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

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trunk/src/brains/Thermo.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

#	Line 1 | Line 1
1	+	/*
2	+	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	+	*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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>
44		#include <iostream>
3	–	using namespace std;
45
46		#ifdef IS_MPI
47		#include <mpi.h>
48		#endif //is_mpi
49
50		#include "brains/Thermo.hpp"
51	<	#include "primitives/SRI.hpp"
11	<	#include "integrators/Integrator.hpp"
51	>	#include "primitives/Molecule.hpp"
52		#include "utils/simError.h"
53	<	#include "math/MatVec3.h"
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	<	#ifdef IS_MPI
63	<	#define __C
17	<	#include "brains/mpiSimulation.hpp"
18	<	#endif // is_mpi
62	>	using namespace std;
63	>	namespace OpenMD {
64
65	<	inline double roundMe( double x ){
66	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
22	<	}
65	>	RealType Thermo::getTranslationalKinetic() {
66	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
67
68	<	Thermo::Thermo( SimInfo* the_info ) {
69	<	info = the_info;
70	<	int baseSeed = the_info->getSeed();
71	<
72	<	gaussStream = new gaussianSPRNG( baseSeed );
73	<	}
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	<	Thermo::~Thermo(){
105	<	delete gaussStream;
33	<	}
104	>	RealType Thermo::getRotationalKinetic() {
105	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
106
107	<	double Thermo::getKinetic(){
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	>
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	<	const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
38	<	double kinetic;
39	<	double amass;
40	<	double aVel[3], aJ[3], I[3][3];
41	<	int i, j, k, kl;
154	>
155
156	<	double kinetic_global;
157	<	vector<StuntDouble *> integrableObjects = info->integrableObjects;
45	<
46	<	kinetic = 0.0;
47	<	kinetic_global = 0.0;
156	>	RealType Thermo::getKinetic() {
157	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
158
159	<	for (kl=0; kl<integrableObjects.size(); kl++) {
160	<	integrableObjects[kl]->getVel(aVel);
161	<	amass = integrableObjects[kl]->getMass();
159	>	if (!snap->hasKineticEnergy) {
160	>	RealType ke = getTranslationalKinetic() + getRotationalKinetic();
161	>	snap->setKineticEnergy(ke);
162	>	}
163	>	return snap->getKineticEnergy();
164	>	}
165
166	<	for(j=0; j<3; j++)
54	<	kinetic += amass*aVel[j]*aVel[j];
166	>	RealType Thermo::getPotential() {
167
168	<	if (integrableObjects[kl]->isDirectional()){
169	<
58	<	integrableObjects[kl]->getJ( aJ );
59	<	integrableObjects[kl]->getI( I );
168	>	// ForceManager computes the potential and stores it in the
169	>	// Snapshot.  All we have to do is report it.
170
171	<	if (integrableObjects[kl]->isLinear()) {
172	<	i = integrableObjects[kl]->linearAxis();
63	<	j = (i+1)%3;
64	<	k = (i+2)%3;
65	<	kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
66	<	} else {
67	<	for (j=0; j<3; j++)
68	<	kinetic += aJ[j]*aJ[j] / I[j][j];
69	<	}
70	<	}
171	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
172	>	return snap->getPotentialEnergy();
173		}
72	–	#ifdef IS_MPI
73	–	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
74	–	MPI_SUM, MPI_COMM_WORLD);
75	–	kinetic = kinetic_global;
76	–	#endif //is_mpi
77	–
78	–	kinetic = kinetic * 0.5 / e_convert;
174
175	<	return kinetic;
81	<	}
175	>	RealType Thermo::getTotalEnergy() {
176
177	<	double Thermo::getPotential(){
84	<
85	<	double potential_local;
86	<	double potential;
87	<	int el, nSRI;
88	<	Molecule* molecules;
177	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
178
179	<	molecules = info->molecules;
180	<	nSRI = info->n_SRI;
179	>	if (!snap->hasTotalEnergy) {
180	>	snap->setTotalEnergy(this->getKinetic() + this->getPotential());
181	>	}
182
183	<	potential_local = 0.0;
94	<	potential = 0.0;
95	<	potential_local += info->lrPot;
96	<
97	<	for( el=0; el<info->n_mol; el++ ){
98	<	potential_local += molecules[el].getPotential();
183	>	return snap->getTotalEnergy();
184		}
185
186	<	// Get total potential for entire system from MPI.
102	<	#ifdef IS_MPI
103	<	MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
104	<	MPI_SUM, MPI_COMM_WORLD);
105	<	#else
106	<	potential = potential_local;
107	<	#endif // is_mpi
186	>	RealType Thermo::getTemperature() {
187
188	<	return potential;
110	<	}
188	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189
190	<	double Thermo::getTotalE(){
190	>	if (!snap->hasTemperature) {
191
192	<	double total;
192	>	RealType temperature = ( 2.0 * this->getKinetic() )
193	>	/ (info_->getNdf()* PhysicalConstants::kb );
194
195	<	total = this->getKinetic() + this->getPotential();
196	<	return total;
197	<	}
195	>	snap->setTemperature(temperature);
196	>	}
197	>
198	>	return snap->getTemperature();
199	>	}
200
201	<	double Thermo::getTemperature(){
201	>	RealType Thermo::getElectronicTemperature() {
202	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203
204	<	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
205	<	double temperature;
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	<	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
235	<	return temperature;
236	<	}
234	>	kinetic *= 0.5;
235	>	eTemp =  (2.0 * kinetic) /
236	>	(info_->getNFluctuatingCharges() * PhysicalConstants::kb );
237	>
238	>	snap->setElectronicTemperature(eTemp);
239	>	}
240
241	<	double Thermo::getVolume() {
241	>	return snap->getElectronicTemperature();
242	>	}
243
131	–	return info->boxVol;
132	–	}
244
245	<	double Thermo::getPressure() {
245	>	RealType Thermo::getVolume() {
246	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247	>	return snap->getVolume();
248	>	}
249
250	<	// Relies on the calculation of the full molecular pressure tensor
251	<
138	<	const double p_convert = 1.63882576e8;
139	<	double press[3][3];
140	<	double pressure;
250	>	RealType Thermo::getPressure() {
251	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252
253	<	this->getPressureTensor(press);
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	<	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
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	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275
276	<	return pressure;
147	<	}
276	>	if (!snap->hasPressureTensor) {
277
278	<	double Thermo::getPressureX() {
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	>	return snap->getPressureTensor();
313	>	}
314
151	–	// Relies on the calculation of the full molecular pressure tensor
152	–
153	–	const double p_convert = 1.63882576e8;
154	–	double press[3][3];
155	–	double pressureX;
315
157	–	this->getPressureTensor(press);
316
159	–	pressureX = p_convert * press[0][0];
317
318	<	return pressureX;
319	<	}
318	>	Vector3d Thermo::getSystemDipole() {
319	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
320
321	<	double Thermo::getPressureY() {
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::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	<	// Relies on the calculation of the full molecular pressure tensor
388	<
389	<	const double p_convert = 1.63882576e8;
390	<	double press[3][3];
170	<	double pressureY;
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	<	this->getPressureTensor(press);
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	<	pressureY = p_convert * press[1][1];
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 pressureY;
419	<	}
418	>	return snap->getSystemDipole();
419	>	}
420
421	<	double Thermo::getPressureZ() {
421	>	// Returns the Heat Flux Vector for the system
422	>	Vector3d Thermo::getHeatFlux(){
423	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
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	<	// Relies on the calculation of the full molecular pressure tensor
439	<
440	<	const double p_convert = 1.63882576e8;
441	<	double press[3][3];
442	<	double pressureZ;
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	<	this->getPressureTensor(press);
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	<	pressureZ = p_convert * press[2][2];
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	<	return pressureZ;
463	<	}
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	<	void Thermo::getPressureTensor(double press[3][3]){
478	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
479	<	// routine derived via viral theorem description in:
480	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
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	<	const double e_convert = 4.184e-4;
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	<	double molmass, volume;
497	<	double vcom[3];
498	<	double p_local[9], p_global[9];
499	<	int i, j, k;
500	<
501	<	for (i=0; i < 9; i++) {
502	<	p_local[i] = 0.0;
503	<	p_global[i] = 0.0;
210	<	}
211	<
212	<	// use velocities of integrableObjects and their masses:
213	<
214	<	for (i=0; i < info->integrableObjects.size(); i++) {
215	<
216	<	molmass = info->integrableObjects[i]->getMass();
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	<	info->integrableObjects[i]->getVel(vcom);
219	<
220	<	p_local[0] += molmass * (vcom[0] * vcom[0]);
221	<	p_local[1] += molmass * (vcom[0] * vcom[1]);
222	<	p_local[2] += molmass * (vcom[0] * vcom[2]);
223	<	p_local[3] += molmass * (vcom[1] * vcom[0]);
224	<	p_local[4] += molmass * (vcom[1] * vcom[1]);
225	<	p_local[5] += molmass * (vcom[1] * vcom[2]);
226	<	p_local[6] += molmass * (vcom[2] * vcom[0]);
227	<	p_local[7] += molmass * (vcom[2] * vcom[1]);
228	<	p_local[8] += molmass * (vcom[2] * vcom[2]);
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
232	–	// Get total for entire system from MPI.
233	–
234	–	#ifdef IS_MPI
235	–	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
236	–	#else
237	–	for (i=0; i<9; i++) {
238	–	p_global[i] = p_local[i];
239	–	}
240	–	#endif // is_mpi
514
515	<	volume = this->getVolume();
515	>	Vector3d Thermo::getComVel(){
516	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
517
518	+	if (!snap->hasCOMvel) {
519
520	<
521	<	for(i = 0; i < 3; i++) {
522	<	for (j = 0; j < 3; j++) {
523	<	k = 3*i + j;
524	<	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
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		}
252	–	}
545
546	<	void Thermo::velocitize() {
547	<
256	<	double aVel[3], aJ[3], I[3][3];
257	<	int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
258	<	double vdrift[3];
259	<	double vbar;
260	<	const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
261	<	double av2;
262	<	double kebar;
263	<	double temperature;
264	<	int nobj;
546	>	Vector3d Thermo::getCom(){
547	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
548
549	<	if (!info->have_target_temp) {
550	<	sprintf( painCave.errMsg,
551	<	"You can't resample the velocities without a targetTemp!\n"
552	<	);
553	<	painCave.isFatal = 1;
554	<	painCave.severity = OOPSE_ERROR;
555	<	simError();
556	<	return;
557	<	}
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	<	nobj = info->integrableObjects.size();
578	<
579	<	temperature   = info->target_temp;
580	<
581	<	kebar = kb * temperature * (double)info->ndfRaw /
582	<	( 2.0 * (double)info->ndf );
282	<
283	<	for(vr = 0; vr < nobj; vr++){
284	<
285	<	// uses equipartition theory to solve for vbar in angstrom/fs
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	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
288	<	vbar = sqrt( av2 );
584	>	if (!(snap->hasCOM && snap->hasCOMvel)) {
585
586	<	// picks random velocities from a gaussian distribution
587	<	// centered on vbar
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	>	* \brief Return inertia 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	<	for (j=0; j<3; j++)
294	<	aVel[j] = vbar * gaussStream->getGaussian();
634	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
635
636	<	info->integrableObjects[vr]->setVel( aVel );
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	<	if(info->integrableObjects[vr]->isDirectional()){
698	>	angularMomentum = snap->getCOMw();
699	>	inertiaTensor = snap->getInertiaTensor();
700	>
701	>	return;
702	>	}
703
300	–	info->integrableObjects[vr]->getI( I );
704
705	<	if (info->integrableObjects[vr]->isLinear()) {
706	<
707	<	l= info->integrableObjects[vr]->linearAxis();
708	<	m = (l+1)%3;
709	<	n = (l+2)%3;
710	<
711	<	aJ[l] = 0.0;
712	<	vbar = sqrt( 2.0 * kebar * I[m][m] );
713	<	aJ[m] = vbar * gaussStream->getGaussian();
714	<	vbar = sqrt( 2.0 * kebar * I[n][n] );
715	<	aJ[n] = vbar * gaussStream->getGaussian();
705	>	Mat3x3d Thermo::getBoundingBox(){
706	>
707	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
708	>
709	>	if (!(snap->hasBoundingBox)) {
710	>
711	>	SimInfo::MoleculeIterator i;
712	>	Molecule::RigidBodyIterator ri;
713	>	Molecule::AtomIterator ai;
714	>	Molecule* mol;
715	>	RigidBody* rb;
716	>	Atom* atom;
717	>	Vector3d pos, bMax, bMin;
718	>	int index = 0;
719	>
720	>	for (mol = info_->beginMolecule(i); mol != NULL;
721	>	mol = info_->nextMolecule(i)) {
722
723	<	} else {
724	<	for (j = 0 ; j < 3; j++) {
725	<	vbar = sqrt( 2.0 * kebar * I[j][j] );
726	<	aJ[j] = vbar * gaussStream->getGaussian();
727	<	}
728	<	} // else isLinear
723	>	//change the positions of atoms which belong to the rigidbodies
724	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
725	>	rb = mol->nextRigidBody(ri)) {
726	>	rb->updateAtoms();
727	>	}
728	>
729	>	for(atom = mol->beginAtom(ai); atom != NULL;
730	>	atom = mol->nextAtom(ai)) {
731	>
732	>	pos = atom->getPos();
733
734	<	info->integrableObjects[vr]->setJ( aJ );
734	>	if (index == 0) {
735	>	bMax = pos;
736	>	bMin = pos;
737	>	} else {
738	>	for (int i = 0; i < 3; i++) {
739	>	bMax[i] = max(bMax[i], pos[i]);
740	>	bMin[i] = min(bMin[i], pos[i]);
741	>	}
742	>	}
743	>	index++;
744	>	}
745	>	}
746
747	<	}//isDirectional
747	>	#ifdef IS_MPI
748	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMax[0], 3, MPI::REALTYPE,
749	>	MPI::MAX);
750
751	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMin[0], 3, MPI::REALTYPE,
752	+	MPI::MIN);
753	+	#endif
754	+	Mat3x3d bBox = Mat3x3d(0.0);
755	+	for (int i = 0; i < 3; i++) {
756	+	bBox(i,i) = bMax[i] - bMin[i];
757	+	}
758	+	snap->setBoundingBox(bBox);
759	+	}
760	+
761	+	return snap->getBoundingBox();
762		}
326	–
327	–	// Get the Center of Mass drift velocity.
328	–
329	–	getCOMVel(vdrift);
763
764	<	//  Corrects for the center of mass drift.
765	<	// sums all the momentum and divides by total mass.
766	<
767	<	for(vd = 0; vd < nobj; vd++){
764	>
765	>	// Returns the angular momentum of the system
766	>	Vector3d Thermo::getAngularMomentum(){
767	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
768
769	<	info->integrableObjects[vd]->getVel(aVel);
770	<
771	<	for (j=0; j < 3; j++)
772	<	aVel[j] -= vdrift[j];
769	>	if (!snap->hasCOMw) {
770	>
771	>	Vector3d com(0.0);
772	>	Vector3d comVel(0.0);
773	>	Vector3d angularMomentum(0.0);
774	>
775	>	getComAll(com, comVel);
776	>
777	>	SimInfo::MoleculeIterator i;
778	>	Molecule* mol;
779	>
780	>	Vector3d thisr(0.0);
781	>	Vector3d thisp(0.0);
782	>
783	>	RealType thisMass;
784	>
785	>	for (mol = info_->beginMolecule(i); mol != NULL;
786	>	mol = info_->nextMolecule(i)) {
787	>	thisMass = mol->getMass();
788	>	thisr = mol->getCom() - com;
789	>	thisp = (mol->getComVel() - comVel) * thisMass;
790
791	<	info->integrableObjects[vd]->setVel( aVel );
791	>	angularMomentum += cross( thisr, thisp );
792	>	}
793	>
794	>	#ifdef IS_MPI
795	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
796	>	angularMomentum.getArrayPointer(), 3,
797	>	MPI::REALTYPE, MPI::SUM);
798	>	#endif
799	>
800	>	snap->setCOMw(angularMomentum);
801	>	}
802	>
803	>	return snap->getCOMw();
804		}
343	–
344	–	}
345	–
346	–	void Thermo::getCOMVel(double vdrift[3]){
347	–
348	–	double mtot, mtot_local;
349	–	double aVel[3], amass;
350	–	double vdrift_local[3];
351	–	int vd, j;
352	–	int nobj;
353	–
354	–	nobj   = info->integrableObjects.size();
355	–
356	–	mtot_local = 0.0;
357	–	vdrift_local[0] = 0.0;
358	–	vdrift_local[1] = 0.0;
359	–	vdrift_local[2] = 0.0;
805
806	<	for(vd = 0; vd < nobj; vd++){
806	>
807	>	/**
808	>	* Returns the Volume of the system based on a ellipsoid with
809	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
810	>	* where R_i are related to the principle inertia moments
811	>	*  R_i = sqrt(C*I_i/N), this reduces to
812	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
813	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
814	>	*/
815	>	RealType Thermo::getGyrationalVolume(){
816	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
817
818	<	amass = info->integrableObjects[vd]->getMass();
819	<	info->integrableObjects[vd]->getVel( aVel );
818	>	if (!snap->hasGyrationalVolume) {
819	>
820	>	Mat3x3d intTensor;
821	>	RealType det;
822	>	Vector3d dummyAngMom;
823	>	RealType sysconstants;
824	>	RealType geomCnst;
825	>	RealType volume;
826	>
827	>	geomCnst = 3.0/2.0;
828	>	/* Get the inertial tensor and angular momentum for free*/
829	>	getInertiaTensor(intTensor, dummyAngMom);
830	>
831	>	det = intTensor.determinant();
832	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
833	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
834
835	<	for(j = 0; j < 3; j++)
836	<	vdrift_local[j] += aVel[j] * amass;
837	<
369	<	mtot_local += amass;
835	>	snap->setGyrationalVolume(volume);
836	>	}
837	>	return snap->getGyrationalVolume();
838		}
839	+
840	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
841	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
842
843	<	#ifdef IS_MPI
373	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
374	<	MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
375	<	#else
376	<	mtot = mtot_local;
377	<	for(vd = 0; vd < 3; vd++) {
378	<	vdrift[vd] = vdrift_local[vd];
379	<	}
380	<	#endif
843	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
844
845	<	for (vd = 0; vd < 3; vd++) {
846	<	vdrift[vd] = vdrift[vd] / mtot;
845	>	Mat3x3d intTensor;
846	>	Vector3d dummyAngMom;
847	>	RealType sysconstants;
848	>	RealType geomCnst;
849	>
850	>	geomCnst = 3.0/2.0;
851	>	/* Get the inertia tensor and angular momentum for free*/
852	>	this->getInertiaTensor(intTensor, dummyAngMom);
853	>
854	>	detI = intTensor.determinant();
855	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
856	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
857	>	snap->setGyrationalVolume(volume);
858	>	} else {
859	>	volume = snap->getGyrationalVolume();
860	>	detI = snap->getInertiaTensor().determinant();
861	>	}
862	>	return;
863		}
864
865	<	}
866	<
867	<	void Thermo::getCOM(double COM[3]){
389	<
390	<	double mtot, mtot_local;
391	<	double aPos[3], amass;
392	<	double COM_local[3];
393	<	int i, j;
394	<	int nobj;
395	<
396	<	mtot_local = 0.0;
397	<	COM_local[0] = 0.0;
398	<	COM_local[1] = 0.0;
399	<	COM_local[2] = 0.0;
400	<
401	<	nobj = info->integrableObjects.size();
402	<	for(i = 0; i < nobj; i++){
865	>	RealType Thermo::getTaggedAtomPairDistance(){
866	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
867	>	Globals* simParams = info_->getSimParams();
868
869	<	amass = info->integrableObjects[i]->getMass();
870	<	info->integrableObjects[i]->getPos( aPos );
869	>	if (simParams->haveTaggedAtomPair() &&
870	>	simParams->havePrintTaggedPairDistance()) {
871	>	if ( simParams->getPrintTaggedPairDistance()) {
872	>
873	>	pair<int, int> tap = simParams->getTaggedAtomPair();
874	>	Vector3d pos1, pos2, rab;
875	>
876	>	#ifdef IS_MPI
877	>	int mol1 = info_->getGlobalMolMembership(tap.first);
878	>	int mol2 = info_->getGlobalMolMembership(tap.second);
879
880	<	for(j = 0; j < 3; j++)
881	<	COM_local[j] += aPos[j] * amass;
409	<
410	<	mtot_local += amass;
411	<	}
880	>	int proc1 = info_->getMolToProc(mol1);
881	>	int proc2 = info_->getMolToProc(mol2);
882
883	<	#ifdef IS_MPI
884	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
885	<	MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
883	>	RealType data[3];
884	>	if (proc1 == worldRank) {
885	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
886	>	pos1 = sd1->getPos();
887	>	data[0] = pos1.x();
888	>	data[1] = pos1.y();
889	>	data[2] = pos1.z();
890	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
891	>	} else {
892	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
893	>	pos1 = Vector3d(data);
894	>	}
895	>
896	>	if (proc2 == worldRank) {
897	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
898	>	pos2 = sd2->getPos();
899	>	data[0] = pos2.x();
900	>	data[1] = pos2.y();
901	>	data[2] = pos2.z();
902	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
903	>	} else {
904	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
905	>	pos2 = Vector3d(data);
906	>	}
907		#else
908	<	mtot = mtot_local;
909	<	for(i = 0; i < 3; i++) {
910	<	COM[i] = COM_local[i];
908	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
909	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
910	>	pos1 = at1->getPos();
911	>	pos2 = at2->getPos();
912	>	#endif
913	>	rab = pos2 - pos1;
914	>	currSnapshot->wrapVector(rab);
915	>	return rab.length();
916	>	}
917	>	return 0.0;
918	>	}
919	>	return 0.0;
920		}
421	–	#endif
422	–
423	–	for (i = 0; i < 3; i++) {
424	–	COM[i] = COM[i] / mtot;
425	–	}
426	–	}
921
922	<	void Thermo::removeCOMdrift() {
923	<	double vdrift[3], aVel[3];
430	<	int vd, j, nobj;
922	>	RealType Thermo::getHullVolume(){
923	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
924
925	<	nobj = info->integrableObjects.size();
925	>	#ifdef HAVE_QHULL
926	>	if (!snap->hasHullVolume) {
927	>	Hull* surfaceMesh_;
928
929	<	// Get the Center of Mass drift velocity.
929	>	Globals* simParams = info_->getSimParams();
930	>	const std::string ht = simParams->getHULL_Method();
931	>
932	>	if (ht == "Convex") {
933	>	surfaceMesh_ = new ConvexHull();
934	>	} else if (ht == "AlphaShape") {
935	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
936	>	} else {
937	>	return 0.0;
938	>	}
939	>
940	>	// Build a vector of stunt doubles to determine if they are
941	>	// surface atoms
942	>	std::vector<StuntDouble*> localSites_;
943	>	Molecule* mol;
944	>	StuntDouble* sd;
945	>	SimInfo::MoleculeIterator i;
946	>	Molecule::IntegrableObjectIterator  j;
947	>
948	>	for (mol = info_->beginMolecule(i); mol != NULL;
949	>	mol = info_->nextMolecule(i)) {
950	>	for (sd = mol->beginIntegrableObject(j);
951	>	sd != NULL;
952	>	sd = mol->nextIntegrableObject(j)) {
953	>	localSites_.push_back(sd);
954	>	}
955	>	}
956	>
957	>	// Compute surface Mesh
958	>	surfaceMesh_->computeHull(localSites_);
959	>	snap->setHullVolume(surfaceMesh_->getVolume());
960
961	<	getCOMVel(vdrift);
962	<
438	<	//  Corrects for the center of mass drift.
439	<	// sums all the momentum and divides by total mass.
961	>	delete surfaceMesh_;
962	>	}
963
964	<	for(vd = 0; vd < nobj; vd++){
965	<
966	<	info->integrableObjects[vd]->getVel(aVel);
967	<
445	<	for (j=0; j < 3; j++)
446	<	aVel[j] -= vdrift[j];
447	<
448	<	info->integrableObjects[vd]->setVel( aVel );
964	>	return snap->getHullVolume();
965	>	#else
966	>	return 0.0;
967	>	#endif
968		}
969	+
970	+
971		}

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

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