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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 1760 by gezelter, Thu Jun 21 19:26:46 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/MultipoleAdapter.hpp"
55
56	<	namespace oopse {
56	>	namespace OpenMD {
57
58		RealType Thermo::getKinetic() {
59		SimInfo::MoleculeIterator miter;
#	Line 103 | Line 105 | namespace oopse {
105
106		#endif //is_mpi
107
108	<	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
108	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
109
110		return kinetic;
111		}
112
113		RealType Thermo::getPotential() {
114		RealType potential = 0.0;
113	–	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	–	RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115
116	<	// Get total potential for entire system from MPI.
117	<
118	<	#ifdef IS_MPI
119	<
120	<	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	<	MPI_COMM_WORLD);
122	<	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123	<
124	<	#else
125	<
126	<	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127	<
128	<	#endif // is_mpi
129	<
116	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
117	>	potential = curSnapshot->getShortRangePotential() + curSnapshot->getLongRangePotential();
118		return potential;
119		}
120
#	Line 139 | Line 127 | namespace oopse {
127
128		RealType Thermo::getTemperature() {
129
130	<	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
130	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
131		return temperature;
132		}
133
134	+	RealType Thermo::getElectronicTemperature() {
135	+	SimInfo::MoleculeIterator miter;
136	+	std::vector<Atom*>::iterator iiter;
137	+	Molecule* mol;
138	+	Atom* atom;
139	+	RealType cvel;
140	+	RealType cmass;
141	+	RealType kinetic = 0.0;
142	+	RealType kinetic_global = 0.0;
143	+
144	+	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
145	+	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
146	+	atom = mol->nextFluctuatingCharge(iiter)) {
147	+	cmass = atom->getChargeMass();
148	+	cvel = atom->getFlucQVel();
149	+
150	+	kinetic += cmass * cvel * cvel;
151	+
152	+	}
153	+	}
154	+
155	+	#ifdef IS_MPI
156	+
157	+	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
158	+	MPI_COMM_WORLD);
159	+	kinetic = kinetic_global;
160	+
161	+	#endif //is_mpi
162	+
163	+	kinetic = kinetic * 0.5;
164	+	return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );
165	+	}
166	+
167	+
168	+
169	+
170		RealType Thermo::getVolume() {
171		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
172		return curSnapshot->getVolume();
#	Line 158 | Line 182 | namespace oopse {
182
183		tensor = getPressureTensor();
184
185	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
185	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
186
187		return pressure;
188		}
#	Line 173 | Line 197 | namespace oopse {
197
198		tensor = getPressureTensor();
199
200	<	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
200	>	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
201
202		return pressure;
203		}
#	Line 208 | Line 232 | namespace oopse {
232
233		RealType volume = this->getVolume();
234		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
235	<	Mat3x3d tau = curSnapshot->statData.getTau();
235	>	Mat3x3d stressTensor = curSnapshot->getStressTensor();
236	>
237	>	pressureTensor =  (p_global +
238	>	PhysicalConstants::energyConvert * stressTensor)/volume;
239
213	–	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
214	–
240		return pressureTensor;
241		}
242
#	Line 228 | Line 253 | namespace oopse {
253		stat[Stats::VOLUME] = getVolume();
254
255		Mat3x3d tensor =getPressureTensor();
256	<	stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);
257	<	stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);
258	<	stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);
256	>	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
257	>	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
258	>	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
259	>	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
260	>	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
261	>	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
262	>	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
263	>	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
264	>	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
265
266	+	// grab the simulation box dipole moment if specified
267	+	if (info_->getCalcBoxDipole()){
268	+	Vector3d totalDipole = getBoxDipole();
269	+	stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
270	+	stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
271	+	stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
272	+	}
273
274	+	Globals* simParams = info_->getSimParams();
275	+	// grab the heat flux if desired
276	+	if (simParams->havePrintHeatFlux()) {
277	+	if (simParams->getPrintHeatFlux()){
278	+	Vector3d heatFlux = getHeatFlux();
279	+	stat[Stats::HEATFLUX_X] = heatFlux(0);
280	+	stat[Stats::HEATFLUX_Y] = heatFlux(1);
281	+	stat[Stats::HEATFLUX_Z] = heatFlux(2);
282	+	}
283	+	}
284	+
285	+	if (simParams->haveTaggedAtomPair() &&
286	+	simParams->havePrintTaggedPairDistance()) {
287	+	if ( simParams->getPrintTaggedPairDistance()) {
288	+
289	+	std::pair<int, int> tap = simParams->getTaggedAtomPair();
290	+	Vector3d pos1, pos2, rab;
291	+
292	+	#ifdef IS_MPI
293	+	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
294	+
295	+	int mol1 = info_->getGlobalMolMembership(tap.first);
296	+	int mol2 = info_->getGlobalMolMembership(tap.second);
297	+	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
298	+
299	+	int proc1 = info_->getMolToProc(mol1);
300	+	int proc2 = info_->getMolToProc(mol2);
301	+
302	+	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
303	+
304	+	RealType data[3];
305	+	if (proc1 == worldRank) {
306	+	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
307	+	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
308	+	pos1 = sd1->getPos();
309	+	data[0] = pos1.x();
310	+	data[1] = pos1.y();
311	+	data[2] = pos1.z();
312	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
313	+	} else {
314	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
315	+	pos1 = Vector3d(data);
316	+	}
317	+
318	+
319	+	if (proc2 == worldRank) {
320	+	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
321	+	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
322	+	pos2 = sd2->getPos();
323	+	data[0] = pos2.x();
324	+	data[1] = pos2.y();
325	+	data[2] = pos2.z();
326	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
327	+	} else {
328	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
329	+	pos2 = Vector3d(data);
330	+	}
331	+	#else
332	+	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
333	+	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
334	+	pos1 = at1->getPos();
335	+	pos2 = at2->getPos();
336	+	#endif
337	+	rab = pos2 - pos1;
338	+	currSnapshot->wrapVector(rab);
339	+	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
340	+	}
341	+	}
342	+
343		/**@todo need refactorying*/
344		//Conserved Quantity is set by integrator and time is set by setTime
345
346		}
347
348	<	} //end namespace oopse
348	>
349	>	Vector3d Thermo::getBoxDipole() {
350	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
351	>	SimInfo::MoleculeIterator miter;
352	>	std::vector<Atom*>::iterator aiter;
353	>	Molecule* mol;
354	>	Atom* atom;
355	>	RealType charge;
356	>	RealType moment(0.0);
357	>	Vector3d ri(0.0);
358	>	Vector3d dipoleVector(0.0);
359	>	Vector3d nPos(0.0);
360	>	Vector3d pPos(0.0);
361	>	RealType nChg(0.0);
362	>	RealType pChg(0.0);
363	>	int nCount = 0;
364	>	int pCount = 0;
365	>
366	>	RealType chargeToC = 1.60217733e-19;
367	>	RealType angstromToM = 1.0e-10;
368	>	RealType debyeToCm = 3.33564095198e-30;
369	>
370	>	for (mol = info_->beginMolecule(miter); mol != NULL;
371	>	mol = info_->nextMolecule(miter)) {
372	>
373	>	for (atom = mol->beginAtom(aiter); atom != NULL;
374	>	atom = mol->nextAtom(aiter)) {
375	>
376	>	if (atom->isCharge() ) {
377	>	charge = 0.0;
378	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
379	>	if (data != NULL) {
380	>
381	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
382	>	charge *= chargeToC;
383	>
384	>	ri = atom->getPos();
385	>	currSnapshot->wrapVector(ri);
386	>	ri *= angstromToM;
387	>
388	>	if (charge < 0.0) {
389	>	nPos += ri;
390	>	nChg -= charge;
391	>	nCount++;
392	>	} else if (charge > 0.0) {
393	>	pPos += ri;
394	>	pChg += charge;
395	>	pCount++;
396	>	}
397	>	}
398	>	}
399	>
400	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
401	>	if (ma.isDipole() ) {
402	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
403	>	moment = ma.getDipoleMoment();
404	>	moment *= debyeToCm;
405	>	dipoleVector += u_i * moment;
406	>	}
407	>	}
408	>	}
409	>
410	>
411	>	#ifdef IS_MPI
412	>	RealType pChg_global, nChg_global;
413	>	int pCount_global, nCount_global;
414	>	Vector3d pPos_global, nPos_global, dipVec_global;
415	>
416	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
417	>	MPI_COMM_WORLD);
418	>	pChg = pChg_global;
419	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
420	>	MPI_COMM_WORLD);
421	>	nChg = nChg_global;
422	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
423	>	MPI_COMM_WORLD);
424	>	pCount = pCount_global;
425	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
426	>	MPI_COMM_WORLD);
427	>	nCount = nCount_global;
428	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
429	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
430	>	pPos = pPos_global;
431	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
432	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
433	>	nPos = nPos_global;
434	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
435	>	dipVec_global.getArrayPointer(), 3,
436	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
437	>	dipoleVector = dipVec_global;
438	>	#endif //is_mpi
439	>
440	>	// first load the accumulated dipole moment (if dipoles were present)
441	>	Vector3d boxDipole = dipoleVector;
442	>	// now include the dipole moment due to charges
443	>	// use the lesser of the positive and negative charge totals
444	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
445	>
446	>	// find the average positions
447	>	if (pCount > 0 && nCount > 0 ) {
448	>	pPos /= pCount;
449	>	nPos /= nCount;
450	>	}
451	>
452	>	// dipole is from the negative to the positive (physics notation)
453	>	boxDipole += (pPos - nPos) * chg_value;
454	>
455	>	return boxDipole;
456	>	}
457	>
458	>	// Returns the Heat Flux Vector for the system
459	>	Vector3d Thermo::getHeatFlux(){
460	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
461	>	SimInfo::MoleculeIterator miter;
462	>	std::vector<StuntDouble*>::iterator iiter;
463	>	Molecule* mol;
464	>	StuntDouble* integrableObject;
465	>	RigidBody::AtomIterator ai;
466	>	Atom* atom;
467	>	Vector3d vel;
468	>	Vector3d angMom;
469	>	Mat3x3d I;
470	>	int i;
471	>	int j;
472	>	int k;
473	>	RealType mass;
474	>
475	>	Vector3d x_a;
476	>	RealType kinetic;
477	>	RealType potential;
478	>	RealType eatom;
479	>	RealType AvgE_a_ = 0;
480	>	// Convective portion of the heat flux
481	>	Vector3d heatFluxJc = V3Zero;
482	>
483	>	/* Calculate convective portion of the heat flux */
484	>	for (mol = info_->beginMolecule(miter); mol != NULL;
485	>	mol = info_->nextMolecule(miter)) {
486	>
487	>	for (integrableObject = mol->beginIntegrableObject(iiter);
488	>	integrableObject != NULL;
489	>	integrableObject = mol->nextIntegrableObject(iiter)) {
490	>
491	>	mass = integrableObject->getMass();
492	>	vel = integrableObject->getVel();
493	>
494	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
495	>
496	>	if (integrableObject->isDirectional()) {
497	>	angMom = integrableObject->getJ();
498	>	I = integrableObject->getI();
499	>
500	>	if (integrableObject->isLinear()) {
501	>	i = integrableObject->linearAxis();
502	>	j = (i + 1) % 3;
503	>	k = (i + 2) % 3;
504	>	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
505	>	} else {
506	>	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
507	>	+ angMom[2]*angMom[2]/I(2, 2);
508	>	}
509	>	}
510	>
511	>	potential = 0.0;
512	>
513	>	if (integrableObject->isRigidBody()) {
514	>	RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject);
515	>	for (atom = rb->beginAtom(ai); atom != NULL;
516	>	atom = rb->nextAtom(ai)) {
517	>	potential +=  atom->getParticlePot();
518	>	}
519	>	} else {
520	>	potential = integrableObject->getParticlePot();
521	>	cerr << "ppot = "  << potential << "\n";
522	>	}
523	>
524	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
525	>	// The potential may not be a 1/2 factor
526	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
527	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
528	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
529	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
530	>	}
531	>	}
532	>
533	>	std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl;
534	>
535	>	/* The J_v vector is reduced in fortan so everyone has the global
536	>	*  Jv. Jc is computed over the local atoms and must be reduced
537	>	*  among all processors.
538	>	*/
539	>	#ifdef IS_MPI
540	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
541	>	MPI::SUM);
542	>	#endif
543	>
544	>	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
545	>
546	>	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
547	>	PhysicalConstants::energyConvert;
548	>
549	>	std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl;
550	>	std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl;
551	>
552	>	// Correct for the fact the flux is 1/V (Jc + Jv)
553	>	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
554	>	}
555	>	} //end namespace OpenMD

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 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

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