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

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trunk/src/brains/Thermo.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1787 by gezelter, Wed Aug 29 18:13:11 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 "Thermo.hpp"
51	<	#include "SRI.hpp"
52	<	#include "Integrator.hpp"
53	<	#include "simError.h"
54	<	#include "MatVec3.h"
50	>	#include "brains/Thermo.hpp"
51	>	#include "primitives/Molecule.hpp"
52	>	#include "utils/simError.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 "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	>	if (atom->isDipole()) {
376	>	dipoleVector += atom->getDipole() * debyeToCm;
377	>	}
378	>	}
379	>	}
380	>
381	>
382	>	#ifdef IS_MPI
383	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
384	>	MPI::SUM);
385	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
386	>	MPI::SUM);
387
388	<	return pressureY;
389	<	}
388	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
389	>	MPI::SUM);
390	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
391	>	MPI::SUM);
392
393	<	double Thermo::getPressureZ() {
393	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
394	>	MPI::REALTYPE, MPI::SUM);
395	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
396	>	MPI::REALTYPE, MPI::SUM);
397
398	<	// Relies on the calculation of the full molecular pressure tensor
399	<
400	<	const double p_convert = 1.63882576e8;
401	<	double press[3][3];
402	<	double pressureZ;
398	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
399	>	3, MPI::REALTYPE, MPI::SUM);
400	>	#endif
401	>
402	>	// first load the accumulated dipole moment (if dipoles were present)
403	>	Vector3d boxDipole = dipoleVector;
404	>	// now include the dipole moment due to charges
405	>	// use the lesser of the positive and negative charge totals
406	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
407	>
408	>	// find the average positions
409	>	if (pCount > 0 && nCount > 0 ) {
410	>	pPos /= pCount;
411	>	nPos /= nCount;
412	>	}
413	>
414	>	// dipole is from the negative to the positive (physics notation)
415	>	boxDipole += (pPos - nPos) * chg_value;
416	>	snap->setSystemDipole(boxDipole);
417	>	}
418
419	<	this->getPressureTensor(press);
419	>	return snap->getSystemDipole();
420	>	}
421
422	<	pressureZ = p_convert * press[2][2];
422	>	// Returns the Heat Flux Vector for the system
423	>	Vector3d Thermo::getHeatFlux(){
424	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
425	>	SimInfo::MoleculeIterator miter;
426	>	vector<StuntDouble*>::iterator iiter;
427	>	Molecule* mol;
428	>	StuntDouble* sd;
429	>	RigidBody::AtomIterator ai;
430	>	Atom* atom;
431	>	Vector3d vel;
432	>	Vector3d angMom;
433	>	Mat3x3d I;
434	>	int i;
435	>	int j;
436	>	int k;
437	>	RealType mass;
438
439	<	return pressureZ;
440	<	}
439	>	Vector3d x_a;
440	>	RealType kinetic;
441	>	RealType potential;
442	>	RealType eatom;
443	>	RealType AvgE_a_ = 0;
444	>	// Convective portion of the heat flux
445	>	Vector3d heatFluxJc = V3Zero;
446
447	+	/* Calculate convective portion of the heat flux */
448	+	for (mol = info_->beginMolecule(miter); mol != NULL;
449	+	mol = info_->nextMolecule(miter)) {
450	+
451	+	for (sd = mol->beginIntegrableObject(iiter);
452	+	sd != NULL;
453	+	sd = mol->nextIntegrableObject(iiter)) {
454	+
455	+	mass = sd->getMass();
456	+	vel = sd->getVel();
457
458	<	void Thermo::getPressureTensor(double press[3][3]){
459	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
460	<	// routine derived via viral theorem description in:
461	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
458	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
459	>
460	>	if (sd->isDirectional()) {
461	>	angMom = sd->getJ();
462	>	I = sd->getI();
463
464	<	const double e_convert = 4.184e-4;
464	>	if (sd->isLinear()) {
465	>	i = sd->linearAxis();
466	>	j = (i + 1) % 3;
467	>	k = (i + 2) % 3;
468	>	kinetic += angMom[j] * angMom[j] / I(j, j)
469	>	+ angMom[k] * angMom[k] / I(k, k);
470	>	} else {
471	>	kinetic += angMom[0]*angMom[0]/I(0, 0)
472	>	+ angMom[1]*angMom[1]/I(1, 1)
473	>	+ angMom[2]*angMom[2]/I(2, 2);
474	>	}
475	>	}
476
477	<	double molmass, volume;
203	<	double vcom[3];
204	<	double p_local[9], p_global[9];
205	<	int i, j, k;
477	>	potential = 0.0;
478
479	<	for (i=0; i < 9; i++) {
480	<	p_local[i] = 0.0;
481	<	p_global[i] = 0.0;
479	>	if (sd->isRigidBody()) {
480	>	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
481	>	for (atom = rb->beginAtom(ai); atom != NULL;
482	>	atom = rb->nextAtom(ai)) {
483	>	potential +=  atom->getParticlePot();
484	>	}
485	>	} else {
486	>	potential = sd->getParticlePot();
487	>	}
488	>
489	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
490	>	// The potential may not be a 1/2 factor
491	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
492	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
493	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
494	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
495	>	}
496	>	}
497	>
498	>	/* The J_v vector is reduced in the forceManager so everyone has
499	>	*  the global Jv. Jc is computed over the local atoms and must be
500	>	*  reduced among all processors.
501	>	*/
502	>	#ifdef IS_MPI
503	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
504	>	MPI::SUM);
505	>	#endif
506	>
507	>	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
508	>
509	>	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
510	>	PhysicalConstants::energyConvert;
511	>
512	>	// Correct for the fact the flux is 1/V (Jc + Jv)
513	>	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
514		}
515
212	–	// use velocities of integrableObjects and their masses:
516
517	<	for (i=0; i < info->integrableObjects.size(); i++) {
517	>	Vector3d Thermo::getComVel(){
518	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
519
520	<	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]);
520	>	if (!snap->hasCOMvel) {
521
522	<	}
523	<
524	<	// Get total for entire system from MPI.
525	<
522	>	SimInfo::MoleculeIterator i;
523	>	Molecule* mol;
524	>
525	>	Vector3d comVel(0.0);
526	>	RealType totalMass(0.0);
527	>
528	>	for (mol = info_->beginMolecule(i); mol != NULL;
529	>	mol = info_->nextMolecule(i)) {
530	>	RealType mass = mol->getMass();
531	>	totalMass += mass;
532	>	comVel += mass * mol->getComVel();
533	>	}
534	>
535		#ifdef IS_MPI
536	<	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
537	<	#else
538	<	for (i=0; i<9; i++) {
539	<	p_global[i] = p_local[i];
536	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
537	>	MPI::SUM);
538	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
539	>	MPI::REALTYPE, MPI::SUM);
540	>	#endif
541	>
542	>	comVel /= totalMass;
543	>	snap->setCOMvel(comVel);
544	>	}
545	>	return snap->getCOMvel();
546		}
240	–	#endif // is_mpi
547
548	<	volume = this->getVolume();
548	>	Vector3d Thermo::getCom(){
549	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
550
551	<
552	<
553	<	for(i = 0; i < 3; i++) {
554	<	for (j = 0; j < 3; j++) {
555	<	k = 3*i + j;
556	<	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
551	>	if (!snap->hasCOM) {
552	>
553	>	SimInfo::MoleculeIterator i;
554	>	Molecule* mol;
555	>
556	>	Vector3d com(0.0);
557	>	RealType totalMass(0.0);
558	>
559	>	for (mol = info_->beginMolecule(i); mol != NULL;
560	>	mol = info_->nextMolecule(i)) {
561	>	RealType mass = mol->getMass();
562	>	totalMass += mass;
563	>	com += mass * mol->getCom();
564	>	}
565	>
566	>	#ifdef IS_MPI
567	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
568	>	MPI::SUM);
569	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
570	>	MPI::REALTYPE, MPI::SUM);
571	>	#endif
572	>
573	>	com /= totalMass;
574	>	snap->setCOM(com);
575		}
576	<	}
577	<	}
576	>	return snap->getCOM();
577	>	}
578
579	<	void Thermo::velocitize() {
580	<
581	<	double aVel[3], aJ[3], I[3][3];
582	<	int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
583	<	double vdrift[3];
584	<	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;
579	>	/**
580	>	* Returns center of mass and center of mass velocity in one
581	>	* function call.
582	>	*/
583	>	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
584	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
585
586	<	if (!info->have_target_temp) {
587	<	sprintf( painCave.errMsg,
588	<	"You can't resample the velocities without a targetTemp!\n"
589	<	);
590	<	painCave.isFatal = 1;
591	<	painCave.severity = OOPSE_ERROR;
592	<	simError();
586	>	if (!(snap->hasCOM && snap->hasCOMvel)) {
587	>
588	>	SimInfo::MoleculeIterator i;
589	>	Molecule* mol;
590	>
591	>	RealType totalMass(0.0);
592	>
593	>	com = 0.0;
594	>	comVel = 0.0;
595	>
596	>	for (mol = info_->beginMolecule(i); mol != NULL;
597	>	mol = info_->nextMolecule(i)) {
598	>	RealType mass = mol->getMass();
599	>	totalMass += mass;
600	>	com += mass * mol->getCom();
601	>	comVel += mass * mol->getComVel();
602	>	}
603	>
604	>	#ifdef IS_MPI
605	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
606	>	MPI::SUM);
607	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
608	>	MPI::REALTYPE, MPI::SUM);
609	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
610	>	MPI::REALTYPE, MPI::SUM);
611	>	#endif
612	>
613	>	com /= totalMass;
614	>	comVel /= totalMass;
615	>	snap->setCOM(com);
616	>	snap->setCOMvel(comVel);
617	>	}
618	>	com = snap->getCOM();
619	>	comVel = snap->getCOMvel();
620		return;
621	<	}
621	>	}
622	>
623	>	/**
624	>	* Return intertia tensor for entire system and angular momentum
625	>	* Vector.
626	>	*
627	>	*
628	>	*
629	>	*    [  Ixx -Ixy  -Ixz ]
630	>	* I =| -Iyx  Iyy  -Iyz |
631	>	*    [ -Izx -Iyz   Izz ]
632	>	*/
633	>	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
634	>	Vector3d &angularMomentum){
635
636	<	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++){
636	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
637
638	<	// uses equipartition theory to solve for vbar in angstrom/fs
639	<
640	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
641	<	vbar = sqrt( av2 );
642	<
643	<	// picks random velocities from a gaussian distribution
644	<	// centered on vbar
645	<
646	<	for (j=0; j<3; j++)
647	<	aVel[j] = vbar * gaussStream->getGaussian();
648	<
649	<	info->integrableObjects[vr]->setVel( aVel );
650	<
651	<	if(info->integrableObjects[vr]->isDirectional()){
652	<
653	<	info->integrableObjects[vr]->getI( I );
654	<
655	<	if (info->integrableObjects[vr]->isLinear()) {
656	<
657	<	l= info->integrableObjects[vr]->linearAxis();
658	<	m = (l+1)%3;
659	<	n = (l+2)%3;
660	<
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();
638	>	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
639	>
640	>	RealType xx = 0.0;
641	>	RealType yy = 0.0;
642	>	RealType zz = 0.0;
643	>	RealType xy = 0.0;
644	>	RealType xz = 0.0;
645	>	RealType yz = 0.0;
646	>	Vector3d com(0.0);
647	>	Vector3d comVel(0.0);
648	>
649	>	getComAll(com, comVel);
650	>
651	>	SimInfo::MoleculeIterator i;
652	>	Molecule* mol;
653	>
654	>	Vector3d thisq(0.0);
655	>	Vector3d thisv(0.0);
656	>
657	>	RealType thisMass = 0.0;
658	>
659	>	for (mol = info_->beginMolecule(i); mol != NULL;
660	>	mol = info_->nextMolecule(i)) {
661
662	<	} else {
663	<	for (j = 0 ; j < 3; j++) {
664	<	vbar = sqrt( 2.0 * kebar * I[j][j] );
665	<	aJ[j] = vbar * gaussStream->getGaussian();
666	<	}
667	<	} // else isLinear
668	<
669	<	info->integrableObjects[vr]->setJ( aJ );
662	>	thisq = mol->getCom()-com;
663	>	thisv = mol->getComVel()-comVel;
664	>	thisMass = mol->getMass();
665	>	// Compute moment of intertia coefficients.
666	>	xx += thisq[0]*thisq[0]*thisMass;
667	>	yy += thisq[1]*thisq[1]*thisMass;
668	>	zz += thisq[2]*thisq[2]*thisMass;
669	>
670	>	// compute products of intertia
671	>	xy += thisq[0]*thisq[1]*thisMass;
672	>	xz += thisq[0]*thisq[2]*thisMass;
673	>	yz += thisq[1]*thisq[2]*thisMass;
674	>
675	>	angularMomentum += cross( thisq, thisv ) * thisMass;
676	>	}
677
678	<	}//isDirectional
679	<
678	>	inertiaTensor(0,0) = yy + zz;
679	>	inertiaTensor(0,1) = -xy;
680	>	inertiaTensor(0,2) = -xz;
681	>	inertiaTensor(1,0) = -xy;
682	>	inertiaTensor(1,1) = xx + zz;
683	>	inertiaTensor(1,2) = -yz;
684	>	inertiaTensor(2,0) = -xz;
685	>	inertiaTensor(2,1) = -yz;
686	>	inertiaTensor(2,2) = xx + yy;
687	>
688	>	#ifdef IS_MPI
689	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
690	>	9, MPI::REALTYPE, MPI::SUM);
691	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
692	>	angularMomentum.getArrayPointer(), 3,
693	>	MPI::REALTYPE, MPI::SUM);
694	>	#endif
695	>
696	>	snap->setCOMw(angularMomentum);
697	>	snap->setInertiaTensor(inertiaTensor);
698	>	}
699	>
700	>	angularMomentum = snap->getCOMw();
701	>	inertiaTensor = snap->getInertiaTensor();
702	>
703	>	return;
704		}
705
706	<	// Get the Center of Mass drift velocity.
707	<
708	<	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++){
706	>	// Returns the angular momentum of the system
707	>	Vector3d Thermo::getAngularMomentum(){
708	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
709
710	<	info->integrableObjects[vd]->getVel(aVel);
711	<
712	<	for (j=0; j < 3; j++)
713	<	aVel[j] -= vdrift[j];
710	>	if (!snap->hasCOMw) {
711	>
712	>	Vector3d com(0.0);
713	>	Vector3d comVel(0.0);
714	>	Vector3d angularMomentum(0.0);
715	>
716	>	getComAll(com, comVel);
717	>
718	>	SimInfo::MoleculeIterator i;
719	>	Molecule* mol;
720	>
721	>	Vector3d thisr(0.0);
722	>	Vector3d thisp(0.0);
723	>
724	>	RealType thisMass;
725	>
726	>	for (mol = info_->beginMolecule(i); mol != NULL;
727	>	mol = info_->nextMolecule(i)) {
728	>	thisMass = mol->getMass();
729	>	thisr = mol->getCom() - com;
730	>	thisp = (mol->getComVel() - comVel) * thisMass;
731
732	<	info->integrableObjects[vd]->setVel( aVel );
732	>	angularMomentum += cross( thisr, thisp );
733	>	}
734	>
735	>	#ifdef IS_MPI
736	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
737	>	angularMomentum.getArrayPointer(), 3,
738	>	MPI::REALTYPE, MPI::SUM);
739	>	#endif
740	>
741	>	snap->setCOMw(angularMomentum);
742	>	}
743	>
744	>	return snap->getCOMw();
745		}
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;
746
747	<	for(vd = 0; vd < nobj; vd++){
747	>
748	>	/**
749	>	* Returns the Volume of the system based on a ellipsoid with
750	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
751	>	* where R_i are related to the principle inertia moments
752	>	*  R_i = sqrt(C*I_i/N), this reduces to
753	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
754	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
755	>	*/
756	>	RealType Thermo::getGyrationalVolume(){
757	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
758
759	<	amass = info->integrableObjects[vd]->getMass();
760	<	info->integrableObjects[vd]->getVel( aVel );
759	>	if (!snap->hasGyrationalVolume) {
760	>
761	>	Mat3x3d intTensor;
762	>	RealType det;
763	>	Vector3d dummyAngMom;
764	>	RealType sysconstants;
765	>	RealType geomCnst;
766	>	RealType volume;
767	>
768	>	geomCnst = 3.0/2.0;
769	>	/* Get the inertial tensor and angular momentum for free*/
770	>	getInertiaTensor(intTensor, dummyAngMom);
771	>
772	>	det = intTensor.determinant();
773	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
774	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
775
776	<	for(j = 0; j < 3; j++)
777	<	vdrift_local[j] += aVel[j] * amass;
778	<
369	<	mtot_local += amass;
776	>	snap->setGyrationalVolume(volume);
777	>	}
778	>	return snap->getGyrationalVolume();
779		}
780	+
781	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
782	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
783
784	<	#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
784	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
785
786	<	for (vd = 0; vd < 3; vd++) {
787	<	vdrift[vd] = vdrift[vd] / mtot;
786	>	Mat3x3d intTensor;
787	>	Vector3d dummyAngMom;
788	>	RealType sysconstants;
789	>	RealType geomCnst;
790	>
791	>	geomCnst = 3.0/2.0;
792	>	/* Get the inertia tensor and angular momentum for free*/
793	>	this->getInertiaTensor(intTensor, dummyAngMom);
794	>
795	>	detI = intTensor.determinant();
796	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
797	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
798	>	snap->setGyrationalVolume(volume);
799	>	} else {
800	>	volume = snap->getGyrationalVolume();
801	>	detI = snap->getInertiaTensor().determinant();
802	>	}
803	>	return;
804		}
805
806	<	}
806	>	RealType Thermo::getTaggedAtomPairDistance(){
807	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
808	>	Globals* simParams = info_->getSimParams();
809	>
810	>	if (simParams->haveTaggedAtomPair() &&
811	>	simParams->havePrintTaggedPairDistance()) {
812	>	if ( simParams->getPrintTaggedPairDistance()) {
813	>
814	>	pair<int, int> tap = simParams->getTaggedAtomPair();
815	>	Vector3d pos1, pos2, rab;
816	>
817	>	#ifdef IS_MPI
818	>	int mol1 = info_->getGlobalMolMembership(tap.first);
819	>	int mol2 = info_->getGlobalMolMembership(tap.second);
820
821	<	void Thermo::getCOM(double COM[3]){
821	>	int proc1 = info_->getMolToProc(mol1);
822	>	int proc2 = info_->getMolToProc(mol2);
823
824	<	double mtot, mtot_local;
825	<	double aPos[3], amass;
826	<	double COM_local[3];
827	<	int i, j;
828	<	int nobj;
824	>	RealType data[3];
825	>	if (proc1 == worldRank) {
826	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
827	>	pos1 = sd1->getPos();
828	>	data[0] = pos1.x();
829	>	data[1] = pos1.y();
830	>	data[2] = pos1.z();
831	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
832	>	} else {
833	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
834	>	pos1 = Vector3d(data);
835	>	}
836
837	<	mtot_local = 0.0;
838	<	COM_local[0] = 0.0;
839	<	COM_local[1] = 0.0;
840	<	COM_local[2] = 0.0;
837	>	if (proc2 == worldRank) {
838	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
839	>	pos2 = sd2->getPos();
840	>	data[0] = pos2.x();
841	>	data[1] = pos2.y();
842	>	data[2] = pos2.z();
843	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
844	>	} else {
845	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
846	>	pos2 = Vector3d(data);
847	>	}
848	>	#else
849	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
850	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
851	>	pos1 = at1->getPos();
852	>	pos2 = at2->getPos();
853	>	#endif
854	>	rab = pos2 - pos1;
855	>	currSnapshot->wrapVector(rab);
856	>	return rab.length();
857	>	}
858	>	return 0.0;
859	>	}
860	>	return 0.0;
861	>	}
862
863	<	nobj = info->integrableObjects.size();
864	<	for(i = 0; i < nobj; i++){
403	<
404	<	amass = info->integrableObjects[i]->getMass();
405	<	info->integrableObjects[i]->getPos( aPos );
863	>	RealType Thermo::getHullVolume(){
864	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
865
866	<	for(j = 0; j < 3; j++)
867	<	COM_local[j] += aPos[j] * amass;
868	<
410	<	mtot_local += amass;
411	<	}
866	>	#ifdef HAVE_QHULL
867	>	if (!snap->hasHullVolume) {
868	>	Hull* surfaceMesh_;
869
870	<	#ifdef IS_MPI
871	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
872	<	MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
870	>	Globals* simParams = info_->getSimParams();
871	>	const std::string ht = simParams->getHULL_Method();
872	>
873	>	if (ht == "Convex") {
874	>	surfaceMesh_ = new ConvexHull();
875	>	} else if (ht == "AlphaShape") {
876	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
877	>	} else {
878	>	return 0.0;
879	>	}
880	>
881	>	// Build a vector of stunt doubles to determine if they are
882	>	// surface atoms
883	>	std::vector<StuntDouble*> localSites_;
884	>	Molecule* mol;
885	>	StuntDouble* sd;
886	>	SimInfo::MoleculeIterator i;
887	>	Molecule::IntegrableObjectIterator  j;
888	>
889	>	for (mol = info_->beginMolecule(i); mol != NULL;
890	>	mol = info_->nextMolecule(i)) {
891	>	for (sd = mol->beginIntegrableObject(j);
892	>	sd != NULL;
893	>	sd = mol->nextIntegrableObject(j)) {
894	>	localSites_.push_back(sd);
895	>	}
896	>	}
897	>
898	>	// Compute surface Mesh
899	>	surfaceMesh_->computeHull(localSites_);
900	>	snap->setHullVolume(surfaceMesh_->getVolume());
901	>	}
902	>	return snap->getHullVolume();
903		#else
904	<	mtot = mtot_local;
418	<	for(i = 0; i < 3; i++) {
419	<	COM[i] = COM_local[i];
420	<	}
904	>	return 0.0;
905		#endif
422	–
423	–	for (i = 0; i < 3; i++) {
424	–	COM[i] = COM[i] / mtot;
906		}
907		}
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 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

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