()) {
463	>	angMom = sd->getJ();
464	>	I = sd->getI();
465	>
466	>	if (sd->isLinear()) {
467	>	i = sd->linearAxis();
468	>	j = (i + 1) % 3;
469	>	k = (i + 2) % 3;
470	>	kinetic += angMom[j] * angMom[j] / I(j, j)
471	>	+ angMom[k] * angMom[k] / I(k, k);
472	>	} else {
473	>	kinetic += angMom[0]*angMom[0]/I(0, 0)
474	>	+ angMom[1]*angMom[1]/I(1, 1)
475	>	+ angMom[2]*angMom[2]/I(2, 2);
476	>	}
477	>	}
478	>
479	>	potential = 0.0;
480	>
481	>	if (sd->isRigidBody()) {
482	>	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
483	>	for (atom = rb->beginAtom(ai); atom != NULL;
484	>	atom = rb->nextAtom(ai)) {
485	>	potential +=  atom->getParticlePot();
486	>	}
487	>	} else {
488	>	potential = sd->getParticlePot();
489	>	}
490	>
491	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
492	>	// The potential may not be a 1/2 factor
493	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
494	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
495	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
496	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
497	>	}
498	>	}
499	>
500	>	/* The J_v vector is reduced in the forceManager so everyone has
501	>	*  the global Jv. Jc is computed over the local atoms and must be
502	>	*  reduced among all processors.
503	>	*/
504	>	#ifdef IS_MPI
505	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
506	>	MPI::SUM);
507	>	#endif
508
509	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
510	+
511	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
512	+	PhysicalConstants::energyConvert;
513	+
514	+	// Correct for the fact the flux is 1/V (Jc + Jv)
515	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
516		}
517
518	<	} //end namespace oopse
518	>
519	>	Vector3d Thermo::getComVel(){
520	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
521	>
522	>	if (!snap->hasCOMvel) {
523	>
524	>	SimInfo::MoleculeIterator i;
525	>	Molecule* mol;
526	>
527	>	Vector3d comVel(0.0);
528	>	RealType totalMass(0.0);
529	>
530	>	for (mol = info_->beginMolecule(i); mol != NULL;
531	>	mol = info_->nextMolecule(i)) {
532	>	RealType mass = mol->getMass();
533	>	totalMass += mass;
534	>	comVel += mass * mol->getComVel();
535	>	}
536	>
537	>	#ifdef IS_MPI
538	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
539	>	MPI::SUM);
540	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
541	>	MPI::REALTYPE, MPI::SUM);
542	>	#endif
543	>
544	>	comVel /= totalMass;
545	>	snap->setCOMvel(comVel);
546	>	}
547	>	return snap->getCOMvel();
548	>	}
549	>
550	>	Vector3d Thermo::getCom(){
551	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
552	>
553	>	if (!snap->hasCOM) {
554	>
555	>	SimInfo::MoleculeIterator i;
556	>	Molecule* mol;
557	>
558	>	Vector3d com(0.0);
559	>	RealType totalMass(0.0);
560	>
561	>	for (mol = info_->beginMolecule(i); mol != NULL;
562	>	mol = info_->nextMolecule(i)) {
563	>	RealType mass = mol->getMass();
564	>	totalMass += mass;
565	>	com += mass * mol->getCom();
566	>	}
567	>
568	>	#ifdef IS_MPI
569	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
570	>	MPI::SUM);
571	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
572	>	MPI::REALTYPE, MPI::SUM);
573	>	#endif
574	>
575	>	com /= totalMass;
576	>	snap->setCOM(com);
577	>	}
578	>	return snap->getCOM();
579	>	}
580	>
581	>	/**
582	>	* Returns center of mass and center of mass velocity in one
583	>	* function call.
584	>	*/
585	>	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
586	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
587	>
588	>	if (!(snap->hasCOM && snap->hasCOMvel)) {
589	>
590	>	SimInfo::MoleculeIterator i;
591	>	Molecule* mol;
592	>
593	>	RealType totalMass(0.0);
594	>
595	>	com = 0.0;
596	>	comVel = 0.0;
597	>
598	>	for (mol = info_->beginMolecule(i); mol != NULL;
599	>	mol = info_->nextMolecule(i)) {
600	>	RealType mass = mol->getMass();
601	>	totalMass += mass;
602	>	com += mass * mol->getCom();
603	>	comVel += mass * mol->getComVel();
604	>	}
605	>
606	>	#ifdef IS_MPI
607	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
608	>	MPI::SUM);
609	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
610	>	MPI::REALTYPE, MPI::SUM);
611	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
612	>	MPI::REALTYPE, MPI::SUM);
613	>	#endif
614	>
615	>	com /= totalMass;
616	>	comVel /= totalMass;
617	>	snap->setCOM(com);
618	>	snap->setCOMvel(comVel);
619	>	}
620	>	com = snap->getCOM();
621	>	comVel = snap->getCOMvel();
622	>	return;
623	>	}
624	>
625	>	/**
626	>	* Return intertia tensor for entire system and angular momentum
627	>	* Vector.
628	>	*
629	>	*
630	>	*
631	>	*    [  Ixx -Ixy  -Ixz ]
632	>	* I =| -Iyx  Iyy  -Iyz |
633	>	*    [ -Izx -Iyz   Izz ]
634	>	*/
635	>	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
636	>	Vector3d &angularMomentum){
637	>
638	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
639	>
640	>	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
641	>
642	>	RealType xx = 0.0;
643	>	RealType yy = 0.0;
644	>	RealType zz = 0.0;
645	>	RealType xy = 0.0;
646	>	RealType xz = 0.0;
647	>	RealType yz = 0.0;
648	>	Vector3d com(0.0);
649	>	Vector3d comVel(0.0);
650	>
651	>	getComAll(com, comVel);
652	>
653	>	SimInfo::MoleculeIterator i;
654	>	Molecule* mol;
655	>
656	>	Vector3d thisq(0.0);
657	>	Vector3d thisv(0.0);
658	>
659	>	RealType thisMass = 0.0;
660	>
661	>	for (mol = info_->beginMolecule(i); mol != NULL;
662	>	mol = info_->nextMolecule(i)) {
663	>
664	>	thisq = mol->getCom()-com;
665	>	thisv = mol->getComVel()-comVel;
666	>	thisMass = mol->getMass();
667	>	// Compute moment of intertia coefficients.
668	>	xx += thisq[0]*thisq[0]*thisMass;
669	>	yy += thisq[1]*thisq[1]*thisMass;
670	>	zz += thisq[2]*thisq[2]*thisMass;
671	>
672	>	// compute products of intertia
673	>	xy += thisq[0]*thisq[1]*thisMass;
674	>	xz += thisq[0]*thisq[2]*thisMass;
675	>	yz += thisq[1]*thisq[2]*thisMass;
676	>
677	>	angularMomentum += cross( thisq, thisv ) * thisMass;
678	>	}
679	>
680	>	inertiaTensor(0,0) = yy + zz;
681	>	inertiaTensor(0,1) = -xy;
682	>	inertiaTensor(0,2) = -xz;
683	>	inertiaTensor(1,0) = -xy;
684	>	inertiaTensor(1,1) = xx + zz;
685	>	inertiaTensor(1,2) = -yz;
686	>	inertiaTensor(2,0) = -xz;
687	>	inertiaTensor(2,1) = -yz;
688	>	inertiaTensor(2,2) = xx + yy;
689	>
690	>	#ifdef IS_MPI
691	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
692	>	9, MPI::REALTYPE, MPI::SUM);
693	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
694	>	angularMomentum.getArrayPointer(), 3,
695	>	MPI::REALTYPE, MPI::SUM);
696	>	#endif
697	>
698	>	snap->setCOMw(angularMomentum);
699	>	snap->setInertiaTensor(inertiaTensor);
700	>	}
701	>
702	>	angularMomentum = snap->getCOMw();
703	>	inertiaTensor = snap->getInertiaTensor();
704	>
705	>	return;
706	>	}
707	>
708	>	// Returns the angular momentum of the system
709	>	Vector3d Thermo::getAngularMomentum(){
710	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
711	>
712	>	if (!snap->hasCOMw) {
713	>
714	>	Vector3d com(0.0);
715	>	Vector3d comVel(0.0);
716	>	Vector3d angularMomentum(0.0);
717	>
718	>	getComAll(com, comVel);
719	>
720	>	SimInfo::MoleculeIterator i;
721	>	Molecule* mol;
722	>
723	>	Vector3d thisr(0.0);
724	>	Vector3d thisp(0.0);
725	>
726	>	RealType thisMass;
727	>
728	>	for (mol = info_->beginMolecule(i); mol != NULL;
729	>	mol = info_->nextMolecule(i)) {
730	>	thisMass = mol->getMass();
731	>	thisr = mol->getCom() - com;
732	>	thisp = (mol->getComVel() - comVel) * thisMass;
733	>
734	>	angularMomentum += cross( thisr, thisp );
735	>	}
736	>
737	>	#ifdef IS_MPI
738	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
739	>	angularMomentum.getArrayPointer(), 3,
740	>	MPI::REALTYPE, MPI::SUM);
741	>	#endif
742	>
743	>	snap->setCOMw(angularMomentum);
744	>	}
745	>
746	>	return snap->getCOMw();
747	>	}
748	>
749	>
750	>	/**
751	>	* Returns the Volume of the system based on a ellipsoid with
752	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
753	>	* where R_i are related to the principle inertia moments
754	>	*  R_i = sqrt(C*I_i/N), this reduces to
755	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
756	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
757	>	*/
758	>	RealType Thermo::getGyrationalVolume(){
759	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
760	>
761	>	if (!snap->hasGyrationalVolume) {
762	>
763	>	Mat3x3d intTensor;
764	>	RealType det;
765	>	Vector3d dummyAngMom;
766	>	RealType sysconstants;
767	>	RealType geomCnst;
768	>	RealType volume;
769	>
770	>	geomCnst = 3.0/2.0;
771	>	/* Get the inertial tensor and angular momentum for free*/
772	>	getInertiaTensor(intTensor, dummyAngMom);
773	>
774	>	det = intTensor.determinant();
775	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
776	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
777	>
778	>	snap->setGyrationalVolume(volume);
779	>	}
780	>	return snap->getGyrationalVolume();
781	>	}
782	>
783	>	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
784	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
785	>
786	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
787	>
788	>	Mat3x3d intTensor;
789	>	Vector3d dummyAngMom;
790	>	RealType sysconstants;
791	>	RealType geomCnst;
792	>
793	>	geomCnst = 3.0/2.0;
794	>	/* Get the inertia tensor and angular momentum for free*/
795	>	this->getInertiaTensor(intTensor, dummyAngMom);
796	>
797	>	detI = intTensor.determinant();
798	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
799	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
800	>	snap->setGyrationalVolume(volume);
801	>	} else {
802	>	volume = snap->getGyrationalVolume();
803	>	detI = snap->getInertiaTensor().determinant();
804	>	}
805	>	return;
806	>	}
807	>
808	>	RealType Thermo::getTaggedAtomPairDistance(){
809	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
810	>	Globals* simParams = info_->getSimParams();
811	>
812	>	if (simParams->haveTaggedAtomPair() &&
813	>	simParams->havePrintTaggedPairDistance()) {
814	>	if ( simParams->getPrintTaggedPairDistance()) {
815	>
816	>	pair<int, int> tap = simParams->getTaggedAtomPair();
817	>	Vector3d pos1, pos2, rab;
818	>
819	>	#ifdef IS_MPI
820	>	int mol1 = info_->getGlobalMolMembership(tap.first);
821	>	int mol2 = info_->getGlobalMolMembership(tap.second);
822	>
823	>	int proc1 = info_->getMolToProc(mol1);
824	>	int proc2 = info_->getMolToProc(mol2);
825	>
826	>	RealType data[3];
827	>	if (proc1 == worldRank) {
828	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
829	>	pos1 = sd1->getPos();
830	>	data[0] = pos1.x();
831	>	data[1] = pos1.y();
832	>	data[2] = pos1.z();
833	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
834	>	} else {
835	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
836	>	pos1 = Vector3d(data);
837	>	}
838	>
839	>	if (proc2 == worldRank) {
840	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
841	>	pos2 = sd2->getPos();
842	>	data[0] = pos2.x();
843	>	data[1] = pos2.y();
844	>	data[2] = pos2.z();
845	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
846	>	} else {
847	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
848	>	pos2 = Vector3d(data);
849	>	}
850	>	#else
851	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
852	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
853	>	pos1 = at1->getPos();
854	>	pos2 = at2->getPos();
855	>	#endif
856	>	rab = pos2 - pos1;
857	>	currSnapshot->wrapVector(rab);
858	>	return rab.length();
859	>	}
860	>	return 0.0;
861	>	}
862	>	return 0.0;
863	>	}
864	>
865	>	RealType Thermo::getHullVolume(){
866	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
867	>
868	>	if (!snap->hasHullVolume) {
869	>
870	>	Hull* surfaceMesh_;
871	>
872	>	Globals* simParams = info_->getSimParams();
873	>	const std::string ht = simParams->getHULL_Method();
874	>
875	>	if (ht == "Convex") {
876	>	surfaceMesh_ = new ConvexHull();
877	>	} else if (ht == "AlphaShape") {
878	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
879	>	} else {
880	>	return 0.0;
881	>	}
882	>
883	>	// Build a vector of stunt doubles to determine if they are
884	>	// surface atoms
885	>	std::vector<StuntDouble*> localSites_;
886	>	Molecule* mol;
887	>	StuntDouble* sd;
888	>	SimInfo::MoleculeIterator i;
889	>	Molecule::IntegrableObjectIterator  j;
890	>
891	>	for (mol = info_->beginMolecule(i); mol != NULL;
892	>	mol = info_->nextMolecule(i)) {
893	>	for (sd = mol->beginIntegrableObject(j);
894	>	sd != NULL;
895	>	sd = mol->nextIntegrableObject(j)) {
896	>	localSites_.push_back(sd);
897	>	}
898	>	}
899	>
900	>	// Compute surface Mesh
901	>	surfaceMesh_->computeHull(localSites_);
902	>	snap->setHullVolume(surfaceMesh_->getVolume());
903	>	}
904	>	return snap->getHullVolume();
905	>	}
906	>	}

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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