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

Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 541 by tim, Sun May 22 21:05:15 2005 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 2014 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		*/
41	–
42	–	#include <math.h>
43	–	#include <iostream>
42
43		#ifdef IS_MPI
44		#include <mpi.h>
45		#endif //is_mpi
46	+
47	+	#include <math.h>
48	+	#include <iostream>
49
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
93	>	MPI_SUM, MPI_COMM_WORLD);
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
144	+	MPI_SUM, MPI_COMM_WORLD);
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 potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
114	<	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	<
120	<	MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
121	<	MPI_COMM_WORLD);
122	<
123	<	#else
124	<
125	<	potential = potential_local;
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
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
231	>	MPI_SUM, MPI_COMM_WORLD);
232	>	#endif
233
234	<
235	<	Mat3x3d tensor;
236	<	double pressure;
234	>	kinetic *= 0.5;
235	>	eTemp =  (2.0 * kinetic) /
236	>	(info_->getNFluctuatingCharges() * PhysicalConstants::kb );
237	>
238	>	snap->setElectronicTemperature(eTemp);
239	>	}
240
241	<	tensor = getPressureTensor();
241	>	return snap->getElectronicTemperature();
242	>	}
243
175	–	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
244
245	<	return pressure;
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	<	}
203	<
298	>
299		#ifdef IS_MPI
300	<	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
301	<	#else
302	<	p_global = p_local;
303	<	#endif // is_mpi
300	>	MPI_Allreduce(MPI_IN_PLACE, p_tens.getArrayPointer(), 9,
301	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
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	>	return snap->getPressureTensor();
313	>	}
314
210	–	double volume = this->getVolume();
211	–	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
212	–	Mat3x3d tau = curSnapshot->statData.getTau();
315
214	–	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
316
317	<	return pressureTensor;
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(MPI_IN_PLACE, &pChg, 1, MPI_REALTYPE,
383	>	MPI_SUM, MPI_COMM_WORLD);
384	>	MPI_Allreduce(MPI_IN_PLACE, &nChg, 1, MPI_REALTYPE,
385	>	MPI_SUM, MPI_COMM_WORLD);
386	>
387	>	MPI_Allreduce(MPI_IN_PLACE, &pCount, 1, MPI_INTEGER,
388	>	MPI_SUM, MPI_COMM_WORLD);
389	>	MPI_Allreduce(MPI_IN_PLACE, &nCount, 1, MPI_INTEGER,
390	>	MPI_SUM, MPI_COMM_WORLD);
391	>
392	>	MPI_Allreduce(MPI_IN_PLACE, pPos.getArrayPointer(), 3,
393	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
394	>	MPI_Allreduce(MPI_IN_PLACE, nPos.getArrayPointer(), 3,
395	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
396	>
397	>	MPI_Allreduce(MPI_IN_PLACE, dipoleVector.getArrayPointer(),
398	>	3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
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(){
422	<	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
423	<	Stats& stat = currSnapshot->statData;
421	>
422	>	Mat3x3d Thermo::getSystemQuadrupole() {
423	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
424	>
425	>	if (!snap->hasSystemQuadrupole) {
426	>	SimInfo::MoleculeIterator miter;
427	>	vector<Atom*>::iterator aiter;
428	>	Molecule* mol;
429	>	Atom* atom;
430	>	RealType charge;
431	>	Vector3d ri(0.0);
432	>	Vector3d dipole(0.0);
433	>	Mat3x3d qpole(0.0);
434	>
435	>	RealType chargeToC = 1.60217733e-19;
436	>	RealType angstromToM = 1.0e-10;
437	>	RealType debyeToCm = 3.33564095198e-30;
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	>	ri = atom->getPos();
446	>	snap->wrapVector(ri);
447	>	ri *= angstromToM;
448	>
449	>	charge = 0.0;
450	>
451	>	FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
452	>	if ( fca.isFixedCharge() ) {
453	>	charge = fca.getCharge();
454	>	}
455	>
456	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
457	>	if ( fqa.isFluctuatingCharge() ) {
458	>	charge += atom->getFlucQPos();
459	>	}
460	>
461	>	charge *= chargeToC;
462	>
463	>	qpole += 0.5 * charge * outProduct(ri, ri);
464	>
465	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
466	>
467	>	if ( ma.isDipole() ) {
468	>	dipole = atom->getDipole() * debyeToCm;
469	>	qpole += 0.5 * outProduct( dipole, ri );
470	>	}
471	>
472	>	if ( ma.isQuadrupole() ) {
473	>	qpole += atom->getQuadrupole() * debyeToCm * angstromToM;
474	>	}
475	>	}
476	>	}
477	>
478	>	#ifdef IS_MPI
479	>	MPI_Allreduce(MPI_IN_PLACE, qpole.getArrayPointer(),
480	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
481	>	#endif
482	>
483	>	snap->setSystemQuadrupole(qpole);
484	>	}
485
486	<	stat[Stats::KINETIC_ENERGY] = getKinetic();
487	<	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();
486	>	return snap->getSystemQuadrupole();
487	>	}
488
489	<	Mat3x3d tensor =getPressureTensor();
490	<	stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);
491	<	stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);
492	<	stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);
489	>	// Returns the Heat Flux Vector for the system
490	>	Vector3d Thermo::getHeatFlux(){
491	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
492	>	SimInfo::MoleculeIterator miter;
493	>	vector<StuntDouble*>::iterator iiter;
494	>	Molecule* mol;
495	>	StuntDouble* sd;
496	>	RigidBody::AtomIterator ai;
497	>	Atom* atom;
498	>	Vector3d vel;
499	>	Vector3d angMom;
500	>	Mat3x3d I;
501	>	int i;
502	>	int j;
503	>	int k;
504	>	RealType mass;
505
506	+	Vector3d x_a;
507	+	RealType kinetic;
508	+	RealType potential;
509	+	RealType eatom;
510	+	// Convective portion of the heat flux
511	+	Vector3d heatFluxJc = V3Zero;
512
513	<	/**@todo need refactorying*/
514	<	//Conserved Quantity is set by integrator and time is set by setTime
513	>	/* Calculate convective portion of the heat flux */
514	>	for (mol = info_->beginMolecule(miter); mol != NULL;
515	>	mol = info_->nextMolecule(miter)) {
516	>
517	>	for (sd = mol->beginIntegrableObject(iiter);
518	>	sd != NULL;
519	>	sd = mol->nextIntegrableObject(iiter)) {
520	>
521	>	mass = sd->getMass();
522	>	vel = sd->getVel();
523	>
524	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
525	>
526	>	if (sd->isDirectional()) {
527	>	angMom = sd->getJ();
528	>	I = sd->getI();
529	>
530	>	if (sd->isLinear()) {
531	>	i = sd->linearAxis();
532	>	j = (i + 1) % 3;
533	>	k = (i + 2) % 3;
534	>	kinetic += angMom[j] * angMom[j] / I(j, j)
535	>	+ angMom[k] * angMom[k] / I(k, k);
536	>	} else {
537	>	kinetic += angMom[0]*angMom[0]/I(0, 0)
538	>	+ angMom[1]*angMom[1]/I(1, 1)
539	>	+ angMom[2]*angMom[2]/I(2, 2);
540	>	}
541	>	}
542	>
543	>	potential = 0.0;
544	>
545	>	if (sd->isRigidBody()) {
546	>	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
547	>	for (atom = rb->beginAtom(ai); atom != NULL;
548	>	atom = rb->nextAtom(ai)) {
549	>	potential +=  atom->getParticlePot();
550	>	}
551	>	} else {
552	>	potential = sd->getParticlePot();
553	>	}
554	>
555	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
556	>	// The potential may not be a 1/2 factor
557	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
558	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
559	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
560	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
561	>	}
562	>	}
563	>
564	>	/* The J_v vector is reduced in the forceManager so everyone has
565	>	*  the global Jv. Jc is computed over the local atoms and must be
566	>	*  reduced among all processors.
567	>	*/
568	>	#ifdef IS_MPI
569	>	MPI_Allreduce(MPI_IN_PLACE, &heatFluxJc[0], 3, MPI_REALTYPE,
570	>	MPI_SUM, MPI_COMM_WORLD);
571	>	#endif
572
573	+	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
574	+
575	+	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
576	+	PhysicalConstants::energyConvert;
577	+
578	+	// Correct for the fact the flux is 1/V (Jc + Jv)
579	+	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
580		}
581
582	<	} //end namespace oopse
582	>
583	>	Vector3d Thermo::getComVel(){
584	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
585	>
586	>	if (!snap->hasCOMvel) {
587	>
588	>	SimInfo::MoleculeIterator i;
589	>	Molecule* mol;
590	>
591	>	Vector3d comVel(0.0);
592	>	RealType totalMass(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	>	comVel += mass * mol->getComVel();
599	>	}
600	>
601	>	#ifdef IS_MPI
602	>	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
603	>	MPI_SUM, MPI_COMM_WORLD);
604	>	MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
605	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
606	>	#endif
607	>
608	>	comVel /= totalMass;
609	>	snap->setCOMvel(comVel);
610	>	}
611	>	return snap->getCOMvel();
612	>	}
613	>
614	>	Vector3d Thermo::getCom(){
615	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
616	>
617	>	if (!snap->hasCOM) {
618	>
619	>	SimInfo::MoleculeIterator i;
620	>	Molecule* mol;
621	>
622	>	Vector3d com(0.0);
623	>	RealType totalMass(0.0);
624	>
625	>	for (mol = info_->beginMolecule(i); mol != NULL;
626	>	mol = info_->nextMolecule(i)) {
627	>	RealType mass = mol->getMass();
628	>	totalMass += mass;
629	>	com += mass * mol->getCom();
630	>	}
631	>
632	>	#ifdef IS_MPI
633	>	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
634	>	MPI_SUM, MPI_COMM_WORLD);
635	>	MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
636	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
637	>	#endif
638	>
639	>	com /= totalMass;
640	>	snap->setCOM(com);
641	>	}
642	>	return snap->getCOM();
643	>	}
644	>
645	>	/**
646	>	* Returns center of mass and center of mass velocity in one
647	>	* function call.
648	>	*/
649	>	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
650	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
651	>
652	>	if (!(snap->hasCOM && snap->hasCOMvel)) {
653	>
654	>	SimInfo::MoleculeIterator i;
655	>	Molecule* mol;
656	>
657	>	RealType totalMass(0.0);
658	>
659	>	com = 0.0;
660	>	comVel = 0.0;
661	>
662	>	for (mol = info_->beginMolecule(i); mol != NULL;
663	>	mol = info_->nextMolecule(i)) {
664	>	RealType mass = mol->getMass();
665	>	totalMass += mass;
666	>	com += mass * mol->getCom();
667	>	comVel += mass * mol->getComVel();
668	>	}
669	>
670	>	#ifdef IS_MPI
671	>	MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
672	>	MPI_SUM, MPI_COMM_WORLD);
673	>	MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
674	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
675	>	MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
676	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
677	>	#endif
678	>
679	>	com /= totalMass;
680	>	comVel /= totalMass;
681	>	snap->setCOM(com);
682	>	snap->setCOMvel(comVel);
683	>	}
684	>	com = snap->getCOM();
685	>	comVel = snap->getCOMvel();
686	>	return;
687	>	}
688	>
689	>	/**
690	>	* \brief Return inertia tensor for entire system and angular momentum
691	>	*  Vector.
692	>	*
693	>	*
694	>	*
695	>	*    [  Ixx -Ixy  -Ixz ]
696	>	* I =| -Iyx  Iyy  -Iyz |
697	>	*    [ -Izx -Iyz   Izz ]
698	>	*/
699	>	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
700	>	Vector3d &angularMomentum){
701	>
702	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
703	>
704	>	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
705	>
706	>	RealType xx = 0.0;
707	>	RealType yy = 0.0;
708	>	RealType zz = 0.0;
709	>	RealType xy = 0.0;
710	>	RealType xz = 0.0;
711	>	RealType yz = 0.0;
712	>	Vector3d com(0.0);
713	>	Vector3d comVel(0.0);
714	>
715	>	getComAll(com, comVel);
716	>
717	>	SimInfo::MoleculeIterator i;
718	>	Molecule* mol;
719	>
720	>	Vector3d thisq(0.0);
721	>	Vector3d thisv(0.0);
722	>
723	>	RealType thisMass = 0.0;
724	>
725	>	for (mol = info_->beginMolecule(i); mol != NULL;
726	>	mol = info_->nextMolecule(i)) {
727	>
728	>	thisq = mol->getCom()-com;
729	>	thisv = mol->getComVel()-comVel;
730	>	thisMass = mol->getMass();
731	>	// Compute moment of intertia coefficients.
732	>	xx += thisq[0]*thisq[0]*thisMass;
733	>	yy += thisq[1]*thisq[1]*thisMass;
734	>	zz += thisq[2]*thisq[2]*thisMass;
735	>
736	>	// compute products of intertia
737	>	xy += thisq[0]*thisq[1]*thisMass;
738	>	xz += thisq[0]*thisq[2]*thisMass;
739	>	yz += thisq[1]*thisq[2]*thisMass;
740	>
741	>	angularMomentum += cross( thisq, thisv ) * thisMass;
742	>	}
743	>
744	>	inertiaTensor(0,0) = yy + zz;
745	>	inertiaTensor(0,1) = -xy;
746	>	inertiaTensor(0,2) = -xz;
747	>	inertiaTensor(1,0) = -xy;
748	>	inertiaTensor(1,1) = xx + zz;
749	>	inertiaTensor(1,2) = -yz;
750	>	inertiaTensor(2,0) = -xz;
751	>	inertiaTensor(2,1) = -yz;
752	>	inertiaTensor(2,2) = xx + yy;
753	>
754	>	#ifdef IS_MPI
755	>	MPI_Allreduce(MPI_IN_PLACE, inertiaTensor.getArrayPointer(),
756	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
757	>	MPI_Allreduce(MPI_IN_PLACE,
758	>	angularMomentum.getArrayPointer(), 3,
759	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
760	>	#endif
761	>
762	>	snap->setCOMw(angularMomentum);
763	>	snap->setInertiaTensor(inertiaTensor);
764	>	}
765	>
766	>	angularMomentum = snap->getCOMw();
767	>	inertiaTensor = snap->getInertiaTensor();
768	>
769	>	return;
770	>	}
771	>
772	>
773	>	Mat3x3d Thermo::getBoundingBox(){
774	>
775	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
776	>
777	>	if (!(snap->hasBoundingBox)) {
778	>
779	>	SimInfo::MoleculeIterator i;
780	>	Molecule::RigidBodyIterator ri;
781	>	Molecule::AtomIterator ai;
782	>	Molecule* mol;
783	>	RigidBody* rb;
784	>	Atom* atom;
785	>	Vector3d pos, bMax, bMin;
786	>	int index = 0;
787	>
788	>	for (mol = info_->beginMolecule(i); mol != NULL;
789	>	mol = info_->nextMolecule(i)) {
790	>
791	>	//change the positions of atoms which belong to the rigidbodies
792	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
793	>	rb = mol->nextRigidBody(ri)) {
794	>	rb->updateAtoms();
795	>	}
796	>
797	>	for(atom = mol->beginAtom(ai); atom != NULL;
798	>	atom = mol->nextAtom(ai)) {
799	>
800	>	pos = atom->getPos();
801	>
802	>	if (index == 0) {
803	>	bMax = pos;
804	>	bMin = pos;
805	>	} else {
806	>	for (int i = 0; i < 3; i++) {
807	>	bMax[i] = max(bMax[i], pos[i]);
808	>	bMin[i] = min(bMin[i], pos[i]);
809	>	}
810	>	}
811	>	index++;
812	>	}
813	>	}
814	>
815	>	#ifdef IS_MPI
816	>	MPI_Allreduce(MPI_IN_PLACE, &bMax[0], 3, MPI_REALTYPE,
817	>	MPI_MAX, MPI_COMM_WORLD);
818	>
819	>	MPI_Allreduce(MPI_IN_PLACE, &bMin[0], 3, MPI_REALTYPE,
820	>	MPI_MIN, MPI_COMM_WORLD);
821	>	#endif
822	>	Mat3x3d bBox = Mat3x3d(0.0);
823	>	for (int i = 0; i < 3; i++) {
824	>	bBox(i,i) = bMax[i] - bMin[i];
825	>	}
826	>	snap->setBoundingBox(bBox);
827	>	}
828	>
829	>	return snap->getBoundingBox();
830	>	}
831	>
832	>
833	>	// Returns the angular momentum of the system
834	>	Vector3d Thermo::getAngularMomentum(){
835	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
836	>
837	>	if (!snap->hasCOMw) {
838	>
839	>	Vector3d com(0.0);
840	>	Vector3d comVel(0.0);
841	>	Vector3d angularMomentum(0.0);
842	>
843	>	getComAll(com, comVel);
844	>
845	>	SimInfo::MoleculeIterator i;
846	>	Molecule* mol;
847	>
848	>	Vector3d thisr(0.0);
849	>	Vector3d thisp(0.0);
850	>
851	>	RealType thisMass;
852	>
853	>	for (mol = info_->beginMolecule(i); mol != NULL;
854	>	mol = info_->nextMolecule(i)) {
855	>	thisMass = mol->getMass();
856	>	thisr = mol->getCom() - com;
857	>	thisp = (mol->getComVel() - comVel) * thisMass;
858	>
859	>	angularMomentum += cross( thisr, thisp );
860	>	}
861	>
862	>	#ifdef IS_MPI
863	>	MPI_Allreduce(MPI_IN_PLACE,
864	>	angularMomentum.getArrayPointer(), 3,
865	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
866	>	#endif
867	>
868	>	snap->setCOMw(angularMomentum);
869	>	}
870	>
871	>	return snap->getCOMw();
872	>	}
873	>
874	>
875	>	/**
876	>	* Returns the Volume of the system based on a ellipsoid with
877	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
878	>	* where R_i are related to the principle inertia moments
879	>	*  R_i = sqrt(C*I_i/N), this reduces to
880	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
881	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
882	>	*/
883	>	RealType Thermo::getGyrationalVolume(){
884	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
885	>
886	>	if (!snap->hasGyrationalVolume) {
887	>
888	>	Mat3x3d intTensor;
889	>	RealType det;
890	>	Vector3d dummyAngMom;
891	>	RealType sysconstants;
892	>	RealType geomCnst;
893	>	RealType volume;
894	>
895	>	geomCnst = 3.0/2.0;
896	>	/* Get the inertial tensor and angular momentum for free*/
897	>	getInertiaTensor(intTensor, dummyAngMom);
898	>
899	>	det = intTensor.determinant();
900	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
901	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
902	>
903	>	snap->setGyrationalVolume(volume);
904	>	}
905	>	return snap->getGyrationalVolume();
906	>	}
907	>
908	>	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
909	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
910	>
911	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
912	>
913	>	Mat3x3d intTensor;
914	>	Vector3d dummyAngMom;
915	>	RealType sysconstants;
916	>	RealType geomCnst;
917	>
918	>	geomCnst = 3.0/2.0;
919	>	/* Get the inertia tensor and angular momentum for free*/
920	>	this->getInertiaTensor(intTensor, dummyAngMom);
921	>
922	>	detI = intTensor.determinant();
923	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
924	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
925	>	snap->setGyrationalVolume(volume);
926	>	} else {
927	>	volume = snap->getGyrationalVolume();
928	>	detI = snap->getInertiaTensor().determinant();
929	>	}
930	>	return;
931	>	}
932	>
933	>	RealType Thermo::getTaggedAtomPairDistance(){
934	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
935	>	Globals* simParams = info_->getSimParams();
936	>
937	>	if (simParams->haveTaggedAtomPair() &&
938	>	simParams->havePrintTaggedPairDistance()) {
939	>	if ( simParams->getPrintTaggedPairDistance()) {
940	>
941	>	pair<int, int> tap = simParams->getTaggedAtomPair();
942	>	Vector3d pos1, pos2, rab;
943	>
944	>	#ifdef IS_MPI
945	>	int mol1 = info_->getGlobalMolMembership(tap.first);
946	>	int mol2 = info_->getGlobalMolMembership(tap.second);
947	>
948	>	int proc1 = info_->getMolToProc(mol1);
949	>	int proc2 = info_->getMolToProc(mol2);
950	>
951	>	RealType data[3];
952	>	if (proc1 == worldRank) {
953	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
954	>	pos1 = sd1->getPos();
955	>	data[0] = pos1.x();
956	>	data[1] = pos1.y();
957	>	data[2] = pos1.z();
958	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
959	>	} else {
960	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
961	>	pos1 = Vector3d(data);
962	>	}
963	>
964	>	if (proc2 == worldRank) {
965	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
966	>	pos2 = sd2->getPos();
967	>	data[0] = pos2.x();
968	>	data[1] = pos2.y();
969	>	data[2] = pos2.z();
970	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
971	>	} else {
972	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
973	>	pos2 = Vector3d(data);
974	>	}
975	>	#else
976	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
977	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
978	>	pos1 = at1->getPos();
979	>	pos2 = at2->getPos();
980	>	#endif
981	>	rab = pos2 - pos1;
982	>	currSnapshot->wrapVector(rab);
983	>	return rab.length();
984	>	}
985	>	return 0.0;
986	>	}
987	>	return 0.0;
988	>	}
989	>
990	>	RealType Thermo::getHullVolume(){
991	>	#ifdef HAVE_QHULL
992	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
993	>	if (!snap->hasHullVolume) {
994	>	Hull* surfaceMesh_;
995	>
996	>	Globals* simParams = info_->getSimParams();
997	>	const std::string ht = simParams->getHULL_Method();
998	>
999	>	if (ht == "Convex") {
1000	>	surfaceMesh_ = new ConvexHull();
1001	>	} else if (ht == "AlphaShape") {
1002	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
1003	>	} else {
1004	>	return 0.0;
1005	>	}
1006	>
1007	>	// Build a vector of stunt doubles to determine if they are
1008	>	// surface atoms
1009	>	std::vector<StuntDouble*> localSites_;
1010	>	Molecule* mol;
1011	>	StuntDouble* sd;
1012	>	SimInfo::MoleculeIterator i;
1013	>	Molecule::IntegrableObjectIterator  j;
1014	>
1015	>	for (mol = info_->beginMolecule(i); mol != NULL;
1016	>	mol = info_->nextMolecule(i)) {
1017	>	for (sd = mol->beginIntegrableObject(j);
1018	>	sd != NULL;
1019	>	sd = mol->nextIntegrableObject(j)) {
1020	>	localSites_.push_back(sd);
1021	>	}
1022	>	}
1023	>
1024	>	// Compute surface Mesh
1025	>	surfaceMesh_->computeHull(localSites_);
1026	>	snap->setHullVolume(surfaceMesh_->getVolume());
1027	>
1028	>	delete surfaceMesh_;
1029	>	}
1030	>
1031	>	return snap->getHullVolume();
1032	>	#else
1033	>	return 0.0;
1034	>	#endif
1035	>	}
1036	>
1037	>
1038	>	}

Comparing trunk/src/brains/Thermo.cpp (property svn:keywords):
Revision 541 by tim, Sun May 22 21:05:15 2005 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 2014 UTC

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