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

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trunk/src/brains/Thermo.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 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 kinetic = 0.0;
77	<	RealType kinetic_global = 0.0;
78	<
70	<	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
71	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
72	<	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	<	RealType mass = integrableObject->getMass();
81	<	Vector3d 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	<	}
96	<
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,
100	<	MPI_COMM_WORLD);
101	<	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() {
111	–	RealType potential = 0.0;
112	–	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
113	–	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,
120	<	MPI_COMM_WORLD);
121	<	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
128	<
129	<	return potential;
183	>	return snap->getTotalEnergy();
184		}
185
132	–	RealType Thermo::getTotalE() {
133	–	RealType total;
134	–
135	–	total = this->getKinetic() + this->getPotential();
136	–	return total;
137	–	}
138	–
186		RealType Thermo::getTemperature() {
140	–
141	–	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
142	–	return temperature;
143	–	}
187
188	<	RealType Thermo::getVolume() {
146	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
147	<	return curSnapshot->getVolume();
148	<	}
188	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189
190	<	RealType Thermo::getPressure() {
190	>	if (!snap->hasTemperature) {
191
192	<	// Relies on the calculation of the full molecular pressure tensor
192	>	RealType temperature = ( 2.0 * this->getKinetic() )
193	>	/ (info_->getNdf()* PhysicalConstants::kb );
194
195	<
196	<	Mat3x3d tensor;
197	<	RealType pressure;
198	<
158	<	tensor = getPressureTensor();
159	<
160	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
161	<
162	<	return pressure;
195	>	snap->setTemperature(temperature);
196	>	}
197	>
198	>	return snap->getTemperature();
199		}
200
201	<	RealType Thermo::getPressure(int direction) {
201	>	RealType Thermo::getElectronicTemperature() {
202	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203
204	<	// Relies on the calculation of the full molecular pressure tensor
205	<
206	<
207	<	Mat3x3d tensor;
208	<	RealType pressure;
209	<
210	<	tensor = getPressureTensor();
211	<
212	<	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
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	<	return pressure;
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* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247	+	return snap->getVolume();
248	+	}
249
250	+	RealType Thermo::getPressure() {
251	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252	+
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;
187	<	Mat3x3d p_local(0.0);
188	<	Mat3x3d p_global(0.0);
274	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275
276	<	SimInfo::MoleculeIterator i;
191	<	std::vector<StuntDouble*>::iterator j;
192	<	Molecule* mol;
193	<	StuntDouble* integrableObject;
194	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
195	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
196	<	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	>	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	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
376	>	if (ma.isDipole() ) {
377	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
378	>	moment = ma.getDipoleMoment();
379	>	moment *= debyeToCm;
380	>	dipoleVector += u_i * moment;
381	>	}
382	>	}
383	>	}
384	>
385	>
386		#ifdef IS_MPI
387	<	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
388	<	#else
389	<	p_global = p_local;
390	<	#endif // is_mpi
387	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
388	>	MPI::SUM);
389	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
390	>	MPI::SUM);
391
392	<	RealType volume = this->getVolume();
393	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
394	<	Mat3x3d tau = curSnapshot->statData.getTau();
392	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
393	>	MPI::SUM);
394	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
395	>	MPI::SUM);
396
397	<	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
397	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
398	>	MPI::REALTYPE, MPI::SUM);
399	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
400	>	MPI::REALTYPE, MPI::SUM);
401
402	<	return pressureTensor;
402	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
403	>	3, MPI::REALTYPE, MPI::SUM);
404	>	#endif
405	>
406	>	// first load the accumulated dipole moment (if dipoles were present)
407	>	Vector3d boxDipole = dipoleVector;
408	>	// now include the dipole moment due to charges
409	>	// use the lesser of the positive and negative charge totals
410	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
411	>
412	>	// find the average positions
413	>	if (pCount > 0 && nCount > 0 ) {
414	>	pPos /= pCount;
415	>	nPos /= nCount;
416	>	}
417	>
418	>	// dipole is from the negative to the positive (physics notation)
419	>	boxDipole += (pPos - nPos) * chg_value;
420	>	snap->setSystemDipole(boxDipole);
421	>	}
422	>
423	>	return snap->getSystemDipole();
424		}
425
426	<	void Thermo::saveStat(){
426	>	// Returns the Heat Flux Vector for the system
427	>	Vector3d Thermo::getHeatFlux(){
428		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
429	<	Stats& stat = currSnapshot->statData;
430	<
431	<	stat[Stats::KINETIC_ENERGY] = getKinetic();
432	<	stat[Stats::POTENTIAL_ENERGY] = getPotential();
433	<	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
434	<	stat[Stats::TEMPERATURE] = getTemperature();
435	<	stat[Stats::PRESSURE] = getPressure();
436	<	stat[Stats::VOLUME] = getVolume();
437	<
438	<	Mat3x3d tensor =getPressureTensor();
439	<	stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);
440	<	stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);
441	<	stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);
429	>	SimInfo::MoleculeIterator miter;
430	>	vector<StuntDouble*>::iterator iiter;
431	>	Molecule* mol;
432	>	StuntDouble* sd;
433	>	RigidBody::AtomIterator ai;
434	>	Atom* atom;
435	>	Vector3d vel;
436	>	Vector3d angMom;
437	>	Mat3x3d I;
438	>	int i;
439	>	int j;
440	>	int k;
441	>	RealType mass;
442
443	+	Vector3d x_a;
444	+	RealType kinetic;
445	+	RealType potential;
446	+	RealType eatom;
447	+	RealType AvgE_a_ = 0;
448	+	// Convective portion of the heat flux
449	+	Vector3d heatFluxJc = V3Zero;
450
451	<	/**@todo need refactorying*/
452	<	//Conserved Quantity is set by integrator and time is set by setTime
451	>	/* Calculate convective portion of the heat flux */
452	>	for (mol = info_->beginMolecule(miter); mol != NULL;
453	>	mol = info_->nextMolecule(miter)) {
454	>
455	>	for (sd = mol->beginIntegrableObject(iiter);
456	>	sd != NULL;
457	>	sd = mol->nextIntegrableObject(iiter)) {
458	>
459	>	mass = sd->getMass();
460	>	vel = sd->getVel();
461	>
462	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
463	>
464	>	if (sd->isDirectional()) {
465	>	angMom = sd->getJ();
466	>	I = sd->getI();
467	>
468	>	if (sd->isLinear()) {
469	>	i = sd->linearAxis();
470	>	j = (i + 1) % 3;
471	>	k = (i + 2) % 3;
472	>	kinetic += angMom[j] * angMom[j] / I(j, j)
473	>	+ angMom[k] * angMom[k] / I(k, k);
474	>	} else {
475	>	kinetic += angMom[0]*angMom[0]/I(0, 0)
476	>	+ angMom[1]*angMom[1]/I(1, 1)
477	>	+ angMom[2]*angMom[2]/I(2, 2);
478	>	}
479	>	}
480	>
481	>	potential = 0.0;
482	>
483	>	if (sd->isRigidBody()) {
484	>	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
485	>	for (atom = rb->beginAtom(ai); atom != NULL;
486	>	atom = rb->nextAtom(ai)) {
487	>	potential +=  atom->getParticlePot();
488	>	}
489	>	} else {
490	>	potential = sd->getParticlePot();
491	>	}
492	>
493	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
494	>	// The potential may not be a 1/2 factor
495	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
496	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
497	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
498	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
499	>	}
500	>	}
501	>
502	>	/* The J_v vector is reduced in the forceManager so everyone has
503	>	*  the global Jv. Jc is computed over the local atoms and must be
504	>	*  reduced among all processors.
505	>	*/
506	>	#ifdef IS_MPI
507	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
508	>	MPI::SUM);
509	>	#endif
510
511	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
512	+
513	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
514	+	PhysicalConstants::energyConvert;
515	+
516	+	// Correct for the fact the flux is 1/V (Jc + Jv)
517	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
518		}
519
520	<	} //end namespace oopse
520	>
521	>	Vector3d Thermo::getComVel(){
522	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
523	>
524	>	if (!snap->hasCOMvel) {
525	>
526	>	SimInfo::MoleculeIterator i;
527	>	Molecule* mol;
528	>
529	>	Vector3d comVel(0.0);
530	>	RealType totalMass(0.0);
531	>
532	>	for (mol = info_->beginMolecule(i); mol != NULL;
533	>	mol = info_->nextMolecule(i)) {
534	>	RealType mass = mol->getMass();
535	>	totalMass += mass;
536	>	comVel += mass * mol->getComVel();
537	>	}
538	>
539	>	#ifdef IS_MPI
540	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
541	>	MPI::SUM);
542	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
543	>	MPI::REALTYPE, MPI::SUM);
544	>	#endif
545	>
546	>	comVel /= totalMass;
547	>	snap->setCOMvel(comVel);
548	>	}
549	>	return snap->getCOMvel();
550	>	}
551	>
552	>	Vector3d Thermo::getCom(){
553	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
554	>
555	>	if (!snap->hasCOM) {
556	>
557	>	SimInfo::MoleculeIterator i;
558	>	Molecule* mol;
559	>
560	>	Vector3d com(0.0);
561	>	RealType totalMass(0.0);
562	>
563	>	for (mol = info_->beginMolecule(i); mol != NULL;
564	>	mol = info_->nextMolecule(i)) {
565	>	RealType mass = mol->getMass();
566	>	totalMass += mass;
567	>	com += mass * mol->getCom();
568	>	}
569	>
570	>	#ifdef IS_MPI
571	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
572	>	MPI::SUM);
573	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
574	>	MPI::REALTYPE, MPI::SUM);
575	>	#endif
576	>
577	>	com /= totalMass;
578	>	snap->setCOM(com);
579	>	}
580	>	return snap->getCOM();
581	>	}
582	>
583	>	/**
584	>	* Returns center of mass and center of mass velocity in one
585	>	* function call.
586	>	*/
587	>	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
588	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
589	>
590	>	if (!(snap->hasCOM && snap->hasCOMvel)) {
591	>
592	>	SimInfo::MoleculeIterator i;
593	>	Molecule* mol;
594	>
595	>	RealType totalMass(0.0);
596	>
597	>	com = 0.0;
598	>	comVel = 0.0;
599	>
600	>	for (mol = info_->beginMolecule(i); mol != NULL;
601	>	mol = info_->nextMolecule(i)) {
602	>	RealType mass = mol->getMass();
603	>	totalMass += mass;
604	>	com += mass * mol->getCom();
605	>	comVel += mass * mol->getComVel();
606	>	}
607	>
608	>	#ifdef IS_MPI
609	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
610	>	MPI::SUM);
611	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
612	>	MPI::REALTYPE, MPI::SUM);
613	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
614	>	MPI::REALTYPE, MPI::SUM);
615	>	#endif
616	>
617	>	com /= totalMass;
618	>	comVel /= totalMass;
619	>	snap->setCOM(com);
620	>	snap->setCOMvel(comVel);
621	>	}
622	>	com = snap->getCOM();
623	>	comVel = snap->getCOMvel();
624	>	return;
625	>	}
626	>
627	>	/**
628	>	* Return intertia tensor for entire system and angular momentum
629	>	* Vector.
630	>	*
631	>	*
632	>	*
633	>	*    [  Ixx -Ixy  -Ixz ]
634	>	* I =| -Iyx  Iyy  -Iyz |
635	>	*    [ -Izx -Iyz   Izz ]
636	>	*/
637	>	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
638	>	Vector3d &angularMomentum){
639	>
640	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
641	>
642	>	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
643	>
644	>	RealType xx = 0.0;
645	>	RealType yy = 0.0;
646	>	RealType zz = 0.0;
647	>	RealType xy = 0.0;
648	>	RealType xz = 0.0;
649	>	RealType yz = 0.0;
650	>	Vector3d com(0.0);
651	>	Vector3d comVel(0.0);
652	>
653	>	getComAll(com, comVel);
654	>
655	>	SimInfo::MoleculeIterator i;
656	>	Molecule* mol;
657	>
658	>	Vector3d thisq(0.0);
659	>	Vector3d thisv(0.0);
660	>
661	>	RealType thisMass = 0.0;
662	>
663	>	for (mol = info_->beginMolecule(i); mol != NULL;
664	>	mol = info_->nextMolecule(i)) {
665	>
666	>	thisq = mol->getCom()-com;
667	>	thisv = mol->getComVel()-comVel;
668	>	thisMass = mol->getMass();
669	>	// Compute moment of intertia coefficients.
670	>	xx += thisq[0]*thisq[0]*thisMass;
671	>	yy += thisq[1]*thisq[1]*thisMass;
672	>	zz += thisq[2]*thisq[2]*thisMass;
673	>
674	>	// compute products of intertia
675	>	xy += thisq[0]*thisq[1]*thisMass;
676	>	xz += thisq[0]*thisq[2]*thisMass;
677	>	yz += thisq[1]*thisq[2]*thisMass;
678	>
679	>	angularMomentum += cross( thisq, thisv ) * thisMass;
680	>	}
681	>
682	>	inertiaTensor(0,0) = yy + zz;
683	>	inertiaTensor(0,1) = -xy;
684	>	inertiaTensor(0,2) = -xz;
685	>	inertiaTensor(1,0) = -xy;
686	>	inertiaTensor(1,1) = xx + zz;
687	>	inertiaTensor(1,2) = -yz;
688	>	inertiaTensor(2,0) = -xz;
689	>	inertiaTensor(2,1) = -yz;
690	>	inertiaTensor(2,2) = xx + yy;
691	>
692	>	#ifdef IS_MPI
693	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
694	>	9, MPI::REALTYPE, MPI::SUM);
695	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
696	>	angularMomentum.getArrayPointer(), 3,
697	>	MPI::REALTYPE, MPI::SUM);
698	>	#endif
699	>
700	>	snap->setCOMw(angularMomentum);
701	>	snap->setInertiaTensor(inertiaTensor);
702	>	}
703	>
704	>	angularMomentum = snap->getCOMw();
705	>	inertiaTensor = snap->getInertiaTensor();
706	>
707	>	return;
708	>	}
709	>
710	>	// Returns the angular momentum of the system
711	>	Vector3d Thermo::getAngularMomentum(){
712	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
713	>
714	>	if (!snap->hasCOMw) {
715	>
716	>	Vector3d com(0.0);
717	>	Vector3d comVel(0.0);
718	>	Vector3d angularMomentum(0.0);
719	>
720	>	getComAll(com, comVel);
721	>
722	>	SimInfo::MoleculeIterator i;
723	>	Molecule* mol;
724	>
725	>	Vector3d thisr(0.0);
726	>	Vector3d thisp(0.0);
727	>
728	>	RealType thisMass;
729	>
730	>	for (mol = info_->beginMolecule(i); mol != NULL;
731	>	mol = info_->nextMolecule(i)) {
732	>	thisMass = mol->getMass();
733	>	thisr = mol->getCom() - com;
734	>	thisp = (mol->getComVel() - comVel) * thisMass;
735	>
736	>	angularMomentum += cross( thisr, thisp );
737	>	}
738	>
739	>	#ifdef IS_MPI
740	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
741	>	angularMomentum.getArrayPointer(), 3,
742	>	MPI::REALTYPE, MPI::SUM);
743	>	#endif
744	>
745	>	snap->setCOMw(angularMomentum);
746	>	}
747	>
748	>	return snap->getCOMw();
749	>	}
750	>
751	>
752	>	/**
753	>	* Returns the Volume of the system based on a ellipsoid with
754	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
755	>	* where R_i are related to the principle inertia moments
756	>	*  R_i = sqrt(C*I_i/N), this reduces to
757	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
758	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
759	>	*/
760	>	RealType Thermo::getGyrationalVolume(){
761	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
762	>
763	>	if (!snap->hasGyrationalVolume) {
764	>
765	>	Mat3x3d intTensor;
766	>	RealType det;
767	>	Vector3d dummyAngMom;
768	>	RealType sysconstants;
769	>	RealType geomCnst;
770	>	RealType volume;
771	>
772	>	geomCnst = 3.0/2.0;
773	>	/* Get the inertial tensor and angular momentum for free*/
774	>	getInertiaTensor(intTensor, dummyAngMom);
775	>
776	>	det = intTensor.determinant();
777	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
778	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
779	>
780	>	snap->setGyrationalVolume(volume);
781	>	}
782	>	return snap->getGyrationalVolume();
783	>	}
784	>
785	>	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
786	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
787	>
788	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
789	>
790	>	Mat3x3d intTensor;
791	>	Vector3d dummyAngMom;
792	>	RealType sysconstants;
793	>	RealType geomCnst;
794	>
795	>	geomCnst = 3.0/2.0;
796	>	/* Get the inertia tensor and angular momentum for free*/
797	>	this->getInertiaTensor(intTensor, dummyAngMom);
798	>
799	>	detI = intTensor.determinant();
800	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
801	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
802	>	snap->setGyrationalVolume(volume);
803	>	} else {
804	>	volume = snap->getGyrationalVolume();
805	>	detI = snap->getInertiaTensor().determinant();
806	>	}
807	>	return;
808	>	}
809	>
810	>	RealType Thermo::getTaggedAtomPairDistance(){
811	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
812	>	Globals* simParams = info_->getSimParams();
813	>
814	>	if (simParams->haveTaggedAtomPair() &&
815	>	simParams->havePrintTaggedPairDistance()) {
816	>	if ( simParams->getPrintTaggedPairDistance()) {
817	>
818	>	pair<int, int> tap = simParams->getTaggedAtomPair();
819	>	Vector3d pos1, pos2, rab;
820	>
821	>	#ifdef IS_MPI
822	>	int mol1 = info_->getGlobalMolMembership(tap.first);
823	>	int mol2 = info_->getGlobalMolMembership(tap.second);
824	>
825	>	int proc1 = info_->getMolToProc(mol1);
826	>	int proc2 = info_->getMolToProc(mol2);
827	>
828	>	RealType data[3];
829	>	if (proc1 == worldRank) {
830	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
831	>	pos1 = sd1->getPos();
832	>	data[0] = pos1.x();
833	>	data[1] = pos1.y();
834	>	data[2] = pos1.z();
835	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
836	>	} else {
837	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
838	>	pos1 = Vector3d(data);
839	>	}
840	>
841	>	if (proc2 == worldRank) {
842	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
843	>	pos2 = sd2->getPos();
844	>	data[0] = pos2.x();
845	>	data[1] = pos2.y();
846	>	data[2] = pos2.z();
847	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
848	>	} else {
849	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
850	>	pos2 = Vector3d(data);
851	>	}
852	>	#else
853	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
854	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
855	>	pos1 = at1->getPos();
856	>	pos2 = at2->getPos();
857	>	#endif
858	>	rab = pos2 - pos1;
859	>	currSnapshot->wrapVector(rab);
860	>	return rab.length();
861	>	}
862	>	return 0.0;
863	>	}
864	>	return 0.0;
865	>	}
866	>
867	>	RealType Thermo::getHullVolume(){
868	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
869	>
870	>	#ifdef HAVE_QHULL
871	>	if (!snap->hasHullVolume) {
872	>	Hull* surfaceMesh_;
873	>
874	>	Globals* simParams = info_->getSimParams();
875	>	const std::string ht = simParams->getHULL_Method();
876	>
877	>	if (ht == "Convex") {
878	>	surfaceMesh_ = new ConvexHull();
879	>	} else if (ht == "AlphaShape") {
880	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
881	>	} else {
882	>	return 0.0;
883	>	}
884	>
885	>	// Build a vector of stunt doubles to determine if they are
886	>	// surface atoms
887	>	std::vector<StuntDouble*> localSites_;
888	>	Molecule* mol;
889	>	StuntDouble* sd;
890	>	SimInfo::MoleculeIterator i;
891	>	Molecule::IntegrableObjectIterator  j;
892	>
893	>	for (mol = info_->beginMolecule(i); mol != NULL;
894	>	mol = info_->nextMolecule(i)) {
895	>	for (sd = mol->beginIntegrableObject(j);
896	>	sd != NULL;
897	>	sd = mol->nextIntegrableObject(j)) {
898	>	localSites_.push_back(sd);
899	>	}
900	>	}
901	>
902	>	// Compute surface Mesh
903	>	surfaceMesh_->computeHull(localSites_);
904	>	snap->setHullVolume(surfaceMesh_->getVolume());
905	>	}
906	>	return snap->getHullVolume();
907	>	#else
908	>	return 0.0;
909	>	#endif
910	>	}
911	>	}

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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