ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/src/brains/Thermo.cpp

Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1666 by chuckv, Wed Dec 14 20:21:54 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41	<
41	>
42		#include <math.h>
43		#include <iostream>
44
#	Line 49 | Line 49
49		#include "brains/Thermo.hpp"
50		#include "primitives/Molecule.hpp"
51		#include "utils/simError.h"
52	<	#include "utils/OOPSEConstant.hpp"
52	>	#include "utils/PhysicalConstants.hpp"
53
54	<	namespace oopse {
54	>	namespace OpenMD {
55
56		RealType Thermo::getKinetic() {
57		SimInfo::MoleculeIterator miter;
58		std::vector<StuntDouble*>::iterator iiter;
59		Molecule* mol;
60	<	StuntDouble* integrableObject;
60	>	StuntDouble* integrableObject;
61		Vector3d vel;
62		Vector3d angMom;
63		Mat3x3d I;
#	Line 67 | Line 67 | namespace oopse {
67		RealType mass;
68		RealType kinetic = 0.0;
69		RealType kinetic_global = 0.0;
70	<
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)) {
74	<
75	<	mass = integrableObject->getMass();
76	<	vel = integrableObject->getVel();
77	<
78	<	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
79	<
80	<	if (integrableObject->isDirectional()) {
81	<	angMom = integrableObject->getJ();
82	<	I = integrableObject->getI();
72	>	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73	>	integrableObject = mol->nextIntegrableObject(iiter)) {
74
75	<	if (integrableObject->isLinear()) {
76	<	i = integrableObject->linearAxis();
77	<	j = (i + 1) % 3;
78	<	k = (i + 2) % 3;
79	<	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
80	<	} else {
81	<	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
82	<	+ angMom[2]*angMom[2]/I(2, 2);
83	<	}
84	<	}
85	<
75	>	mass = integrableObject->getMass();
76	>	vel = integrableObject->getVel();
77	>
78	>	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
79	>
80	>	if (integrableObject->isDirectional()) {
81	>	angMom = integrableObject->getJ();
82	>	I = integrableObject->getI();
83	>
84	>	if (integrableObject->isLinear()) {
85	>	i = integrableObject->linearAxis();
86	>	j = (i + 1) % 3;
87	>	k = (i + 2) % 3;
88	>	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
89	>	} else {
90	>	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
91	>	+ angMom[2]*angMom[2]/I(2, 2);
92	>	}
93	>	}
94	>
95		}
96		}
97	<
97	>
98		#ifdef IS_MPI
99
100		MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
#	Line 103 | Line 103 | namespace oopse {
103
104		#endif //is_mpi
105
106	<	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
106	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
107
108		return kinetic;
109		}
#	Line 138 | Line 138 | namespace oopse {
138		}
139
140		RealType Thermo::getTemperature() {
141	<
142	<	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
141	>
142	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143		return temperature;
144		}
145
146	<	RealType Thermo::getVolume() {
146	>	RealType Thermo::getVolume() {
147		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148		return curSnapshot->getVolume();
149		}
#	Line 158 | Line 158 | namespace oopse {
158
159		tensor = getPressureTensor();
160
161	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
161	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162
163		return pressure;
164		}
#	Line 167 | Line 167 | namespace oopse {
167
168		// Relies on the calculation of the full molecular pressure tensor
169
170	<
170	>
171		Mat3x3d tensor;
172		RealType pressure;
173
174		tensor = getPressureTensor();
175
176	<	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
176	>	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
177
178		return pressure;
179		}
#	Line 189 | Line 189 | namespace oopse {
189		SimInfo::MoleculeIterator i;
190		std::vector<StuntDouble*>::iterator j;
191		Molecule* mol;
192	<	StuntDouble* integrableObject;
192	>	StuntDouble* integrableObject;
193		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195	<	integrableObject = mol->nextIntegrableObject(j)) {
194	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195	>	integrableObject = mol->nextIntegrableObject(j)) {
196
197	<	RealType mass = integrableObject->getMass();
198	<	Vector3d vcom = integrableObject->getVel();
199	<	p_local += mass * outProduct(vcom, vcom);
197	>	RealType mass = integrableObject->getMass();
198	>	Vector3d vcom = integrableObject->getVel();
199	>	p_local += mass * outProduct(vcom, vcom);
200		}
201		}
202	<
202	>
203		#ifdef IS_MPI
204		MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205		#else
#	Line 210 | Line 210 | namespace oopse {
210		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211		Mat3x3d tau = curSnapshot->statData.getTau();
212
213	<	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
214	<
213	>	pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
214	>
215		return pressureTensor;
216		}
217
#	Line 219 | Line 219 | namespace oopse {
219		void Thermo::saveStat(){
220		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221		Stats& stat = currSnapshot->statData;
222	<
222	>
223		stat[Stats::KINETIC_ENERGY] = getKinetic();
224		stat[Stats::POTENTIAL_ENERGY] = getPotential();
225		stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
226		stat[Stats::TEMPERATURE] = getTemperature();
227		stat[Stats::PRESSURE] = getPressure();
228	<	stat[Stats::VOLUME] = getVolume();
228	>	stat[Stats::VOLUME] = getVolume();
229
230		Mat3x3d tensor =getPressureTensor();
231	<	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
232	<	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
233	<	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
234	<	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
235	<	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
236	<	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
237	<	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
238	<	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
239	<	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
231	>	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
232	>	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
233	>	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
234	>	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
235	>	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
236	>	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
237	>	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
238	>	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
239	>	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
240	>	Vector3d GKappa_t = getThermalHelfand();
241	>	stat[Stats::THERMAL_HELFANDMOMENT_X] = GKappa_t.x();
242	>	stat[Stats::THERMAL_HELFANDMOMENT_Y] = GKappa_t.y();
243	>	stat[Stats::THERMAL_HELFANDMOMENT_Z] = GKappa_t.z();
244
241	–
245		Globals* simParams = info_->getSimParams();
246
247	<	if (simParams->haveTaggedAtomPair() &&
247	>	if (simParams->haveTaggedAtomPair() &&
248		simParams->havePrintTaggedPairDistance()) {
249		if ( simParams->getPrintTaggedPairDistance()) {
250	<
250	>
251		std::pair<int, int> tap = simParams->getTaggedAtomPair();
252		Vector3d pos1, pos2, rab;
253
254	<	#ifdef IS_MPI
254	>	#ifdef IS_MPI
255		std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
256
257	<	int mol1 = info_->getGlobalMolMembership(tap.first);
258	<	int mol2 = info_->getGlobalMolMembership(tap.second);
257	>	int mol1 = info_->getGlobalMolMembership(tap.first);
258	>	int mol2 = info_->getGlobalMolMembership(tap.second);
259		std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
260
261		int proc1 = info_->getMolToProc(mol1);
#	Line 260 | Line 263 | namespace oopse {
263
264		std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
265
266	<	RealType data[3];
266	>	RealType data[3];
267		if (proc1 == worldRank) {
268		StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
269		std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
270		pos1 = sd1->getPos();
271		data[0] = pos1.x();
272		data[1] = pos1.y();
273	<	data[2] = pos1.z();
273	>	data[2] = pos1.z();
274		MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
275		} else {
276		MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
#	Line 281 | Line 284 | namespace oopse {
284		pos2 = sd2->getPos();
285		data[0] = pos2.x();
286		data[1] = pos2.y();
287	<	data[2] = pos2.z();
287	>	data[2] = pos2.z();
288		MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
289		} else {
290		MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
#	Line 292 | Line 295 | namespace oopse {
295		StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
296		pos1 = at1->getPos();
297		pos2 = at2->getPos();
298	<	#endif
298	>	#endif
299		rab = pos2 - pos1;
300		currSnapshot->wrapVector(rab);
301		stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
302		}
303		}
304	<
304	>
305		/**@todo need refactorying*/
306		//Conserved Quantity is set by integrator and time is set by setTime
307	<
307	>
308		}
309
310	<	} //end namespace oopse
310	>
311	>
312	>	Vector3d Thermo::getBoxDipole() {
313	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
314	>	SimInfo::MoleculeIterator miter;
315	>	std::vector<Atom*>::iterator aiter;
316	>	Molecule* mol;
317	>	Atom* atom;
318	>	RealType charge;
319	>	RealType moment(0.0);
320	>	Vector3d ri(0.0);
321	>	Vector3d dipoleVector(0.0);
322	>	Vector3d nPos(0.0);
323	>	Vector3d pPos(0.0);
324	>	RealType nChg(0.0);
325	>	RealType pChg(0.0);
326	>	int nCount = 0;
327	>	int pCount = 0;
328	>
329	>	RealType chargeToC = 1.60217733e-19;
330	>	RealType angstromToM = 1.0e-10;    RealType debyeToCm = 3.33564095198e-30;
331	>
332	>	for (mol = info_->beginMolecule(miter); mol != NULL;
333	>	mol = info_->nextMolecule(miter)) {
334	>
335	>	for (atom = mol->beginAtom(aiter); atom != NULL;
336	>	atom = mol->nextAtom(aiter)) {
337	>
338	>	if (atom->isCharge() ) {
339	>	charge = 0.0;
340	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
341	>	if (data != NULL) {
342	>
343	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
344	>	charge *= chargeToC;
345	>
346	>	ri = atom->getPos();
347	>	currSnapshot->wrapVector(ri);
348	>	ri *= angstromToM;
349	>
350	>	if (charge < 0.0) {
351	>	nPos += ri;
352	>	nChg -= charge;
353	>	nCount++;
354	>	} else if (charge > 0.0) {
355	>	pPos += ri;
356	>	pChg += charge;
357	>	pCount++;
358	>	}
359	>	}
360	>	}
361	>
362	>	if (atom->isDipole() ) {
363	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
364	>	GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
365	>	if (data != NULL) {
366	>	moment = (dynamic_cast<DoubleGenericData*>(data))->getData();
367	>
368	>	moment *= debyeToCm;
369	>	dipoleVector += u_i * moment;
370	>	}
371	>	}
372	>	}
373	>	}
374	>
375	>
376	>	#ifdef IS_MPI
377	>	RealType pChg_global, nChg_global;
378	>	int pCount_global, nCount_global;
379	>	Vector3d pPos_global, nPos_global, dipVec_global;
380	>
381	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
382	>	MPI_COMM_WORLD);
383	>	pChg = pChg_global;
384	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
385	>	MPI_COMM_WORLD);
386	>	nChg = nChg_global;
387	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
388	>	MPI_COMM_WORLD);
389	>	pCount = pCount_global;
390	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
391	>	MPI_COMM_WORLD);
392	>	nCount = nCount_global;
393	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
394	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
395	>	pPos = pPos_global;
396	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
397	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
398	>	nPos = nPos_global;
399	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
400	>	dipVec_global.getArrayPointer(), 3,
401	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
402	>	dipoleVector = dipVec_global;
403	>	#endif //is_mpi
404	>
405	>	// first load the accumulated dipole moment (if dipoles were present)
406	>	Vector3d boxDipole = dipoleVector;
407	>	// now include the dipole moment due to charges
408	>	// use the lesser of the positive and negative charge totals
409	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
410	>
411	>	// find the average positions
412	>	if (pCount > 0 && nCount > 0 ) {
413	>	pPos /= pCount;
414	>	nPos /= nCount;
415	>	}
416	>
417	>	// dipole is from the negative to the positive (physics notation)
418	>	boxDipole += (pPos - nPos) * chg_value;
419	>
420	>	return boxDipole;
421	>	}
422	>
423	>	Vector3d Thermo::getThermalHelfand() {
424	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
425	>	SimInfo::MoleculeIterator miter;
426	>	std::vector<Atom*>::iterator aiter;
427	>	Molecule* mol;
428	>	Atom* atom;
429	>	RealType mass;
430	>	Vector3d velocity;
431	>	Vector3d x_a;
432	>	RealType kinetic;
433	>	RealType potential;
434	>	RealType eatom;
435	>	RealType AvgE_a_ = 0;
436	>	Vector3d GKappa_t = V3Zero;
437	>	Vector3d ThermalHelfandMoment;
438	>
439	>	for (mol = info_->beginMolecule(miter); mol != NULL;
440	>	mol = info_->nextMolecule(miter)) {
441	>
442	>	for (atom = mol->beginAtom(aiter); atom != NULL;
443	>	atom = mol->nextAtom(aiter)) {
444	>
445	>	mass = atom->getMass();
446	>	velocity = atom->getVel();
447	>	kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
448	>	velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
449	>	potential =  atom->getParticlePot();
450	>	eatom += (kinetic + potential)/2.0;
451	>	}
452	>	}
453	>
454	>	int natoms = info_->getNGlobalAtoms();
455	>	#ifdef IS_MPI
456	>
457	>	MPI_Allreduce(&eatom, &AvgE_a_, 1, MPI_REALTYPE, MPI_SUM,
458	>	MPI_COMM_WORLD);
459	>	#else
460	>	AvgE_a_ = eatom;
461	>	#endif
462	>	AvgE_a_ = AvgE_a_/RealType(natoms);
463	>
464	>	for (mol = info_->beginMolecule(miter); mol != NULL;
465	>	mol = info_->nextMolecule(miter)) {
466	>
467	>	for (atom = mol->beginAtom(aiter); atom != NULL;
468	>	atom = mol->nextAtom(aiter)) {
469	>
470	>	/* We think that x_a is relative to the total box and should be a wrapped coordinate */
471	>	x_a = atom->getPos();
472	>	currSnapshot->wrapVector(x_a);
473	>	potential =  atom->getParticlePot();
474	>	velocity = atom->getVel();
475	>	kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
476	>	velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
477	>	eatom += (kinetic + potential)/2.0
478	>	GKappa_t += x_a*(eatom-AvgE_a_);
479	>	}
480	>	}
481	>	#ifdef IS_MPI
482	>	MPI_Allreduce(GKappa_t.getArrayPointer(), ThermalHelfandMoment.getArrayPointer(), 3,
483	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
484	>	#else
485	>	ThermalHelfandMoment = GKappa_t;
486	>	#endif
487	>	return ThermalHelfandMoment;
488	>
489	>	}
490	>
491	>
492	>
493	>	} //end namespace OpenMD

Comparing trunk/src/brains/Thermo.cpp (property svn:keywords):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1666 by chuckv, Wed Dec 14 20:21:54 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines