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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 1764 by gezelter, Tue Jul 3 18:32:27 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	>	#include "math/ConvexHull.hpp"
58	>	#include "math/AlphaHull.hpp"
59
60	<	#ifdef IS_MPI
61	<	#define __C
17	<	#include "brains/mpiSimulation.hpp"
18	<	#endif // is_mpi
60	>	using namespace std;
61	>	namespace OpenMD {
62
63	<	inline double roundMe( double x ){
64	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
22	<	}
63	>	RealType Thermo::getTranslationalKinetic() {
64	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
65
66	<	Thermo::Thermo( SimInfo* the_info ) {
67	<	info = the_info;
68	<	int baseSeed = the_info->getSeed();
69	<
70	<	gaussStream = new gaussianSPRNG( baseSeed );
71	<	}
66	>	if (!snap->hasTranslationalKineticEnergy) {
67	>	SimInfo::MoleculeIterator miter;
68	>	vector<StuntDouble*>::iterator iiter;
69	>	Molecule* mol;
70	>	StuntDouble* sd;
71	>	Vector3d vel;
72	>	RealType mass;
73	>	RealType kinetic(0.0);
74	>
75	>	for (mol = info_->beginMolecule(miter); mol != NULL;
76	>	mol = info_->nextMolecule(miter)) {
77	>
78	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
79	>	sd = mol->nextIntegrableObject(iiter)) {
80	>
81	>	mass = sd->getMass();
82	>	vel = sd->getVel();
83	>
84	>	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
85	>
86	>	}
87	>	}
88	>
89	>	#ifdef IS_MPI
90	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
91	>	MPI::SUM);
92	>	#endif
93	>
94	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
95	>
96	>
97	>	snap->setTranslationalKineticEnergy(kinetic);
98	>	}
99	>	return snap->getTranslationalKineticEnergy();
100	>	}
101
102	<	Thermo::~Thermo(){
103	<	delete gaussStream;
33	<	}
102	>	RealType Thermo::getRotationalKinetic() {
103	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
104
105	<	double Thermo::getKinetic(){
106	<
107	<	const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
108	<	double kinetic;
109	<	double amass;
110	<	double aVel[3], aJ[3], I[3][3];
111	<	int i, j, k, kl;
112	<
113	<	double kinetic_global;
114	<	vector<StuntDouble *> integrableObjects = info->integrableObjects;
115	<
116	<	kinetic = 0.0;
117	<	kinetic_global = 0.0;
118	<
119	<	for (kl=0; kl<integrableObjects.size(); kl++) {
120	<	integrableObjects[kl]->getVel(aVel);
121	<	amass = integrableObjects[kl]->getMass();
122	<
123	<	for(j=0; j<3; j++)
124	<	kinetic += amass*aVel[j]*aVel[j];
125	<
126	<	if (integrableObjects[kl]->isDirectional()){
127	<
128	<	integrableObjects[kl]->getJ( aJ );
129	<	integrableObjects[kl]->getI( I );
130	<
131	<	if (integrableObjects[kl]->isLinear()) {
132	<	i = integrableObjects[kl]->linearAxis();
133	<	j = (i+1)%3;
134	<	k = (i+2)%3;
135	<	kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
136	<	} else {
137	<	for (j=0; j<3; j++)
68	<	kinetic += aJ[j]*aJ[j] / I[j][j];
105	>	if (!snap->hasRotationalKineticEnergy) {
106	>	SimInfo::MoleculeIterator miter;
107	>	vector<StuntDouble*>::iterator iiter;
108	>	Molecule* mol;
109	>	StuntDouble* sd;
110	>	Vector3d angMom;
111	>	Mat3x3d I;
112	>	int i, j, k;
113	>	RealType kinetic(0.0);
114	>
115	>	for (mol = info_->beginMolecule(miter); mol != NULL;
116	>	mol = info_->nextMolecule(miter)) {
117	>
118	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
119	>	sd = mol->nextIntegrableObject(iiter)) {
120	>
121	>	if (sd->isDirectional()) {
122	>	angMom = sd->getJ();
123	>	I = sd->getI();
124	>
125	>	if (sd->isLinear()) {
126	>	i = sd->linearAxis();
127	>	j = (i + 1) % 3;
128	>	k = (i + 2) % 3;
129	>	kinetic += angMom[j] * angMom[j] / I(j, j)
130	>	+ angMom[k] * angMom[k] / I(k, k);
131	>	} else {
132	>	kinetic += angMom[0]*angMom[0]/I(0, 0)
133	>	+ angMom[1]*angMom[1]/I(1, 1)
134	>	+ angMom[2]*angMom[2]/I(2, 2);
135	>	}
136	>	}
137	>	}
138		}
139	<	}
71	<	}
139	>
140		#ifdef IS_MPI
141	<	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
142	<	MPI_SUM, MPI_COMM_WORLD);
143	<	kinetic = kinetic_global;
144	<	#endif //is_mpi
145	<
146	<	kinetic = kinetic * 0.5 / e_convert;
141	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
142	>	MPI::SUM);
143	>	#endif
144	>
145	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
146	>
147	>	snap->setRotationalKineticEnergy(kinetic);
148	>	}
149	>	return snap->getRotationalKineticEnergy();
150	>	}
151
152	<	return kinetic;
81	<	}
152	>
153
154	<	double Thermo::getPotential(){
155	<
85	<	double potential_local;
86	<	double potential;
87	<	int el, nSRI;
88	<	Molecule* molecules;
154	>	RealType Thermo::getKinetic() {
155	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
156
157	<	molecules = info->molecules;
158	<	nSRI = info->n_SRI;
159	<
160	<	potential_local = 0.0;
161	<	potential = 0.0;
95	<	potential_local += info->lrPot;
96	<
97	<	for( el=0; el<info->n_mol; el++ ){
98	<	potential_local += molecules[el].getPotential();
157	>	if (!snap->hasKineticEnergy) {
158	>	RealType ke = getTranslationalKinetic() + getRotationalKinetic();
159	>	snap->setKineticEnergy(ke);
160	>	}
161	>	return snap->getKineticEnergy();
162		}
163
164	<	// 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
164	>	RealType Thermo::getPotential() {
165
166	<	return potential;
167	<	}
166	>	// ForceManager computes the potential and stores it in the
167	>	// Snapshot.  All we have to do is report it.
168
169	<	double Thermo::getTotalE(){
169	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
170	>	return snap->getPotentialEnergy();
171	>	}
172
173	<	double total;
173	>	RealType Thermo::getTotalEnergy() {
174
175	<	total = this->getKinetic() + this->getPotential();
117	<	return total;
118	<	}
175	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
176
177	<	double Thermo::getTemperature(){
177	>	if (!snap->hasTotalEnergy) {
178	>	snap->setTotalEnergy(this->getKinetic() + this->getPotential());
179	>	}
180
181	<	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
182	<	double temperature;
181	>	return snap->getTotalEnergy();
182	>	}
183
184	<	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126	<	return temperature;
127	<	}
184	>	RealType Thermo::getTemperature() {
185
186	<	double Thermo::getVolume() {
186	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
187
188	<	return info->boxVol;
132	<	}
188	>	if (!snap->hasTemperature) {
189
190	<	double Thermo::getPressure() {
190	>	RealType temperature = ( 2.0 * this->getKinetic() )
191	>	/ (info_->getNdf()* PhysicalConstants::kb );
192
193	<	// Relies on the calculation of the full molecular pressure tensor
194	<
195	<	const double p_convert = 1.63882576e8;
196	<	double press[3][3];
197	<	double pressure;
193	>	snap->setTemperature(temperature);
194	>	}
195	>
196	>	return snap->getTemperature();
197	>	}
198
199	<	this->getPressureTensor(press);
199	>	RealType Thermo::getElectronicTemperature() {
200	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
201
202	<	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
202	>	if (!snap->hasElectronicTemperature) {
203	>
204	>	SimInfo::MoleculeIterator miter;
205	>	vector<Atom*>::iterator iiter;
206	>	Molecule* mol;
207	>	Atom* atom;
208	>	RealType cvel;
209	>	RealType cmass;
210	>	RealType kinetic(0.0);
211	>	RealType eTemp;
212	>
213	>	for (mol = info_->beginMolecule(miter); mol != NULL;
214	>	mol = info_->nextMolecule(miter)) {
215	>
216	>	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
217	>	atom = mol->nextFluctuatingCharge(iiter)) {
218	>
219	>	cmass = atom->getChargeMass();
220	>	cvel = atom->getFlucQVel();
221	>
222	>	kinetic += cmass * cvel * cvel;
223	>
224	>	}
225	>	}
226	>
227	>	#ifdef IS_MPI
228	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
229	>	MPI::SUM);
230	>	#endif
231
232	<	return pressure;
233	<	}
232	>	kinetic *= 0.5;
233	>	eTemp =  (2.0 * kinetic) /
234	>	(info_->getNFluctuatingCharges() * PhysicalConstants::kb );
235	>
236	>	snap->setElectronicTemperature(eTemp);
237	>	}
238
239	<	double Thermo::getPressureX() {
239	>	return snap->getElectronicTemperature();
240	>	}
241
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;
242
243	<	this->getPressureTensor(press);
243	>	RealType Thermo::getVolume() {
244	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
245	>	return snap->getVolume();
246	>	}
247
248	<	pressureX = p_convert * press[0][0];
248	>	RealType Thermo::getPressure() {
249	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
250
251	<	return pressureX;
252	<	}
251	>	if (!snap->hasPressure) {
252	>	// Relies on the calculation of the full molecular pressure tensor
253	>
254	>	Mat3x3d tensor;
255	>	RealType pressure;
256	>
257	>	tensor = getPressureTensor();
258	>
259	>	pressure = PhysicalConstants::pressureConvert *
260	>	(tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
261	>
262	>	snap->setPressure(pressure);
263	>	}
264	>
265	>	return snap->getPressure();
266	>	}
267
268	<	double Thermo::getPressureY() {
268	>	Mat3x3d Thermo::getPressureTensor() {
269	>	// returns pressure tensor in units amu*fs^-2*Ang^-1
270	>	// routine derived via viral theorem description in:
271	>	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
272	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
273
274	<	// 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;
274	>	if (!snap->hasPressureTensor) {
275
276	<	this->getPressureTensor(press);
276	>	Mat3x3d pressureTensor;
277	>	Mat3x3d p_tens(0.0);
278	>	RealType mass;
279	>	Vector3d vcom;
280	>
281	>	SimInfo::MoleculeIterator i;
282	>	vector<StuntDouble*>::iterator j;
283	>	Molecule* mol;
284	>	StuntDouble* sd;
285	>	for (mol = info_->beginMolecule(i); mol != NULL;
286	>	mol = info_->nextMolecule(i)) {
287	>
288	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
289	>	sd = mol->nextIntegrableObject(j)) {
290	>
291	>	mass = sd->getMass();
292	>	vcom = sd->getVel();
293	>	p_tens += mass * outProduct(vcom, vcom);
294	>	}
295	>	}
296	>
297	>	#ifdef IS_MPI
298	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, p_tens.getArrayPointer(), 9,
299	>	MPI::REALTYPE, MPI::SUM);
300	>	#endif
301	>
302	>	RealType volume = this->getVolume();
303	>	Mat3x3d stressTensor = snap->getStressTensor();
304	>
305	>	pressureTensor =  (p_tens +
306	>	PhysicalConstants::energyConvert * stressTensor)/volume;
307	>
308	>	snap->setPressureTensor(pressureTensor);
309	>	}
310	>	return snap->getPressureTensor();
311	>	}
312
174	–	pressureY = p_convert * press[1][1];
313
176	–	return pressureY;
177	–	}
314
179	–	double Thermo::getPressureZ() {
315
316	<	// Relies on the calculation of the full molecular pressure tensor
317	<
183	<	const double p_convert = 1.63882576e8;
184	<	double press[3][3];
185	<	double pressureZ;
316	>	Vector3d Thermo::getSystemDipole() {
317	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
318
319	<	this->getPressureTensor(press);
319	>	if (!snap->hasSystemDipole) {
320	>	SimInfo::MoleculeIterator miter;
321	>	vector<Atom*>::iterator aiter;
322	>	Molecule* mol;
323	>	Atom* atom;
324	>	RealType charge;
325	>	RealType moment(0.0);
326	>	Vector3d ri(0.0);
327	>	Vector3d dipoleVector(0.0);
328	>	Vector3d nPos(0.0);
329	>	Vector3d pPos(0.0);
330	>	RealType nChg(0.0);
331	>	RealType pChg(0.0);
332	>	int nCount = 0;
333	>	int pCount = 0;
334	>
335	>	RealType chargeToC = 1.60217733e-19;
336	>	RealType angstromToM = 1.0e-10;
337	>	RealType debyeToCm = 3.33564095198e-30;
338	>
339	>	for (mol = info_->beginMolecule(miter); mol != NULL;
340	>	mol = info_->nextMolecule(miter)) {
341	>
342	>	for (atom = mol->beginAtom(aiter); atom != NULL;
343	>	atom = mol->nextAtom(aiter)) {
344	>
345	>	charge = 0.0;
346	>
347	>	FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
348	>	if ( fca.isFixedCharge() ) {
349	>	charge = fca.getCharge();
350	>	}
351	>
352	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
353	>	if ( fqa.isFluctuatingCharge() ) {
354	>	charge += atom->getFlucQPos();
355	>	}
356	>
357	>	charge *= chargeToC;
358	>
359	>	ri = atom->getPos();
360	>	snap->wrapVector(ri);
361	>	ri *= angstromToM;
362	>
363	>	if (charge < 0.0) {
364	>	nPos += ri;
365	>	nChg -= charge;
366	>	nCount++;
367	>	} else if (charge > 0.0) {
368	>	pPos += ri;
369	>	pChg += charge;
370	>	pCount++;
371	>	}
372	>
373	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
374	>	if (ma.isDipole() ) {
375	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
376	>	moment = ma.getDipoleMoment();
377	>	moment *= debyeToCm;
378	>	dipoleVector += u_i * moment;
379	>	}
380	>	}
381	>	}
382	>
383	>
384	>	#ifdef IS_MPI
385	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
386	>	MPI::SUM);
387	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
388	>	MPI::SUM);
389
390	<	pressureZ = p_convert * press[2][2];
390	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
391	>	MPI::SUM);
392	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
393	>	MPI::SUM);
394
395	<	return pressureZ;
396	<	}
395	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
396	>	MPI::REALTYPE, MPI::SUM);
397	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
398	>	MPI::REALTYPE, MPI::SUM);
399
400	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
401	+	3, MPI::REALTYPE, MPI::SUM);
402	+	#endif
403	+
404	+	// first load the accumulated dipole moment (if dipoles were present)
405	+	Vector3d boxDipole = dipoleVector;
406	+	// now include the dipole moment due to charges
407	+	// use the lesser of the positive and negative charge totals
408	+	RealType chg_value = nChg <= pChg ? nChg : pChg;
409	+
410	+	// find the average positions
411	+	if (pCount > 0 && nCount > 0 ) {
412	+	pPos /= pCount;
413	+	nPos /= nCount;
414	+	}
415	+
416	+	// dipole is from the negative to the positive (physics notation)
417	+	boxDipole += (pPos - nPos) * chg_value;
418	+	snap->setSystemDipole(boxDipole);
419	+	}
420
421	<	void Thermo::getPressureTensor(double press[3][3]){
422	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
197	<	// routine derived via viral theorem description in:
198	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
421	>	return snap->getSystemDipole();
422	>	}
423
424	<	const double e_convert = 4.184e-4;
424	>	// Returns the Heat Flux Vector for the system
425	>	Vector3d Thermo::getHeatFlux(){
426	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
427	>	SimInfo::MoleculeIterator miter;
428	>	vector<StuntDouble*>::iterator iiter;
429	>	Molecule* mol;
430	>	StuntDouble* sd;
431	>	RigidBody::AtomIterator ai;
432	>	Atom* atom;
433	>	Vector3d vel;
434	>	Vector3d angMom;
435	>	Mat3x3d I;
436	>	int i;
437	>	int j;
438	>	int k;
439	>	RealType mass;
440
441	<	double molmass, volume;
442	<	double vcom[3];
443	<	double p_local[9], p_global[9];
444	<	int i, j, k;
441	>	Vector3d x_a;
442	>	RealType kinetic;
443	>	RealType potential;
444	>	RealType eatom;
445	>	RealType AvgE_a_ = 0;
446	>	// Convective portion of the heat flux
447	>	Vector3d heatFluxJc = V3Zero;
448
449	<	for (i=0; i < 9; i++) {
450	<	p_local[i] = 0.0;
451	<	p_global[i] = 0.0;
452	<	}
449	>	/* Calculate convective portion of the heat flux */
450	>	for (mol = info_->beginMolecule(miter); mol != NULL;
451	>	mol = info_->nextMolecule(miter)) {
452	>
453	>	for (sd = mol->beginIntegrableObject(iiter);
454	>	sd != NULL;
455	>	sd = mol->nextIntegrableObject(iiter)) {
456	>
457	>	mass = sd->getMass();
458	>	vel = sd->getVel();
459
460	<	// use velocities of integrableObjects and their masses:
460	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
461	>
462	>	if (sd->isDirectional()) {
463	>	angMom = sd->getJ();
464	>	I = sd->getI();
465
466	<	for (i=0; i < info->integrableObjects.size(); i++) {
466	>	if (sd->isLinear()) {
467	>	i = sd->linearAxis();
468	>	j = (i + 1) % 3;
469	>	k = (i + 2) % 3;
470	>	kinetic += angMom[j] * angMom[j] / I(j, j)
471	>	+ angMom[k] * angMom[k] / I(k, k);
472	>	} else {
473	>	kinetic += angMom[0]*angMom[0]/I(0, 0)
474	>	+ angMom[1]*angMom[1]/I(1, 1)
475	>	+ angMom[2]*angMom[2]/I(2, 2);
476	>	}
477	>	}
478
479	<	molmass = info->integrableObjects[i]->getMass();
479	>	potential = 0.0;
480	>
481	>	if (sd->isRigidBody()) {
482	>	RigidBody* rb = dynamic_cast<RigidBody*>(sd);
483	>	for (atom = rb->beginAtom(ai); atom != NULL;
484	>	atom = rb->nextAtom(ai)) {
485	>	potential +=  atom->getParticlePot();
486	>	}
487	>	} else {
488	>	potential = sd->getParticlePot();
489	>	}
490	>
491	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
492	>	// The potential may not be a 1/2 factor
493	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
494	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
495	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
496	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
497	>	}
498	>	}
499	>
500	>	/* The J_v vector is reduced in the forceManager so everyone has
501	>	*  the global Jv. Jc is computed over the local atoms and must be
502	>	*  reduced among all processors.
503	>	*/
504	>	#ifdef IS_MPI
505	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
506	>	MPI::SUM);
507	>	#endif
508
509	<	info->integrableObjects[i]->getVel(vcom);
510	<
511	<	p_local[0] += molmass * (vcom[0] * vcom[0]);
512	<	p_local[1] += molmass * (vcom[0] * vcom[1]);
513	<	p_local[2] += molmass * (vcom[0] * vcom[2]);
514	<	p_local[3] += molmass * (vcom[1] * vcom[0]);
515	<	p_local[4] += molmass * (vcom[1] * vcom[1]);
516	<	p_local[5] += molmass * (vcom[1] * vcom[2]);
517	<	p_local[6] += molmass * (vcom[2] * vcom[0]);
518	<	p_local[7] += molmass * (vcom[2] * vcom[1]);
519	<	p_local[8] += molmass * (vcom[2] * vcom[2]);
520	<
521	<	}
522	<
523	<	// Get total for entire system from MPI.
524	<
509	>	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
510	>
511	>	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
512	>	PhysicalConstants::energyConvert;
513	>
514	>	// Correct for the fact the flux is 1/V (Jc + Jv)
515	>	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
516	>	}
517	>
518	>
519	>	Vector3d Thermo::getComVel(){
520	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
521	>
522	>	if (!snap->hasCOMvel) {
523	>
524	>	SimInfo::MoleculeIterator i;
525	>	Molecule* mol;
526	>
527	>	Vector3d comVel(0.0);
528	>	RealType totalMass(0.0);
529	>
530	>	for (mol = info_->beginMolecule(i); mol != NULL;
531	>	mol = info_->nextMolecule(i)) {
532	>	RealType mass = mol->getMass();
533	>	totalMass += mass;
534	>	comVel += mass * mol->getComVel();
535	>	}
536	>
537		#ifdef IS_MPI
538	<	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
539	<	#else
540	<	for (i=0; i<9; i++) {
541	<	p_global[i] = p_local[i];
538	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
539	>	MPI::SUM);
540	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
541	>	MPI::REALTYPE, MPI::SUM);
542	>	#endif
543	>
544	>	comVel /= totalMass;
545	>	snap->setCOMvel(comVel);
546	>	}
547	>	return snap->getCOMvel();
548		}
240	–	#endif // is_mpi
549
550	<	volume = this->getVolume();
550	>	Vector3d Thermo::getCom(){
551	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
552
553	<
554	<
555	<	for(i = 0; i < 3; i++) {
556	<	for (j = 0; j < 3; j++) {
557	<	k = 3*i + j;
558	<	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
553	>	if (!snap->hasCOM) {
554	>
555	>	SimInfo::MoleculeIterator i;
556	>	Molecule* mol;
557	>
558	>	Vector3d com(0.0);
559	>	RealType totalMass(0.0);
560	>
561	>	for (mol = info_->beginMolecule(i); mol != NULL;
562	>	mol = info_->nextMolecule(i)) {
563	>	RealType mass = mol->getMass();
564	>	totalMass += mass;
565	>	com += mass * mol->getCom();
566	>	}
567	>
568	>	#ifdef IS_MPI
569	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
570	>	MPI::SUM);
571	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
572	>	MPI::REALTYPE, MPI::SUM);
573	>	#endif
574	>
575	>	com /= totalMass;
576	>	snap->setCOM(com);
577		}
578	<	}
579	<	}
578	>	return snap->getCOM();
579	>	}
580
581	<	void Thermo::velocitize() {
582	<
583	<	double aVel[3], aJ[3], I[3][3];
584	<	int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
585	<	double vdrift[3];
586	<	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;
581	>	/**
582	>	* Returns center of mass and center of mass velocity in one
583	>	* function call.
584	>	*/
585	>	void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
586	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
587
588	<	if (!info->have_target_temp) {
589	<	sprintf( painCave.errMsg,
590	<	"You can't resample the velocities without a targetTemp!\n"
591	<	);
592	<	painCave.isFatal = 1;
593	<	painCave.severity = OOPSE_ERROR;
594	<	simError();
588	>	if (!(snap->hasCOM && snap->hasCOMvel)) {
589	>
590	>	SimInfo::MoleculeIterator i;
591	>	Molecule* mol;
592	>
593	>	RealType totalMass(0.0);
594	>
595	>	com = 0.0;
596	>	comVel = 0.0;
597	>
598	>	for (mol = info_->beginMolecule(i); mol != NULL;
599	>	mol = info_->nextMolecule(i)) {
600	>	RealType mass = mol->getMass();
601	>	totalMass += mass;
602	>	com += mass * mol->getCom();
603	>	comVel += mass * mol->getComVel();
604	>	}
605	>
606	>	#ifdef IS_MPI
607	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
608	>	MPI::SUM);
609	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
610	>	MPI::REALTYPE, MPI::SUM);
611	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
612	>	MPI::REALTYPE, MPI::SUM);
613	>	#endif
614	>
615	>	com /= totalMass;
616	>	comVel /= totalMass;
617	>	snap->setCOM(com);
618	>	snap->setCOMvel(comVel);
619	>	}
620	>	com = snap->getCOM();
621	>	comVel = snap->getCOMvel();
622		return;
623	<	}
623	>	}
624	>
625	>	/**
626	>	* Return intertia tensor for entire system and angular momentum
627	>	* Vector.
628	>	*
629	>	*
630	>	*
631	>	*    [  Ixx -Ixy  -Ixz ]
632	>	* I =| -Iyx  Iyy  -Iyz |
633	>	*    [ -Izx -Iyz   Izz ]
634	>	*/
635	>	void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
636	>	Vector3d &angularMomentum){
637
638	<	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++){
638	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
639
640	<	// uses equipartition theory to solve for vbar in angstrom/fs
641	<
642	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
643	<	vbar = sqrt( av2 );
644	<
645	<	// picks random velocities from a gaussian distribution
646	<	// centered on vbar
647	<
648	<	for (j=0; j<3; j++)
649	<	aVel[j] = vbar * gaussStream->getGaussian();
650	<
651	<	info->integrableObjects[vr]->setVel( aVel );
652	<
653	<	if(info->integrableObjects[vr]->isDirectional()){
654	<
655	<	info->integrableObjects[vr]->getI( I );
656	<
657	<	if (info->integrableObjects[vr]->isLinear()) {
658	<
659	<	l= info->integrableObjects[vr]->linearAxis();
660	<	m = (l+1)%3;
661	<	n = (l+2)%3;
662	<
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();
640	>	if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
641	>
642	>	RealType xx = 0.0;
643	>	RealType yy = 0.0;
644	>	RealType zz = 0.0;
645	>	RealType xy = 0.0;
646	>	RealType xz = 0.0;
647	>	RealType yz = 0.0;
648	>	Vector3d com(0.0);
649	>	Vector3d comVel(0.0);
650	>
651	>	getComAll(com, comVel);
652	>
653	>	SimInfo::MoleculeIterator i;
654	>	Molecule* mol;
655	>
656	>	Vector3d thisq(0.0);
657	>	Vector3d thisv(0.0);
658	>
659	>	RealType thisMass = 0.0;
660	>
661	>	for (mol = info_->beginMolecule(i); mol != NULL;
662	>	mol = info_->nextMolecule(i)) {
663
664	<	} else {
665	<	for (j = 0 ; j < 3; j++) {
666	<	vbar = sqrt( 2.0 * kebar * I[j][j] );
667	<	aJ[j] = vbar * gaussStream->getGaussian();
668	<	}
669	<	} // else isLinear
670	<
671	<	info->integrableObjects[vr]->setJ( aJ );
664	>	thisq = mol->getCom()-com;
665	>	thisv = mol->getComVel()-comVel;
666	>	thisMass = mol->getMass();
667	>	// Compute moment of intertia coefficients.
668	>	xx += thisq[0]*thisq[0]*thisMass;
669	>	yy += thisq[1]*thisq[1]*thisMass;
670	>	zz += thisq[2]*thisq[2]*thisMass;
671	>
672	>	// compute products of intertia
673	>	xy += thisq[0]*thisq[1]*thisMass;
674	>	xz += thisq[0]*thisq[2]*thisMass;
675	>	yz += thisq[1]*thisq[2]*thisMass;
676	>
677	>	angularMomentum += cross( thisq, thisv ) * thisMass;
678	>	}
679
680	<	}//isDirectional
681	<
680	>	inertiaTensor(0,0) = yy + zz;
681	>	inertiaTensor(0,1) = -xy;
682	>	inertiaTensor(0,2) = -xz;
683	>	inertiaTensor(1,0) = -xy;
684	>	inertiaTensor(1,1) = xx + zz;
685	>	inertiaTensor(1,2) = -yz;
686	>	inertiaTensor(2,0) = -xz;
687	>	inertiaTensor(2,1) = -yz;
688	>	inertiaTensor(2,2) = xx + yy;
689	>
690	>	#ifdef IS_MPI
691	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
692	>	9, MPI::REALTYPE, MPI::SUM);
693	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
694	>	angularMomentum.getArrayPointer(), 3,
695	>	MPI::REALTYPE, MPI::SUM);
696	>	#endif
697	>
698	>	snap->setCOMw(angularMomentum);
699	>	snap->setInertiaTensor(inertiaTensor);
700	>	}
701	>
702	>	angularMomentum = snap->getCOMw();
703	>	inertiaTensor = snap->getInertiaTensor();
704	>
705	>	return;
706		}
707
708	<	// Get the Center of Mass drift velocity.
709	<
710	<	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++){
708	>	// Returns the angular momentum of the system
709	>	Vector3d Thermo::getAngularMomentum(){
710	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
711
712	<	info->integrableObjects[vd]->getVel(aVel);
713	<
714	<	for (j=0; j < 3; j++)
715	<	aVel[j] -= vdrift[j];
712	>	if (!snap->hasCOMw) {
713	>
714	>	Vector3d com(0.0);
715	>	Vector3d comVel(0.0);
716	>	Vector3d angularMomentum(0.0);
717	>
718	>	getComAll(com, comVel);
719	>
720	>	SimInfo::MoleculeIterator i;
721	>	Molecule* mol;
722	>
723	>	Vector3d thisr(0.0);
724	>	Vector3d thisp(0.0);
725	>
726	>	RealType thisMass;
727	>
728	>	for (mol = info_->beginMolecule(i); mol != NULL;
729	>	mol = info_->nextMolecule(i)) {
730	>	thisMass = mol->getMass();
731	>	thisr = mol->getCom() - com;
732	>	thisp = (mol->getComVel() - comVel) * thisMass;
733
734	<	info->integrableObjects[vd]->setVel( aVel );
734	>	angularMomentum += cross( thisr, thisp );
735	>	}
736	>
737	>	#ifdef IS_MPI
738	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
739	>	angularMomentum.getArrayPointer(), 3,
740	>	MPI::REALTYPE, MPI::SUM);
741	>	#endif
742	>
743	>	snap->setCOMw(angularMomentum);
744	>	}
745	>
746	>	return snap->getCOMw();
747		}
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;
748
749	<	for(vd = 0; vd < nobj; vd++){
749	>
750	>	/**
751	>	* Returns the Volume of the system based on a ellipsoid with
752	>	* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
753	>	* where R_i are related to the principle inertia moments
754	>	*  R_i = sqrt(C*I_i/N), this reduces to
755	>	*  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
756	>	* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
757	>	*/
758	>	RealType Thermo::getGyrationalVolume(){
759	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
760
761	<	amass = info->integrableObjects[vd]->getMass();
762	<	info->integrableObjects[vd]->getVel( aVel );
761	>	if (!snap->hasGyrationalVolume) {
762	>
763	>	Mat3x3d intTensor;
764	>	RealType det;
765	>	Vector3d dummyAngMom;
766	>	RealType sysconstants;
767	>	RealType geomCnst;
768	>	RealType volume;
769	>
770	>	geomCnst = 3.0/2.0;
771	>	/* Get the inertial tensor and angular momentum for free*/
772	>	getInertiaTensor(intTensor, dummyAngMom);
773	>
774	>	det = intTensor.determinant();
775	>	sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
776	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
777
778	<	for(j = 0; j < 3; j++)
779	<	vdrift_local[j] += aVel[j] * amass;
780	<
369	<	mtot_local += amass;
778	>	snap->setGyrationalVolume(volume);
779	>	}
780	>	return snap->getGyrationalVolume();
781		}
782	+
783	+	void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
784	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
785
786	<	#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
786	>	if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
787
788	<	for (vd = 0; vd < 3; vd++) {
789	<	vdrift[vd] = vdrift[vd] / mtot;
788	>	Mat3x3d intTensor;
789	>	Vector3d dummyAngMom;
790	>	RealType sysconstants;
791	>	RealType geomCnst;
792	>
793	>	geomCnst = 3.0/2.0;
794	>	/* Get the inertia tensor and angular momentum for free*/
795	>	this->getInertiaTensor(intTensor, dummyAngMom);
796	>
797	>	detI = intTensor.determinant();
798	>	sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
799	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
800	>	snap->setGyrationalVolume(volume);
801	>	} else {
802	>	volume = snap->getGyrationalVolume();
803	>	detI = snap->getInertiaTensor().determinant();
804	>	}
805	>	return;
806		}
807
808	<	}
809	<
810	<	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++){
808	>	RealType Thermo::getTaggedAtomPairDistance(){
809	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
810	>	Globals* simParams = info_->getSimParams();
811
812	<	amass = info->integrableObjects[i]->getMass();
813	<	info->integrableObjects[i]->getPos( aPos );
812	>	if (simParams->haveTaggedAtomPair() &&
813	>	simParams->havePrintTaggedPairDistance()) {
814	>	if ( simParams->getPrintTaggedPairDistance()) {
815	>
816	>	pair<int, int> tap = simParams->getTaggedAtomPair();
817	>	Vector3d pos1, pos2, rab;
818	>
819	>	#ifdef IS_MPI
820	>	int mol1 = info_->getGlobalMolMembership(tap.first);
821	>	int mol2 = info_->getGlobalMolMembership(tap.second);
822
823	<	for(j = 0; j < 3; j++)
824	<	COM_local[j] += aPos[j] * amass;
409	<
410	<	mtot_local += amass;
411	<	}
823	>	int proc1 = info_->getMolToProc(mol1);
824	>	int proc2 = info_->getMolToProc(mol2);
825
826	<	#ifdef IS_MPI
827	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
828	<	MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
826	>	RealType data[3];
827	>	if (proc1 == worldRank) {
828	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
829	>	pos1 = sd1->getPos();
830	>	data[0] = pos1.x();
831	>	data[1] = pos1.y();
832	>	data[2] = pos1.z();
833	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
834	>	} else {
835	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
836	>	pos1 = Vector3d(data);
837	>	}
838	>
839	>	if (proc2 == worldRank) {
840	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
841	>	pos2 = sd2->getPos();
842	>	data[0] = pos2.x();
843	>	data[1] = pos2.y();
844	>	data[2] = pos2.z();
845	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
846	>	} else {
847	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
848	>	pos2 = Vector3d(data);
849	>	}
850		#else
851	<	mtot = mtot_local;
852	<	for(i = 0; i < 3; i++) {
853	<	COM[i] = COM_local[i];
851	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
852	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
853	>	pos1 = at1->getPos();
854	>	pos2 = at2->getPos();
855	>	#endif
856	>	rab = pos2 - pos1;
857	>	currSnapshot->wrapVector(rab);
858	>	return rab.length();
859	>	}
860	>	return 0.0;
861	>	}
862	>	return 0.0;
863		}
864	<	#endif
864	>
865	>	RealType Thermo::getHullVolume(){
866	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
867
868	<	for (i = 0; i < 3; i++) {
424	<	COM[i] = COM[i] / mtot;
425	<	}
426	<	}
868	>	if (!snap->hasHullVolume) {
869
870	<	void Thermo::removeCOMdrift() {
429	<	double vdrift[3], aVel[3];
430	<	int vd, j, nobj;
870	>	Hull* surfaceMesh_;
871
872	<	nobj = info->integrableObjects.size();
873	<
874	<	// Get the Center of Mass drift velocity.
875	<
876	<	getCOMVel(vdrift);
877	<
878	<	//  Corrects for the center of mass drift.
879	<	// sums all the momentum and divides by total mass.
880	<
881	<	for(vd = 0; vd < nobj; vd++){
882	<
883	<	info->integrableObjects[vd]->getVel(aVel);
884	<
885	<	for (j=0; j < 3; j++)
886	<	aVel[j] -= vdrift[j];
887	<
888	<	info->integrableObjects[vd]->setVel( aVel );
889	<	}
872	>	Globals* simParams = info_->getSimParams();
873	>	const std::string ht = simParams->getHULL_Method();
874	>
875	>	if (ht == "Convex") {
876	>	surfaceMesh_ = new ConvexHull();
877	>	} else if (ht == "AlphaShape") {
878	>	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
879	>	} else {
880	>	return 0.0;
881	>	}
882	>
883	>	// Build a vector of stunt doubles to determine if they are
884	>	// surface atoms
885	>	std::vector<StuntDouble*> localSites_;
886	>	Molecule* mol;
887	>	StuntDouble* sd;
888	>	SimInfo::MoleculeIterator i;
889	>	Molecule::IntegrableObjectIterator  j;
890	>
891	>	for (mol = info_->beginMolecule(i); mol != NULL;
892	>	mol = info_->nextMolecule(i)) {
893	>	for (sd = mol->beginIntegrableObject(j);
894	>	sd != NULL;
895	>	sd = mol->nextIntegrableObject(j)) {
896	>	localSites_.push_back(sd);
897	>	}
898	>	}
899	>
900	>	// Compute surface Mesh
901	>	surfaceMesh_->computeHull(localSites_);
902	>	snap->setHullVolume(surfaceMesh_->getVolume());
903	>	}
904	>	return snap->getHullVolume();
905	>	}
906		}

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 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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