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

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trunk/src/brains/Thermo.cpp (file contents), Revision 833 by tim, Fri Dec 30 21:25:56 2005 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1850 by gezelter, Wed Feb 20 15:39:39 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	<	double Thermo::getKinetic() {
66	<	SimInfo::MoleculeIterator miter;
58	<	std::vector<StuntDouble*>::iterator iiter;
59	<	Molecule* mol;
60	<	StuntDouble* integrableObject;
61	<	Vector3d vel;
62	<	Vector3d angMom;
63	<	Mat3x3d I;
64	<	int i;
65	<	int j;
66	<	int k;
67	<	double kinetic = 0.0;
68	<	double kinetic_global = 0.0;
69	<
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	<	double mass = integrableObject->getMass();
69	<	Vector3d vel = integrableObject->getVel();
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	>	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	<	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
104	>	RealType Thermo::getRotationalKinetic() {
105	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
106
107	<	if (integrableObject->isDirectional()) {
108	<	angMom = integrableObject->getJ();
109	<	I = integrableObject->getI();
110	<
111	<	if (integrableObject->isLinear()) {
112	<	i = integrableObject->linearAxis();
113	<	j = (i + 1) % 3;
114	<	k = (i + 2) % 3;
115	<	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
116	<	} else {
117	<	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
118	<	+ angMom[2]*angMom[2]/I(2, 2);
119	<	}
120	<	}
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_DOUBLE, 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	<	double Thermo::getPotential() {
111	<	double potential = 0.0;
112	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
113	<	double shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
166	>	RealType Thermo::getPotential() {
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
172	<
119	<	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
120	<	MPI_COMM_WORLD);
121	<	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
122	<
123	<	#else
124	<
125	<	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
126	<
127	<	#endif // is_mpi
128	<
129	<	return potential;
171	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
172	>	return snap->getPotentialEnergy();
173		}
174
175	<	double Thermo::getTotalE() {
133	<	double total;
175	>	RealType Thermo::getTotalEnergy() {
176
177	<	total = this->getKinetic() + this->getPotential();
136	<	return total;
137	<	}
177	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
178
179	<	double Thermo::getTemperature() {
180	<
181	<	double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
142	<	return temperature;
143	<	}
179	>	if (!snap->hasTotalEnergy) {
180	>	snap->setTotalEnergy(this->getKinetic() + this->getPotential());
181	>	}
182
183	<	double Thermo::getVolume() {
146	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
147	<	return curSnapshot->getVolume();
183	>	return snap->getTotalEnergy();
184		}
185
186	<	double Thermo::getPressure() {
186	>	RealType Thermo::getTemperature() {
187
188	<	// Relies on the calculation of the full molecular pressure tensor
188	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189
190	+	if (!snap->hasTemperature) {
191
192	<	Mat3x3d tensor;
193	<	double pressure;
192	>	RealType temperature = ( 2.0 * this->getKinetic() )
193	>	/ (info_->getNdf()* PhysicalConstants::kb );
194
195	<	tensor = getPressureTensor();
196	<
197	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
198	<
162	<	return pressure;
195	>	snap->setTemperature(temperature);
196	>	}
197	>
198	>	return snap->getTemperature();
199		}
200
201	<	double 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	<	double 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	<	double 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_DOUBLE, 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	<	double 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;
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	<	return pressureTensor;
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	>	return snap->getSystemDipole();
419		}
420
421	<	void Thermo::saveStat(){
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();
432	<
433	<	Mat3x3d tensor =getPressureTensor();
434	<	stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);
435	<	stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);
436	<	stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);
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	+	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	<	/**@todo need refactorying*/
446	<	//Conserved Quantity is set by integrator and time is set by setTime
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	>	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	<	} //end namespace oopse
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	>	* Return intertia 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	>	// Returns the angular momentum of the system
705	>	Vector3d Thermo::getAngularMomentum(){
706	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
707	>
708	>	if (!snap->hasCOMw) {
709	>
710	>	Vector3d com(0.0);
711	>	Vector3d comVel(0.0);
712	>	Vector3d angularMomentum(0.0);
713	>
714	>	getComAll(com, comVel);
715	>
716	>	SimInfo::MoleculeIterator i;
717	>	Molecule* mol;
718	>
719	>	Vector3d thisr(0.0);
720	>	Vector3d thisp(0.0);
721	>
722	>	RealType thisMass;
723	>
724	>	for (mol = info_->beginMolecule(i); mol != NULL;
725	>	mol = info_->nextMolecule(i)) {
726	>	thisMass = mol->getMass();
727	>	thisr = mol->getCom() - com;
728	>	thisp = (mol->getComVel() - comVel) * thisMass;
729	>
730	>	angularMomentum += cross( thisr, thisp );
731	>	}
732	>
733	>	#ifdef IS_MPI
734	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
735	>	angularMomentum.getArrayPointer(), 3,
736	>	MPI::REALTYPE, MPI::SUM);
737	>	#endif
738	>
739	>	snap->setCOMw(angularMomentum);
740	>	}
741	>
742	>	return snap->getCOMw();
743	>	}
744	>
745	>
746	>	/**
747	>	* Returns the Volume of the system based on a ellipsoid with
748	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
749	>	* where R_i are related to the principle inertia moments
750	>	*  R_i = sqrt(C*I_i/N), this reduces to
751	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
752	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
753	>	*/
754	>	RealType Thermo::getGyrationalVolume(){
755	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
756	>
757	>	if (!snap->hasGyrationalVolume) {
758	>
759	>	Mat3x3d intTensor;
760	>	RealType det;
761	>	Vector3d dummyAngMom;
762	>	RealType sysconstants;
763	>	RealType geomCnst;
764	>	RealType volume;
765	>
766	>	geomCnst = 3.0/2.0;
767	>	/* Get the inertial tensor and angular momentum for free*/
768	>	getInertiaTensor(intTensor, dummyAngMom);
769	>
770	>	det = intTensor.determinant();
771	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
772	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
773	>
774	>	snap->setGyrationalVolume(volume);
775	>	}
776	>	return snap->getGyrationalVolume();
777	>	}
778	>
779	>	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
780	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
781	>
782	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
783	>
784	>	Mat3x3d intTensor;
785	>	Vector3d dummyAngMom;
786	>	RealType sysconstants;
787	>	RealType geomCnst;
788	>
789	>	geomCnst = 3.0/2.0;
790	>	/* Get the inertia tensor and angular momentum for free*/
791	>	this->getInertiaTensor(intTensor, dummyAngMom);
792	>
793	>	detI = intTensor.determinant();
794	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
795	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
796	>	snap->setGyrationalVolume(volume);
797	>	} else {
798	>	volume = snap->getGyrationalVolume();
799	>	detI = snap->getInertiaTensor().determinant();
800	>	}
801	>	return;
802	>	}
803	>
804	>	RealType Thermo::getTaggedAtomPairDistance(){
805	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
806	>	Globals* simParams = info_->getSimParams();
807	>
808	>	if (simParams->haveTaggedAtomPair() &&
809	>	simParams->havePrintTaggedPairDistance()) {
810	>	if ( simParams->getPrintTaggedPairDistance()) {
811	>
812	>	pair<int, int> tap = simParams->getTaggedAtomPair();
813	>	Vector3d pos1, pos2, rab;
814	>
815	>	#ifdef IS_MPI
816	>	int mol1 = info_->getGlobalMolMembership(tap.first);
817	>	int mol2 = info_->getGlobalMolMembership(tap.second);
818	>
819	>	int proc1 = info_->getMolToProc(mol1);
820	>	int proc2 = info_->getMolToProc(mol2);
821	>
822	>	RealType data[3];
823	>	if (proc1 == worldRank) {
824	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
825	>	pos1 = sd1->getPos();
826	>	data[0] = pos1.x();
827	>	data[1] = pos1.y();
828	>	data[2] = pos1.z();
829	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
830	>	} else {
831	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
832	>	pos1 = Vector3d(data);
833	>	}
834	>
835	>	if (proc2 == worldRank) {
836	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
837	>	pos2 = sd2->getPos();
838	>	data[0] = pos2.x();
839	>	data[1] = pos2.y();
840	>	data[2] = pos2.z();
841	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
842	>	} else {
843	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
844	>	pos2 = Vector3d(data);
845	>	}
846	>	#else
847	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
848	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
849	>	pos1 = at1->getPos();
850	>	pos2 = at2->getPos();
851	>	#endif
852	>	rab = pos2 - pos1;
853	>	currSnapshot->wrapVector(rab);
854	>	return rab.length();
855	>	}
856	>	return 0.0;
857	>	}
858	>	return 0.0;
859	>	}
860	>
861	>	RealType Thermo::getHullVolume(){
862	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
863	>
864	>	#ifdef HAVE_QHULL
865	>	if (!snap->hasHullVolume) {
866	>	Hull* surfaceMesh_;
867	>
868	>	Globals* simParams = info_->getSimParams();
869	>	const std::string ht = simParams->getHULL_Method();
870	>
871	>	if (ht == "Convex") {
872	>	surfaceMesh_ = new ConvexHull();
873	>	} else if (ht == "AlphaShape") {
874	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
875	>	} else {
876	>	return 0.0;
877	>	}
878	>
879	>	// Build a vector of stunt doubles to determine if they are
880	>	// surface atoms
881	>	std::vector<StuntDouble*> localSites_;
882	>	Molecule* mol;
883	>	StuntDouble* sd;
884	>	SimInfo::MoleculeIterator i;
885	>	Molecule::IntegrableObjectIterator  j;
886	>
887	>	for (mol = info_->beginMolecule(i); mol != NULL;
888	>	mol = info_->nextMolecule(i)) {
889	>	for (sd = mol->beginIntegrableObject(j);
890	>	sd != NULL;
891	>	sd = mol->nextIntegrableObject(j)) {
892	>	localSites_.push_back(sd);
893	>	}
894	>	}
895	>
896	>	// Compute surface Mesh
897	>	surfaceMesh_->computeHull(localSites_);
898	>	snap->setHullVolume(surfaceMesh_->getVolume());
899	>	}
900	>	return snap->getHullVolume();
901	>	#else
902	>	return 0.0;
903	>	#endif
904	>	}
905	>	}

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 833 by tim, Fri Dec 30 21:25:56 2005 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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