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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 1767 by gezelter, Fri Jul 6 22:01:58 2012 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, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	+	*/
42	+
43		#include <math.h>
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);
254	<
255	<	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
256	<
257	<	return pressure;
258	<	}
259	<
260	<	double Thermo::getPressureX() {
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	<	// Relies on the calculation of the full molecular pressure tensor
271	<
272	<	const double p_convert = 1.63882576e8;
273	<	double press[3][3];
274	<	double pressureX;
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	<	this->getPressureTensor(press);
276	>	if (!snap->hasPressureTensor) {
277
278	<	pressureX = p_convert * press[0][0];
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
161	–	return pressureX;
162	–	}
315
164	–	double Thermo::getPressureY() {
316
166	–	// Relies on the calculation of the full molecular pressure tensor
167	–
168	–	const double p_convert = 1.63882576e8;
169	–	double press[3][3];
170	–	double pressureY;
317
318	<	this->getPressureTensor(press);
318	>	Vector3d Thermo::getSystemDipole() {
319	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
320
321	<	pressureY = p_convert * press[1][1];
321	>	if (!snap->hasSystemDipole) {
322	>	SimInfo::MoleculeIterator miter;
323	>	vector<Atom*>::iterator aiter;
324	>	Molecule* mol;
325	>	Atom* atom;
326	>	RealType charge;
327	>	RealType moment(0.0);
328	>	Vector3d ri(0.0);
329	>	Vector3d dipoleVector(0.0);
330	>	Vector3d nPos(0.0);
331	>	Vector3d pPos(0.0);
332	>	RealType nChg(0.0);
333	>	RealType pChg(0.0);
334	>	int nCount = 0;
335	>	int pCount = 0;
336	>
337	>	RealType chargeToC = 1.60217733e-19;
338	>	RealType angstromToM = 1.0e-10;
339	>	RealType debyeToCm = 3.33564095198e-30;
340	>
341	>	for (mol = info_->beginMolecule(miter); mol != NULL;
342	>	mol = info_->nextMolecule(miter)) {
343	>
344	>	for (atom = mol->beginAtom(aiter); atom != NULL;
345	>	atom = mol->nextAtom(aiter)) {
346	>
347	>	charge = 0.0;
348	>
349	>	FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
350	>	if ( fca.isFixedCharge() ) {
351	>	charge = fca.getCharge();
352	>	}
353	>
354	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
355	>	if ( fqa.isFluctuatingCharge() ) {
356	>	charge += atom->getFlucQPos();
357	>	}
358	>
359	>	charge *= chargeToC;
360	>
361	>	ri = atom->getPos();
362	>	snap->wrapVector(ri);
363	>	ri *= angstromToM;
364	>
365	>	if (charge < 0.0) {
366	>	nPos += ri;
367	>	nChg -= charge;
368	>	nCount++;
369	>	} else if (charge > 0.0) {
370	>	pPos += ri;
371	>	pChg += charge;
372	>	pCount++;
373	>	}
374	>
375	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
376	>	if (ma.isDipole() ) {
377	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
378	>	moment = ma.getDipoleMoment();
379	>	moment *= debyeToCm;
380	>	dipoleVector += u_i * moment;
381	>	}
382	>	}
383	>	}
384	>
385	>
386	>	#ifdef IS_MPI
387	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
388	>	MPI::SUM);
389	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
390	>	MPI::SUM);
391
392	<	return pressureY;
393	<	}
392	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
393	>	MPI::SUM);
394	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
395	>	MPI::SUM);
396
397	<	double Thermo::getPressureZ() {
397	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
398	>	MPI::REALTYPE, MPI::SUM);
399	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
400	>	MPI::REALTYPE, MPI::SUM);
401
402	<	// Relies on the calculation of the full molecular pressure tensor
403	<
404	<	const double p_convert = 1.63882576e8;
405	<	double press[3][3];
406	<	double pressureZ;
402	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
403	>	3, MPI::REALTYPE, MPI::SUM);
404	>	#endif
405	>
406	>	// first load the accumulated dipole moment (if dipoles were present)
407	>	Vector3d boxDipole = dipoleVector;
408	>	// now include the dipole moment due to charges
409	>	// use the lesser of the positive and negative charge totals
410	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
411	>
412	>	// find the average positions
413	>	if (pCount > 0 && nCount > 0 ) {
414	>	pPos /= pCount;
415	>	nPos /= nCount;
416	>	}
417	>
418	>	// dipole is from the negative to the positive (physics notation)
419	>	boxDipole += (pPos - nPos) * chg_value;
420	>	snap->setSystemDipole(boxDipole);
421	>	}
422
423	<	this->getPressureTensor(press);
423	>	return snap->getSystemDipole();
424	>	}
425
426	<	pressureZ = p_convert * press[2][2];
426	>	// Returns the Heat Flux Vector for the system
427	>	Vector3d Thermo::getHeatFlux(){
428	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
429	>	SimInfo::MoleculeIterator miter;
430	>	vector<StuntDouble*>::iterator iiter;
431	>	Molecule* mol;
432	>	StuntDouble* sd;
433	>	RigidBody::AtomIterator ai;
434	>	Atom* atom;
435	>	Vector3d vel;
436	>	Vector3d angMom;
437	>	Mat3x3d I;
438	>	int i;
439	>	int j;
440	>	int k;
441	>	RealType mass;
442
443	<	return pressureZ;
444	<	}
443	>	Vector3d x_a;
444	>	RealType kinetic;
445	>	RealType potential;
446	>	RealType eatom;
447	>	RealType AvgE_a_ = 0;
448	>	// Convective portion of the heat flux
449	>	Vector3d heatFluxJc = V3Zero;
450
451	+	/* Calculate convective portion of the heat flux */
452	+	for (mol = info_->beginMolecule(miter); mol != NULL;
453	+	mol = info_->nextMolecule(miter)) {
454	+
455	+	for (sd = mol->beginIntegrableObject(iiter);
456	+	sd != NULL;
457	+	sd = mol->nextIntegrableObject(iiter)) {
458	+
459	+	mass = sd->getMass();
460	+	vel = sd->getVel();
461
462	<	void Thermo::getPressureTensor(double press[3][3]){
463	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
464	<	// routine derived via viral theorem description in:
465	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
462	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
463	>
464	>	if (sd->isDirectional()) {
465	>	angMom = sd->getJ();
466	>	I = sd->getI();
467
468	<	const double e_convert = 4.184e-4;
468	>	if (sd->isLinear()) {
469	>	i = sd->linearAxis();
470	>	j = (i + 1) % 3;
471	>	k = (i + 2) % 3;
472	>	kinetic += angMom[j] * angMom[j] / I(j, j)
473	>	+ angMom[k] * angMom[k] / I(k, k);
474	>	} else {
475	>	kinetic += angMom[0]*angMom[0]/I(0, 0)
476	>	+ angMom[1]*angMom[1]/I(1, 1)
477	>	+ angMom[2]*angMom[2]/I(2, 2);
478	>	}
479	>	}
480
481	<	double molmass, volume;
203	<	double vcom[3];
204	<	double p_local[9], p_global[9];
205	<	int i, j, k;
481	>	potential = 0.0;
482
483	<	for (i=0; i < 9; i++) {
484	<	p_local[i] = 0.0;
485	<	p_global[i] = 0.0;
483	>	if (sd->isRigidBody()) {
484	>	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
485	>	for (atom = rb->beginAtom(ai); atom != NULL;
486	>	atom = rb->nextAtom(ai)) {
487	>	potential +=  atom->getParticlePot();
488	>	}
489	>	} else {
490	>	potential = sd->getParticlePot();
491	>	}
492	>
493	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
494	>	// The potential may not be a 1/2 factor
495	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
496	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
497	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
498	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
499	>	}
500	>	}
501	>
502	>	/* The J_v vector is reduced in the forceManager so everyone has
503	>	*  the global Jv. Jc is computed over the local atoms and must be
504	>	*  reduced among all processors.
505	>	*/
506	>	#ifdef IS_MPI
507	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
508	>	MPI::SUM);
509	>	#endif
510	>
511	>	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
512	>
513	>	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
514	>	PhysicalConstants::energyConvert;
515	>
516	>	// Correct for the fact the flux is 1/V (Jc + Jv)
517	>	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
518		}
519
212	–	// use velocities of integrableObjects and their masses:
520
521	<	for (i=0; i < info->integrableObjects.size(); i++) {
521	>	Vector3d Thermo::getComVel(){
522	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
523
524	<	molmass = info->integrableObjects[i]->getMass();
217	<
218	<	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]);
524	>	if (!snap->hasCOMvel) {
525
526	<	}
527	<
528	<	// Get total for entire system from MPI.
529	<
526	>	SimInfo::MoleculeIterator i;
527	>	Molecule* mol;
528	>
529	>	Vector3d comVel(0.0);
530	>	RealType totalMass(0.0);
531	>
532	>	for (mol = info_->beginMolecule(i); mol != NULL;
533	>	mol = info_->nextMolecule(i)) {
534	>	RealType mass = mol->getMass();
535	>	totalMass += mass;
536	>	comVel += mass * mol->getComVel();
537	>	}
538	>
539		#ifdef IS_MPI
540	<	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
541	<	#else
542	<	for (i=0; i<9; i++) {
543	<	p_global[i] = p_local[i];
540	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
541	>	MPI::SUM);
542	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
543	>	MPI::REALTYPE, MPI::SUM);
544	>	#endif
545	>
546	>	comVel /= totalMass;
547	>	snap->setCOMvel(comVel);
548	>	}
549	>	return snap->getCOMvel();
550		}
240	–	#endif // is_mpi
551
552	<	volume = this->getVolume();
552	>	Vector3d Thermo::getCom(){
553	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
554
555	<
556	<
557	<	for(i = 0; i < 3; i++) {
558	<	for (j = 0; j < 3; j++) {
559	<	k = 3*i + j;
560	<	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
555	>	if (!snap->hasCOM) {
556	>
557	>	SimInfo::MoleculeIterator i;
558	>	Molecule* mol;
559	>
560	>	Vector3d com(0.0);
561	>	RealType totalMass(0.0);
562	>
563	>	for (mol = info_->beginMolecule(i); mol != NULL;
564	>	mol = info_->nextMolecule(i)) {
565	>	RealType mass = mol->getMass();
566	>	totalMass += mass;
567	>	com += mass * mol->getCom();
568	>	}
569	>
570	>	#ifdef IS_MPI
571	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
572	>	MPI::SUM);
573	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
574	>	MPI::REALTYPE, MPI::SUM);
575	>	#endif
576	>
577	>	com /= totalMass;
578	>	snap->setCOM(com);
579		}
580	<	}
581	<	}
580	>	return snap->getCOM();
581	>	}
582
583	<	void Thermo::velocitize() {
584	<
585	<	double aVel[3], aJ[3], I[3][3];
586	<	int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
587	<	double vdrift[3];
588	<	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;
583	>	/**
584	>	* Returns center of mass and center of mass velocity in one
585	>	* function call.
586	>	*/
587	>	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
588	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
589
590	<	if (!info->have_target_temp) {
591	<	sprintf( painCave.errMsg,
592	<	"You can't resample the velocities without a targetTemp!\n"
593	<	);
594	<	painCave.isFatal = 1;
595	<	painCave.severity = OOPSE_ERROR;
596	<	simError();
590	>	if (!(snap->hasCOM && snap->hasCOMvel)) {
591	>
592	>	SimInfo::MoleculeIterator i;
593	>	Molecule* mol;
594	>
595	>	RealType totalMass(0.0);
596	>
597	>	com = 0.0;
598	>	comVel = 0.0;
599	>
600	>	for (mol = info_->beginMolecule(i); mol != NULL;
601	>	mol = info_->nextMolecule(i)) {
602	>	RealType mass = mol->getMass();
603	>	totalMass += mass;
604	>	com += mass * mol->getCom();
605	>	comVel += mass * mol->getComVel();
606	>	}
607	>
608	>	#ifdef IS_MPI
609	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
610	>	MPI::SUM);
611	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
612	>	MPI::REALTYPE, MPI::SUM);
613	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
614	>	MPI::REALTYPE, MPI::SUM);
615	>	#endif
616	>
617	>	com /= totalMass;
618	>	comVel /= totalMass;
619	>	snap->setCOM(com);
620	>	snap->setCOMvel(comVel);
621	>	}
622	>	com = snap->getCOM();
623	>	comVel = snap->getCOMvel();
624		return;
625	<	}
625	>	}
626	>
627	>	/**
628	>	* Return intertia tensor for entire system and angular momentum
629	>	* Vector.
630	>	*
631	>	*
632	>	*
633	>	*    [  Ixx -Ixy  -Ixz ]
634	>	* I =| -Iyx  Iyy  -Iyz |
635	>	*    [ -Izx -Iyz   Izz ]
636	>	*/
637	>	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
638	>	Vector3d &angularMomentum){
639
640	<	nobj = info->integrableObjects.size();
277	<
278	<	temperature   = info->target_temp;
279	<
280	<	kebar = kb * temperature * (double)info->ndfRaw /
281	<	( 2.0 * (double)info->ndf );
282	<
283	<	for(vr = 0; vr < nobj; vr++){
640	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
641
642	<	// uses equipartition theory to solve for vbar in angstrom/fs
643	<
644	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
645	<	vbar = sqrt( av2 );
646	<
647	<	// picks random velocities from a gaussian distribution
648	<	// centered on vbar
649	<
650	<	for (j=0; j<3; j++)
651	<	aVel[j] = vbar * gaussStream->getGaussian();
652	<
653	<	info->integrableObjects[vr]->setVel( aVel );
654	<
655	<	if(info->integrableObjects[vr]->isDirectional()){
656	<
657	<	info->integrableObjects[vr]->getI( I );
658	<
659	<	if (info->integrableObjects[vr]->isLinear()) {
660	<
661	<	l= info->integrableObjects[vr]->linearAxis();
662	<	m = (l+1)%3;
663	<	n = (l+2)%3;
664	<
308	<	aJ[l] = 0.0;
309	<	vbar = sqrt( 2.0 * kebar * I[m][m] );
310	<	aJ[m] = vbar * gaussStream->getGaussian();
311	<	vbar = sqrt( 2.0 * kebar * I[n][n] );
312	<	aJ[n] = vbar * gaussStream->getGaussian();
642	>	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
643	>
644	>	RealType xx = 0.0;
645	>	RealType yy = 0.0;
646	>	RealType zz = 0.0;
647	>	RealType xy = 0.0;
648	>	RealType xz = 0.0;
649	>	RealType yz = 0.0;
650	>	Vector3d com(0.0);
651	>	Vector3d comVel(0.0);
652	>
653	>	getComAll(com, comVel);
654	>
655	>	SimInfo::MoleculeIterator i;
656	>	Molecule* mol;
657	>
658	>	Vector3d thisq(0.0);
659	>	Vector3d thisv(0.0);
660	>
661	>	RealType thisMass = 0.0;
662	>
663	>	for (mol = info_->beginMolecule(i); mol != NULL;
664	>	mol = info_->nextMolecule(i)) {
665
666	<	} else {
667	<	for (j = 0 ; j < 3; j++) {
668	<	vbar = sqrt( 2.0 * kebar * I[j][j] );
669	<	aJ[j] = vbar * gaussStream->getGaussian();
670	<	}
671	<	} // else isLinear
672	<
673	<	info->integrableObjects[vr]->setJ( aJ );
666	>	thisq = mol->getCom()-com;
667	>	thisv = mol->getComVel()-comVel;
668	>	thisMass = mol->getMass();
669	>	// Compute moment of intertia coefficients.
670	>	xx += thisq[0]*thisq[0]*thisMass;
671	>	yy += thisq[1]*thisq[1]*thisMass;
672	>	zz += thisq[2]*thisq[2]*thisMass;
673	>
674	>	// compute products of intertia
675	>	xy += thisq[0]*thisq[1]*thisMass;
676	>	xz += thisq[0]*thisq[2]*thisMass;
677	>	yz += thisq[1]*thisq[2]*thisMass;
678	>
679	>	angularMomentum += cross( thisq, thisv ) * thisMass;
680	>	}
681
682	<	}//isDirectional
683	<
682	>	inertiaTensor(0,0) = yy + zz;
683	>	inertiaTensor(0,1) = -xy;
684	>	inertiaTensor(0,2) = -xz;
685	>	inertiaTensor(1,0) = -xy;
686	>	inertiaTensor(1,1) = xx + zz;
687	>	inertiaTensor(1,2) = -yz;
688	>	inertiaTensor(2,0) = -xz;
689	>	inertiaTensor(2,1) = -yz;
690	>	inertiaTensor(2,2) = xx + yy;
691	>
692	>	#ifdef IS_MPI
693	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
694	>	9, MPI::REALTYPE, MPI::SUM);
695	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
696	>	angularMomentum.getArrayPointer(), 3,
697	>	MPI::REALTYPE, MPI::SUM);
698	>	#endif
699	>
700	>	snap->setCOMw(angularMomentum);
701	>	snap->setInertiaTensor(inertiaTensor);
702	>	}
703	>
704	>	angularMomentum = snap->getCOMw();
705	>	inertiaTensor = snap->getInertiaTensor();
706	>
707	>	return;
708		}
709
710	<	// Get the Center of Mass drift velocity.
711	<
712	<	getCOMVel(vdrift);
330	<
331	<	//  Corrects for the center of mass drift.
332	<	// sums all the momentum and divides by total mass.
333	<
334	<	for(vd = 0; vd < nobj; vd++){
710	>	// Returns the angular momentum of the system
711	>	Vector3d Thermo::getAngularMomentum(){
712	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
713
714	<	info->integrableObjects[vd]->getVel(aVel);
715	<
716	<	for (j=0; j < 3; j++)
717	<	aVel[j] -= vdrift[j];
714	>	if (!snap->hasCOMw) {
715	>
716	>	Vector3d com(0.0);
717	>	Vector3d comVel(0.0);
718	>	Vector3d angularMomentum(0.0);
719	>
720	>	getComAll(com, comVel);
721	>
722	>	SimInfo::MoleculeIterator i;
723	>	Molecule* mol;
724	>
725	>	Vector3d thisr(0.0);
726	>	Vector3d thisp(0.0);
727	>
728	>	RealType thisMass;
729	>
730	>	for (mol = info_->beginMolecule(i); mol != NULL;
731	>	mol = info_->nextMolecule(i)) {
732	>	thisMass = mol->getMass();
733	>	thisr = mol->getCom() - com;
734	>	thisp = (mol->getComVel() - comVel) * thisMass;
735
736	<	info->integrableObjects[vd]->setVel( aVel );
736	>	angularMomentum += cross( thisr, thisp );
737	>	}
738	>
739	>	#ifdef IS_MPI
740	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
741	>	angularMomentum.getArrayPointer(), 3,
742	>	MPI::REALTYPE, MPI::SUM);
743	>	#endif
744	>
745	>	snap->setCOMw(angularMomentum);
746	>	}
747	>
748	>	return snap->getCOMw();
749		}
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;
750
751	<	for(vd = 0; vd < nobj; vd++){
751	>
752	>	/**
753	>	* Returns the Volume of the system based on a ellipsoid with
754	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
755	>	* where R_i are related to the principle inertia moments
756	>	*  R_i = sqrt(C*I_i/N), this reduces to
757	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
758	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
759	>	*/
760	>	RealType Thermo::getGyrationalVolume(){
761	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
762
763	<	amass = info->integrableObjects[vd]->getMass();
764	<	info->integrableObjects[vd]->getVel( aVel );
763	>	if (!snap->hasGyrationalVolume) {
764	>
765	>	Mat3x3d intTensor;
766	>	RealType det;
767	>	Vector3d dummyAngMom;
768	>	RealType sysconstants;
769	>	RealType geomCnst;
770	>	RealType volume;
771	>
772	>	geomCnst = 3.0/2.0;
773	>	/* Get the inertial tensor and angular momentum for free*/
774	>	getInertiaTensor(intTensor, dummyAngMom);
775	>
776	>	det = intTensor.determinant();
777	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
778	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
779
780	<	for(j = 0; j < 3; j++)
781	<	vdrift_local[j] += aVel[j] * amass;
782	<
369	<	mtot_local += amass;
780	>	snap->setGyrationalVolume(volume);
781	>	}
782	>	return snap->getGyrationalVolume();
783		}
784	+
785	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
786	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
787
788	<	#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
788	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
789
790	<	for (vd = 0; vd < 3; vd++) {
791	<	vdrift[vd] = vdrift[vd] / mtot;
790	>	Mat3x3d intTensor;
791	>	Vector3d dummyAngMom;
792	>	RealType sysconstants;
793	>	RealType geomCnst;
794	>
795	>	geomCnst = 3.0/2.0;
796	>	/* Get the inertia tensor and angular momentum for free*/
797	>	this->getInertiaTensor(intTensor, dummyAngMom);
798	>
799	>	detI = intTensor.determinant();
800	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
801	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
802	>	snap->setGyrationalVolume(volume);
803	>	} else {
804	>	volume = snap->getGyrationalVolume();
805	>	detI = snap->getInertiaTensor().determinant();
806	>	}
807	>	return;
808		}
809
810	<	}
810	>	RealType Thermo::getTaggedAtomPairDistance(){
811	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
812	>	Globals* simParams = info_->getSimParams();
813	>
814	>	if (simParams->haveTaggedAtomPair() &&
815	>	simParams->havePrintTaggedPairDistance()) {
816	>	if ( simParams->getPrintTaggedPairDistance()) {
817	>
818	>	pair<int, int> tap = simParams->getTaggedAtomPair();
819	>	Vector3d pos1, pos2, rab;
820	>
821	>	#ifdef IS_MPI
822	>	int mol1 = info_->getGlobalMolMembership(tap.first);
823	>	int mol2 = info_->getGlobalMolMembership(tap.second);
824
825	<	void Thermo::getCOM(double COM[3]){
825	>	int proc1 = info_->getMolToProc(mol1);
826	>	int proc2 = info_->getMolToProc(mol2);
827
828	<	double mtot, mtot_local;
829	<	double aPos[3], amass;
830	<	double COM_local[3];
831	<	int i, j;
832	<	int nobj;
828	>	RealType data[3];
829	>	if (proc1 == worldRank) {
830	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
831	>	pos1 = sd1->getPos();
832	>	data[0] = pos1.x();
833	>	data[1] = pos1.y();
834	>	data[2] = pos1.z();
835	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
836	>	} else {
837	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
838	>	pos1 = Vector3d(data);
839	>	}
840
841	<	mtot_local = 0.0;
842	<	COM_local[0] = 0.0;
843	<	COM_local[1] = 0.0;
844	<	COM_local[2] = 0.0;
841	>	if (proc2 == worldRank) {
842	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
843	>	pos2 = sd2->getPos();
844	>	data[0] = pos2.x();
845	>	data[1] = pos2.y();
846	>	data[2] = pos2.z();
847	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
848	>	} else {
849	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
850	>	pos2 = Vector3d(data);
851	>	}
852	>	#else
853	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
854	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
855	>	pos1 = at1->getPos();
856	>	pos2 = at2->getPos();
857	>	#endif
858	>	rab = pos2 - pos1;
859	>	currSnapshot->wrapVector(rab);
860	>	return rab.length();
861	>	}
862	>	return 0.0;
863	>	}
864	>	return 0.0;
865	>	}
866
867	<	nobj = info->integrableObjects.size();
868	<	for(i = 0; i < nobj; i++){
403	<
404	<	amass = info->integrableObjects[i]->getMass();
405	<	info->integrableObjects[i]->getPos( aPos );
867	>	RealType Thermo::getHullVolume(){
868	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
869
870	<	for(j = 0; j < 3; j++)
871	<	COM_local[j] += aPos[j] * amass;
872	<
410	<	mtot_local += amass;
411	<	}
870	>	#ifdef HAVE_QHULL
871	>	if (!snap->hasHullVolume) {
872	>	Hull* surfaceMesh_;
873
874	<	#ifdef IS_MPI
875	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
876	<	MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
874	>	Globals* simParams = info_->getSimParams();
875	>	const std::string ht = simParams->getHULL_Method();
876	>
877	>	if (ht == "Convex") {
878	>	surfaceMesh_ = new ConvexHull();
879	>	} else if (ht == "AlphaShape") {
880	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
881	>	} else {
882	>	return 0.0;
883	>	}
884	>
885	>	// Build a vector of stunt doubles to determine if they are
886	>	// surface atoms
887	>	std::vector<StuntDouble*> localSites_;
888	>	Molecule* mol;
889	>	StuntDouble* sd;
890	>	SimInfo::MoleculeIterator i;
891	>	Molecule::IntegrableObjectIterator  j;
892	>
893	>	for (mol = info_->beginMolecule(i); mol != NULL;
894	>	mol = info_->nextMolecule(i)) {
895	>	for (sd = mol->beginIntegrableObject(j);
896	>	sd != NULL;
897	>	sd = mol->nextIntegrableObject(j)) {
898	>	localSites_.push_back(sd);
899	>	}
900	>	}
901	>
902	>	// Compute surface Mesh
903	>	surfaceMesh_->computeHull(localSites_);
904	>	snap->setHullVolume(surfaceMesh_->getVolume());
905	>	}
906	>	return snap->getHullVolume();
907		#else
908	<	mtot = mtot_local;
418	<	for(i = 0; i < 3; i++) {
419	<	COM[i] = COM_local[i];
420	<	}
908	>	return 0.0;
909		#endif
422	–
423	–	for (i = 0; i < 3; i++) {
424	–	COM[i] = COM[i] / mtot;
910		}
911		}
427	–
428	–	void Thermo::removeCOMdrift() {
429	–	double vdrift[3], aVel[3];
430	–	int vd, j, nobj;
431	–
432	–	nobj = info->integrableObjects.size();
433	–
434	–	// Get the Center of Mass drift velocity.
435	–
436	–	getCOMVel(vdrift);
437	–
438	–	//  Corrects for the center of mass drift.
439	–	// sums all the momentum and divides by total mass.
440	–
441	–	for(vd = 0; vd < nobj; vd++){
442	–
443	–	info->integrableObjects[vd]->getVel(aVel);
444	–
445	–	for (j=0; j < 3; j++)
446	–	aVel[j] -= vdrift[j];
447	–
448	–	info->integrableObjects[vd]->setVel( aVel );
449	–	}
450	–	}

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 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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