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

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trunk/src/brains/Snapshot.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	Line 1 | Line 1
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
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 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	<	/**
44	<	* @file Snapshot.cpp
45	<	* @author tlin
46	<	* @date 11/11/2004
47	<	* @time 10:56am
48	<	* @version 1.0
48	<	*/
43	>	/**
44	>	* @file Snapshot.cpp
45	>	* @author tlin
46	>	* @date 11/11/2004
47	>	* @version 1.0
48	>	*/
49
50		#include "brains/Snapshot.hpp"
51		#include "utils/NumericConstant.hpp"
52		#include "utils/simError.h"
53		#include "utils/Utility.hpp"
54	<	namespace oopse {
54	>	#include <cstdio>
55
56	<	void  Snapshot::setHmat(const Mat3x3d& m) {
57	<	const double orthoTolerance = NumericConstant::epsilon;
58	<	hmat_ = m;
59	<	invHmat_ = hmat_.inverse();
56	>	namespace OpenMD {
57	>
58	>	Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) :
59	>	atomData(nAtoms), rigidbodyData(nRigidbodies),
60	>	cgData(nCutoffGroups, DataStorage::dslPosition),
61	>	orthoTolerance_(1e-6) {
62
63	<	//prepare fortran Hmat
64	<	double fortranHmat[9];
65	<	double fortranInvHmat[9];
66	<	hmat_.getArray(fortranHmat);
67	<	invHmat_.getArray(fortranInvHmat);
63	>	frameData.id = -1;
64	>	frameData.currentTime = 0;
65	>	frameData.hmat = Mat3x3d(0.0);
66	>	frameData.invHmat = Mat3x3d(0.0);
67	>	frameData.orthoRhombic = false;
68	>	frameData.bondPotential = 0.0;
69	>	frameData.bendPotential = 0.0;
70	>	frameData.torsionPotential = 0.0;
71	>	frameData.inversionPotential = 0.0;
72	>	frameData.lrPotentials = potVec(0.0);
73	>	frameData.excludedPotentials = potVec(0.0);
74	>	frameData.restraintPotential = 0.0;
75	>	frameData.rawPotential = 0.0;
76	>	frameData.xyArea = 0.0;
77	>	frameData.volume = 0.0;
78	>	frameData.thermostat = make_pair(0.0, 0.0);
79	>	frameData.electronicThermostat = make_pair(0.0, 0.0);
80	>	frameData.barostat = Mat3x3d(0.0);
81	>	frameData.stressTensor = Mat3x3d(0.0);
82	>	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
83
84	<	//determine whether the box is orthoTolerance or not
85	<	int oldOrthoRhombic = orthoRhombic_;
84	>	clearDerivedProperties();
85	>	}
86	>
87	>	Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
88	>	int storageLayout) :
89	>	atomData(nAtoms, storageLayout),
90	>	rigidbodyData(nRigidbodies, storageLayout),
91	>	cgData(nCutoffGroups, DataStorage::dslPosition),
92	>	orthoTolerance_(1e-6) {
93
94	<	double smallDiag = fabs(hmat_(0, 0));
95	<	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
96	<	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
97	<	double tol = smallDiag * orthoTolerance;
94	>	frameData.id = -1;
95	>	frameData.currentTime = 0;
96	>	frameData.hmat = Mat3x3d(0.0);
97	>	frameData.invHmat = Mat3x3d(0.0);
98	>	frameData.orthoRhombic = false;
99	>	frameData.bondPotential = 0.0;
100	>	frameData.bendPotential = 0.0;
101	>	frameData.torsionPotential = 0.0;
102	>	frameData.inversionPotential = 0.0;
103	>	frameData.lrPotentials = potVec(0.0);
104	>	frameData.excludedPotentials = potVec(0.0);
105	>	frameData.restraintPotential = 0.0;
106	>	frameData.rawPotential = 0.0;
107	>	frameData.xyArea = 0.0;
108	>	frameData.volume = 0.0;
109	>	frameData.thermostat = make_pair(0.0, 0.0);
110	>	frameData.electronicThermostat = make_pair(0.0, 0.0);
111	>	frameData.barostat = Mat3x3d(0.0);
112	>	frameData.stressTensor = Mat3x3d(0.0);
113	>	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
114
115	<	orthoRhombic_ = 1;
115	>	clearDerivedProperties();
116	>	}
117
118	<	for (int i = 0; i < 3; i++ ) {
119	<	for (int j = 0 ; j < 3; j++) {
120	<	if (i != j) {
121	<	if (orthoRhombic_) {
122	<	if ( fabs(hmat_(i, j)) >= tol)
123	<	orthoRhombic_ = 0;
124	<	}
125	<	}
126	<	}
127	<	}
118	>	void Snapshot::clearDerivedProperties() {
119	>	frameData.totalEnergy = 0.0;
120	>	frameData.translationalKinetic = 0.0;
121	>	frameData.rotationalKinetic = 0.0;
122	>	frameData.kineticEnergy = 0.0;
123	>	frameData.potentialEnergy = 0.0;
124	>	frameData.shortRangePotential = 0.0;
125	>	frameData.longRangePotential = 0.0;
126	>	frameData.pressure = 0.0;
127	>	frameData.temperature = 0.0;
128	>	frameData.pressureTensor = Mat3x3d(0.0);
129	>	frameData.systemDipole = Vector3d(0.0);
130	>	frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
131	>	frameData.electronicTemperature = 0.0;
132	>	frameData.COM = V3Zero;
133	>	frameData.COMvel = V3Zero;
134	>	frameData.COMw = V3Zero;
135
136	<	if( oldOrthoRhombic != orthoRhombic_ ){
136	>	hasTotalEnergy = false;
137	>	hasTranslationalKineticEnergy = false;
138	>	hasRotationalKineticEnergy = false;
139	>	hasKineticEnergy = false;
140	>	hasShortRangePotential = false;
141	>	hasLongRangePotential = false;
142	>	hasPotentialEnergy = false;
143	>	hasXYarea = false;
144	>	hasVolume = false;
145	>	hasPressure = false;
146	>	hasTemperature = false;
147	>	hasElectronicTemperature = false;
148	>	hasCOM = false;
149	>	hasCOMvel = false;
150	>	hasCOMw = false;
151	>	hasPressureTensor = false;
152	>	hasSystemDipole = false;
153	>	hasConvectiveHeatFlux = false;
154	>	hasInertiaTensor = false;
155	>	hasGyrationalVolume = false;
156	>	hasHullVolume = false;
157	>	hasConservedQuantity = false;
158	>	}
159
160	<	if( orthoRhombic_ ) {
161	<	sprintf( painCave.errMsg,
162	<	"OOPSE is switching from the default Non-Orthorhombic\n"
163	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
164	<	"\tThis is usually a good thing, but if you wan't the\n"
165	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
166	<	"\tvariable ( currently set to %G ) smaller.\n",
167	<	orthoTolerance);
168	<	painCave.severity = OOPSE_INFO;
169	<	simError();
170	<	}
171	<	else {
172	<	sprintf( painCave.errMsg,
173	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
174	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
175	<	"\tThis is usually because the box has deformed under\n"
176	<	"\tNPTf integration. If you wan't to live on the edge with\n"
177	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
178	<	"\tvariable ( currently set to %G ) larger.\n",
179	<	orthoTolerance);
180	<	painCave.severity = OOPSE_WARNING;
181	<	simError();
182	<	}
183	<	}
160	>	/** Returns the id of this Snapshot */
161	>	int Snapshot::getID() {
162	>	return frameData.id;
163	>	}
164	>
165	>	/** Sets the id of this Snapshot */
166	>	void Snapshot::setID(int id) {
167	>	frameData.id = id;
168	>	}
169	>
170	>	int Snapshot::getSize() {
171	>	return atomData.getSize() + rigidbodyData.getSize();
172	>	}
173	>
174	>	/** Returns the number of atoms */
175	>	int Snapshot::getNumberOfAtoms() {
176	>	return atomData.getSize();
177	>	}
178	>
179	>	/** Returns the number of rigid bodies */
180	>	int Snapshot::getNumberOfRigidBodies() {
181	>	return rigidbodyData.getSize();
182	>	}
183	>
184	>	/** Returns the number of rigid bodies */
185	>	int Snapshot::getNumberOfCutoffGroups() {
186	>	return cgData.getSize();
187	>	}
188	>
189	>	/** Returns the H-Matrix */
190	>	Mat3x3d Snapshot::getHmat() {
191	>	return frameData.hmat;
192	>	}
193
194	<	//notify fortran simulation box has changed
195	<	setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
196	<	}
194	>	/** Sets the H-Matrix */
195	>	void Snapshot::setHmat(const Mat3x3d& m) {
196	>	hasVolume = false;
197	>	frameData.hmat = m;
198	>	frameData.invHmat = frameData.hmat.inverse();
199	>
200	>	//determine whether the box is orthoTolerance or not
201	>	bool oldOrthoRhombic = frameData.orthoRhombic;
202	>
203	>	RealType smallDiag = fabs(frameData.hmat(0, 0));
204	>	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
205	>	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
206	>	RealType tol = smallDiag * orthoTolerance_;
207
208	+	frameData.orthoRhombic = true;
209
210	<	void Snapshot::wrapVector(Vector3d& pos) {
210	>	for (int i = 0; i < 3; i++ ) {
211	>	for (int j = 0 ; j < 3; j++) {
212	>	if (i != j) {
213	>	if (frameData.orthoRhombic) {
214	>	if ( fabs(frameData.hmat(i, j)) >= tol)
215	>	frameData.orthoRhombic = false;
216	>	}
217	>	}
218	>	}
219	>	}
220	>
221	>	if( oldOrthoRhombic != frameData.orthoRhombic){
222	>
223	>	if( frameData.orthoRhombic ) {
224	>	sprintf( painCave.errMsg,
225	>	"OpenMD is switching from the default Non-Orthorhombic\n"
226	>	"\tto the faster Orthorhombic periodic boundary computations.\n"
227	>	"\tThis is usually a good thing, but if you want the\n"
228	>	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
229	>	"\tvariable ( currently set to %G ) smaller.\n",
230	>	orthoTolerance_);
231	>	painCave.severity = OPENMD_INFO;
232	>	simError();
233	>	}
234	>	else {
235	>	sprintf( painCave.errMsg,
236	>	"OpenMD is switching from the faster Orthorhombic to the more\n"
237	>	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
238	>	"\tThis is usually because the box has deformed under\n"
239	>	"\tNPTf integration. If you want to live on the edge with\n"
240	>	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
241	>	"\tvariable ( currently set to %G ) larger.\n",
242	>	orthoTolerance_);
243	>	painCave.severity = OPENMD_WARNING;
244	>	simError();
245	>	}
246	>	}
247	>	}
248	>
249	>	/** Returns the inverse H-Matrix */
250	>	Mat3x3d Snapshot::getInvHmat() {
251	>	return frameData.invHmat;
252	>	}
253
254	<	int i;
255	<	Vector3d scaled;
254	>	RealType Snapshot::getXYarea() {
255	>	if (!hasXYarea) {
256	>	Vector3d x = frameData.hmat.getColumn(0);
257	>	Vector3d y = frameData.hmat.getColumn(1);
258	>	frameData.xyArea = cross(x,y).length();
259	>	hasXYarea = true;
260	>	}
261	>	return frameData.xyArea;
262	>	}
263
264	<	if( !orthoRhombic_ ){
264	>	RealType Snapshot::getVolume() {
265	>	if (!hasVolume) {
266	>	frameData.volume = frameData.hmat.determinant();
267	>	hasVolume = true;
268	>	}
269	>	return frameData.volume;
270	>	}
271
272	<	// calc the scaled coordinates.
273	<	scaled = invHmat_* pos;
272	>	void Snapshot::setVolume(RealType vol) {
273	>	hasVolume = true;
274	>	frameData.volume = vol;
275	>	}
276
277	<	// wrap the scaled coordinates
278	<	for (i = 0; i < 3; ++i) {
132	<	scaled[i] -= roundMe(scaled[i]);
133	<	}
134	<
135	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
136	<	pos = hmat_ * scaled;
137	<
138	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
277	>	/** Wrap a vector according to periodic boundary conditions */
278	>	void Snapshot::wrapVector(Vector3d& pos) {
279
280	<	// calc the scaled coordinates.
281	<	for (i=0; i<3; i++) {
282	<	scaled[i] = pos[i] * invHmat_(i, i);
283	<	}
284	<
285	<	// wrap the scaled coordinates
286	<	for (i = 0; i < 3; ++i) {
287	<	scaled[i] -= roundMe(scaled[i]);
288	<	}
280	>	Vector3d scaled = scaleVector(pos);
281	>
282	>	for (int i = 0; i < 3; i++)
283	>	scaled[i] -= roundMe(scaled[i]);
284	>
285	>	if( !frameData.orthoRhombic )
286	>	pos = frameData.hmat * scaled;
287	>	else {
288	>
289	>	// calc the wrapped real coordinates from the wrapped scaled coordinates
290	>	for (int i=0; i<3; i++) {
291	>	pos[i] = scaled[i] * frameData.hmat(i, i);
292	>	}
293	>	}
294	>	}
295
296	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
297	<	for (i=0; i<3; i++) {
298	<	pos[i] = scaled[i] * hmat_(i, i);
299	<	}
300	<
296	>	/** Scaling a vector to multiples of the periodic box */
297	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
298	>
299	>	Vector3d scaled;
300	>
301	>	if( !frameData.orthoRhombic )
302	>	scaled = frameData.invHmat * pos;
303	>	else {
304	>	// calc the scaled coordinates.
305	>	for (int i=0; i<3; i++)
306	>	scaled[i] = pos[i] * frameData.invHmat(i, i);
307		}
308
309	<	}
309	>	return scaled;
310	>	}
311
312	<	}
312	>	void Snapshot::setCOM(const Vector3d& com) {
313	>	frameData.COM = com;
314	>	hasCOM = true;
315	>	}
316
317	+	void Snapshot::setCOMvel(const Vector3d& comVel) {
318	+	frameData.COMvel = comVel;
319	+	hasCOMvel = true;
320	+	}
321	+
322	+	void Snapshot::setCOMw(const Vector3d& comw) {
323	+	frameData.COMw = comw;
324	+	hasCOMw = true;
325	+	}
326	+
327	+	Vector3d Snapshot::getCOM() {
328	+	return frameData.COM;
329	+	}
330	+
331	+	Vector3d Snapshot::getCOMvel() {
332	+	return frameData.COMvel;
333	+	}
334	+
335	+	Vector3d Snapshot::getCOMw() {
336	+	return frameData.COMw;
337	+	}
338	+
339	+	RealType Snapshot::getTime() {
340	+	return frameData.currentTime;
341	+	}
342	+
343	+	void Snapshot::increaseTime(RealType dt) {
344	+	setTime(getTime() + dt);
345	+	}
346	+
347	+	void Snapshot::setTime(RealType time) {
348	+	frameData.currentTime = time;
349	+	}
350	+
351	+	void Snapshot::setBondPotential(RealType bp) {
352	+	frameData.bondPotential = bp;
353	+	}
354	+
355	+	void Snapshot::setBendPotential(RealType bp) {
356	+	frameData.bendPotential = bp;
357	+	}
358	+
359	+	void Snapshot::setTorsionPotential(RealType tp) {
360	+	frameData.torsionPotential = tp;
361	+	}
362	+
363	+	void Snapshot::setInversionPotential(RealType ip) {
364	+	frameData.inversionPotential = ip;
365	+	}
366	+
367	+
368	+	RealType Snapshot::getBondPotential() {
369	+	return frameData.bondPotential;
370	+	}
371	+	RealType Snapshot::getBendPotential() {
372	+	return frameData.bendPotential;
373	+	}
374	+	RealType Snapshot::getTorsionPotential() {
375	+	return frameData.torsionPotential;
376	+	}
377	+	RealType Snapshot::getInversionPotential() {
378	+	return frameData.inversionPotential;
379	+	}
380	+
381	+	RealType Snapshot::getShortRangePotential() {
382	+	if (!hasShortRangePotential) {
383	+	frameData.shortRangePotential = frameData.bondPotential;
384	+	frameData.shortRangePotential += frameData.bendPotential;
385	+	frameData.shortRangePotential += frameData.torsionPotential;
386	+	frameData.shortRangePotential += frameData.inversionPotential;
387	+	hasShortRangePotential = true;
388	+	}
389	+	return frameData.shortRangePotential;
390	+	}
391	+
392	+	void Snapshot::setLongRangePotential(potVec lrPot) {
393	+	frameData.lrPotentials = lrPot;
394	+	}
395	+
396	+	RealType Snapshot::getLongRangePotential() {
397	+	if (!hasLongRangePotential) {
398	+	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
399	+	frameData.longRangePotential += frameData.lrPotentials[i];
400	+	}
401	+	hasLongRangePotential = true;
402	+	}
403	+	return frameData.longRangePotential;
404	+	}
405	+
406	+	potVec Snapshot::getLongRangePotentials() {
407	+	return frameData.lrPotentials;
408	+	}
409	+
410	+	RealType Snapshot::getPotentialEnergy() {
411	+	if (!hasPotentialEnergy) {
412	+	frameData.potentialEnergy = this->getLongRangePotential();
413	+	frameData.potentialEnergy += this->getShortRangePotential();
414	+	hasPotentialEnergy = true;
415	+	}
416	+	return frameData.potentialEnergy;
417	+	}
418	+
419	+	void Snapshot::setExcludedPotentials(potVec exPot) {
420	+	frameData.excludedPotentials = exPot;
421	+	}
422	+
423	+	potVec Snapshot::getExcludedPotentials() {
424	+	return frameData.excludedPotentials;
425	+	}
426	+
427	+	void Snapshot::setRestraintPotential(RealType rp) {
428	+	frameData.restraintPotential = rp;
429	+	}
430	+
431	+	RealType Snapshot::getRestraintPotential() {
432	+	return frameData.restraintPotential;
433	+	}
434	+
435	+	void Snapshot::setRawPotential(RealType rp) {
436	+	frameData.rawPotential = rp;
437	+	}
438	+
439	+	RealType Snapshot::getRawPotential() {
440	+	return frameData.rawPotential;
441	+	}
442	+
443	+	RealType Snapshot::getTranslationalKineticEnergy() {
444	+	return frameData.translationalKinetic;
445	+	}
446	+
447	+	RealType Snapshot::getRotationalKineticEnergy() {
448	+	return frameData.rotationalKinetic;
449	+	}
450	+
451	+	RealType Snapshot::getKineticEnergy() {
452	+	return frameData.kineticEnergy;
453	+	}
454	+
455	+	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
456	+	hasTranslationalKineticEnergy = true;
457	+	frameData.translationalKinetic = tke;
458	+	}
459	+
460	+	void Snapshot::setRotationalKineticEnergy(RealType rke) {
461	+	hasRotationalKineticEnergy = true;
462	+	frameData.rotationalKinetic = rke;
463	+	}
464	+
465	+	void Snapshot::setKineticEnergy(RealType ke) {
466	+	hasKineticEnergy = true;
467	+	frameData.kineticEnergy = ke;
468	+	}
469	+
470	+	RealType Snapshot::getTotalEnergy() {
471	+	return frameData.totalEnergy;
472	+	}
473	+
474	+	void Snapshot::setTotalEnergy(RealType te) {
475	+	hasTotalEnergy = true;
476	+	frameData.totalEnergy = te;
477	+	}
478	+
479	+	RealType Snapshot::getConservedQuantity() {
480	+	return frameData.conservedQuantity;
481	+	}
482	+
483	+	void Snapshot::setConservedQuantity(RealType cq) {
484	+	hasConservedQuantity = true;
485	+	frameData.conservedQuantity = cq;
486	+	}
487	+
488	+	RealType Snapshot::getTemperature() {
489	+	return frameData.temperature;
490	+	}
491	+
492	+	void Snapshot::setTemperature(RealType temp) {
493	+	hasTemperature = true;
494	+	frameData.temperature = temp;
495	+	}
496	+
497	+	RealType Snapshot::getElectronicTemperature() {
498	+	return frameData.electronicTemperature;
499	+	}
500	+
501	+	void Snapshot::setElectronicTemperature(RealType eTemp) {
502	+	hasElectronicTemperature = true;
503	+	frameData.electronicTemperature = eTemp;
504	+	}
505	+
506	+	RealType Snapshot::getPressure() {
507	+	return frameData.pressure;
508	+	}
509	+
510	+	void Snapshot::setPressure(RealType pressure) {
511	+	hasPressure = true;
512	+	frameData.pressure = pressure;
513	+	}
514	+
515	+	Mat3x3d Snapshot::getPressureTensor() {
516	+	return frameData.pressureTensor;
517	+	}
518	+
519	+
520	+	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
521	+	hasPressureTensor = true;
522	+	frameData.pressureTensor = pressureTensor;
523	+	}
524	+
525	+	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
526	+	frameData.stressTensor = stressTensor;
527	+	}
528	+
529	+	Mat3x3d  Snapshot::getStressTensor() {
530	+	return frameData.stressTensor;
531	+	}
532	+
533	+	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
534	+	frameData.conductiveHeatFlux = chf;
535	+	}
536	+
537	+	Vector3d Snapshot::getConductiveHeatFlux() {
538	+	return frameData.conductiveHeatFlux;
539	+	}
540	+
541	+	Vector3d Snapshot::getConvectiveHeatFlux() {
542	+	return frameData.convectiveHeatFlux;
543	+	}
544	+
545	+	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
546	+	hasConvectiveHeatFlux = true;
547	+	frameData.convectiveHeatFlux = chf;
548	+	}
549	+
550	+	Vector3d Snapshot::getHeatFlux() {
551	+	// BE CAREFUL WITH UNITS
552	+	return getConductiveHeatFlux() + getConvectiveHeatFlux();
553	+	}
554	+
555	+	Vector3d Snapshot::getSystemDipole() {
556	+	return frameData.systemDipole;
557	+	}
558	+
559	+	void Snapshot::setSystemDipole(const Vector3d& bd) {
560	+	hasSystemDipole = true;
561	+	frameData.systemDipole = bd;
562	+	}
563	+
564	+	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
565	+	frameData.thermostat = thermostat;
566	+	}
567	+
568	+	pair<RealType, RealType> Snapshot::getThermostat() {
569	+	return frameData.thermostat;
570	+	}
571	+
572	+	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
573	+	frameData.electronicThermostat = eTherm;
574	+	}
575	+
576	+	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
577	+	return frameData.electronicThermostat;
578	+	}
579	+
580	+	void Snapshot::setBarostat(const Mat3x3d& barostat) {
581	+	frameData.barostat = barostat;
582	+	}
583	+
584	+	Mat3x3d Snapshot::getBarostat() {
585	+	return frameData.barostat;
586	+	}
587	+
588	+	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
589	+	frameData.inertiaTensor = inertiaTensor;
590	+	hasInertiaTensor = true;
591	+	}
592	+
593	+	Mat3x3d Snapshot::getInertiaTensor() {
594	+	return frameData.inertiaTensor;
595	+	}
596	+
597	+	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
598	+	frameData.gyrationalVolume = gyrationalVolume;
599	+	hasGyrationalVolume = true;
600	+	}
601	+
602	+	RealType Snapshot::getGyrationalVolume() {
603	+	return frameData.gyrationalVolume;
604	+	}
605	+
606	+	void Snapshot::setHullVolume(const RealType hullVolume) {
607	+	frameData.hullVolume = hullVolume;
608	+	hasHullVolume = true;
609	+	}
610	+
611	+	RealType Snapshot::getHullVolume() {
612	+	return frameData.hullVolume;
613	+	}
614	+
615	+	void Snapshot::setOrthoTolerance(RealType ot) {
616	+	orthoTolerance_ = ot;
617	+	}
618	+	}

Comparing:
trunk/src/brains/Snapshot.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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