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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 1850 by gezelter, Wed Feb 20 15:39:39 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	<	/**
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	>	// It is finally time to suppress these warnings once and for
224	>	// all.  They were annoying and not very informative.
225
226	<	int i;
227	<	Vector3d scaled;
226	>	// if( frameData.orthoRhombic ) {
227	>	//   sprintf( painCave.errMsg,
228	>	//         "OpenMD is switching from the default Non-Orthorhombic\n"
229	>	//         "\tto the faster Orthorhombic periodic boundary computations.\n"
230	>	//         "\tThis is usually a good thing, but if you want the\n"
231	>	//         "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
232	>	//         "\tvariable ( currently set to %G ) smaller.\n",
233	>	//         orthoTolerance_);
234	>	//   painCave.severity = OPENMD_INFO;
235	>	//   simError();
236	>	// }
237	>	// else {
238	>	//   sprintf( painCave.errMsg,
239	>	//         "OpenMD is switching from the faster Orthorhombic to the more\n"
240	>	//         "\tflexible Non-Orthorhombic periodic boundary computations.\n"
241	>	//         "\tThis is usually because the box has deformed under\n"
242	>	//         "\tNPTf integration. If you want to live on the edge with\n"
243	>	//         "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
244	>	//         "\tvariable ( currently set to %G ) larger.\n",
245	>	//         orthoTolerance_);
246	>	//   painCave.severity = OPENMD_WARNING;
247	>	//   simError();
248	>	// }
249	>	}
250	>	}
251	>
252	>	/** Returns the inverse H-Matrix */
253	>	Mat3x3d Snapshot::getInvHmat() {
254	>	return frameData.invHmat;
255	>	}
256
257	<	if( !orthoRhombic_ ){
257	>	RealType Snapshot::getXYarea() {
258	>	if (!hasXYarea) {
259	>	Vector3d x = frameData.hmat.getColumn(0);
260	>	Vector3d y = frameData.hmat.getColumn(1);
261	>	frameData.xyArea = cross(x,y).length();
262	>	hasXYarea = true;
263	>	}
264	>	return frameData.xyArea;
265	>	}
266
267	<	// calc the scaled coordinates.
268	<	scaled = invHmat_* pos;
267	>	RealType Snapshot::getVolume() {
268	>	if (!hasVolume) {
269	>	frameData.volume = frameData.hmat.determinant();
270	>	hasVolume = true;
271	>	}
272	>	return frameData.volume;
273	>	}
274
275	<	// wrap the scaled coordinates
276	<	for (i = 0; i < 3; ++i) {
277	<	scaled[i] -= roundMe(scaled[i]);
278	<	}
275	>	void Snapshot::setVolume(RealType vol) {
276	>	hasVolume = true;
277	>	frameData.volume = vol;
278	>	}
279
280	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
281	<	pos = hmat_ * scaled;
137	<
138	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
280	>	/** Wrap a vector according to periodic boundary conditions */
281	>	void Snapshot::wrapVector(Vector3d& pos) {
282
283	<	// calc the scaled coordinates.
284	<	for (i=0; i<3; i++) {
285	<	scaled[i] = pos[i] * invHmat_(i, i);
286	<	}
287	<
288	<	// wrap the scaled coordinates
289	<	for (i = 0; i < 3; ++i) {
290	<	scaled[i] -= roundMe(scaled[i]);
291	<	}
283	>	Vector3d scaled = scaleVector(pos);
284	>
285	>	for (int i = 0; i < 3; i++)
286	>	scaled[i] -= roundMe(scaled[i]);
287	>
288	>	if( !frameData.orthoRhombic )
289	>	pos = frameData.hmat * scaled;
290	>	else {
291	>
292	>	// calc the wrapped real coordinates from the wrapped scaled coordinates
293	>	for (int i=0; i<3; i++) {
294	>	pos[i] = scaled[i] * frameData.hmat(i, i);
295	>	}
296	>	}
297	>	}
298
299	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
300	<	for (i=0; i<3; i++) {
301	<	pos[i] = scaled[i] * hmat_(i, i);
302	<	}
303	<
299	>	/** Scaling a vector to multiples of the periodic box */
300	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
301	>
302	>	Vector3d scaled;
303	>
304	>	if( !frameData.orthoRhombic )
305	>	scaled = frameData.invHmat * pos;
306	>	else {
307	>	// calc the scaled coordinates.
308	>	for (int i=0; i<3; i++)
309	>	scaled[i] = pos[i] * frameData.invHmat(i, i);
310		}
311
312	<	}
312	>	return scaled;
313	>	}
314
315	<	}
315	>	void Snapshot::setCOM(const Vector3d& com) {
316	>	frameData.COM = com;
317	>	hasCOM = true;
318	>	}
319
320	+	void Snapshot::setCOMvel(const Vector3d& comVel) {
321	+	frameData.COMvel = comVel;
322	+	hasCOMvel = true;
323	+	}
324	+
325	+	void Snapshot::setCOMw(const Vector3d& comw) {
326	+	frameData.COMw = comw;
327	+	hasCOMw = true;
328	+	}
329	+
330	+	Vector3d Snapshot::getCOM() {
331	+	return frameData.COM;
332	+	}
333	+
334	+	Vector3d Snapshot::getCOMvel() {
335	+	return frameData.COMvel;
336	+	}
337	+
338	+	Vector3d Snapshot::getCOMw() {
339	+	return frameData.COMw;
340	+	}
341	+
342	+	RealType Snapshot::getTime() {
343	+	return frameData.currentTime;
344	+	}
345	+
346	+	void Snapshot::increaseTime(RealType dt) {
347	+	setTime(getTime() + dt);
348	+	}
349	+
350	+	void Snapshot::setTime(RealType time) {
351	+	frameData.currentTime = time;
352	+	}
353	+
354	+	void Snapshot::setBondPotential(RealType bp) {
355	+	frameData.bondPotential = bp;
356	+	}
357	+
358	+	void Snapshot::setBendPotential(RealType bp) {
359	+	frameData.bendPotential = bp;
360	+	}
361	+
362	+	void Snapshot::setTorsionPotential(RealType tp) {
363	+	frameData.torsionPotential = tp;
364	+	}
365	+
366	+	void Snapshot::setInversionPotential(RealType ip) {
367	+	frameData.inversionPotential = ip;
368	+	}
369	+
370	+
371	+	RealType Snapshot::getBondPotential() {
372	+	return frameData.bondPotential;
373	+	}
374	+	RealType Snapshot::getBendPotential() {
375	+	return frameData.bendPotential;
376	+	}
377	+	RealType Snapshot::getTorsionPotential() {
378	+	return frameData.torsionPotential;
379	+	}
380	+	RealType Snapshot::getInversionPotential() {
381	+	return frameData.inversionPotential;
382	+	}
383	+
384	+	RealType Snapshot::getShortRangePotential() {
385	+	if (!hasShortRangePotential) {
386	+	frameData.shortRangePotential = frameData.bondPotential;
387	+	frameData.shortRangePotential += frameData.bendPotential;
388	+	frameData.shortRangePotential += frameData.torsionPotential;
389	+	frameData.shortRangePotential += frameData.inversionPotential;
390	+	hasShortRangePotential = true;
391	+	}
392	+	return frameData.shortRangePotential;
393	+	}
394	+
395	+	void Snapshot::setLongRangePotential(potVec lrPot) {
396	+	frameData.lrPotentials = lrPot;
397	+	}
398	+
399	+	RealType Snapshot::getLongRangePotential() {
400	+	if (!hasLongRangePotential) {
401	+	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
402	+	frameData.longRangePotential += frameData.lrPotentials[i];
403	+	}
404	+	hasLongRangePotential = true;
405	+	}
406	+	return frameData.longRangePotential;
407	+	}
408	+
409	+	potVec Snapshot::getLongRangePotentials() {
410	+	return frameData.lrPotentials;
411	+	}
412	+
413	+	RealType Snapshot::getPotentialEnergy() {
414	+	if (!hasPotentialEnergy) {
415	+	frameData.potentialEnergy = this->getLongRangePotential();
416	+	frameData.potentialEnergy += this->getShortRangePotential();
417	+	hasPotentialEnergy = true;
418	+	}
419	+	return frameData.potentialEnergy;
420	+	}
421	+
422	+	void Snapshot::setExcludedPotentials(potVec exPot) {
423	+	frameData.excludedPotentials = exPot;
424	+	}
425	+
426	+	potVec Snapshot::getExcludedPotentials() {
427	+	return frameData.excludedPotentials;
428	+	}
429	+
430	+	void Snapshot::setRestraintPotential(RealType rp) {
431	+	frameData.restraintPotential = rp;
432	+	}
433	+
434	+	RealType Snapshot::getRestraintPotential() {
435	+	return frameData.restraintPotential;
436	+	}
437	+
438	+	void Snapshot::setRawPotential(RealType rp) {
439	+	frameData.rawPotential = rp;
440	+	}
441	+
442	+	RealType Snapshot::getRawPotential() {
443	+	return frameData.rawPotential;
444	+	}
445	+
446	+	RealType Snapshot::getTranslationalKineticEnergy() {
447	+	return frameData.translationalKinetic;
448	+	}
449	+
450	+	RealType Snapshot::getRotationalKineticEnergy() {
451	+	return frameData.rotationalKinetic;
452	+	}
453	+
454	+	RealType Snapshot::getKineticEnergy() {
455	+	return frameData.kineticEnergy;
456	+	}
457	+
458	+	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
459	+	hasTranslationalKineticEnergy = true;
460	+	frameData.translationalKinetic = tke;
461	+	}
462	+
463	+	void Snapshot::setRotationalKineticEnergy(RealType rke) {
464	+	hasRotationalKineticEnergy = true;
465	+	frameData.rotationalKinetic = rke;
466	+	}
467	+
468	+	void Snapshot::setKineticEnergy(RealType ke) {
469	+	hasKineticEnergy = true;
470	+	frameData.kineticEnergy = ke;
471	+	}
472	+
473	+	RealType Snapshot::getTotalEnergy() {
474	+	return frameData.totalEnergy;
475	+	}
476	+
477	+	void Snapshot::setTotalEnergy(RealType te) {
478	+	hasTotalEnergy = true;
479	+	frameData.totalEnergy = te;
480	+	}
481	+
482	+	RealType Snapshot::getConservedQuantity() {
483	+	return frameData.conservedQuantity;
484	+	}
485	+
486	+	void Snapshot::setConservedQuantity(RealType cq) {
487	+	hasConservedQuantity = true;
488	+	frameData.conservedQuantity = cq;
489	+	}
490	+
491	+	RealType Snapshot::getTemperature() {
492	+	return frameData.temperature;
493	+	}
494	+
495	+	void Snapshot::setTemperature(RealType temp) {
496	+	hasTemperature = true;
497	+	frameData.temperature = temp;
498	+	}
499	+
500	+	RealType Snapshot::getElectronicTemperature() {
501	+	return frameData.electronicTemperature;
502	+	}
503	+
504	+	void Snapshot::setElectronicTemperature(RealType eTemp) {
505	+	hasElectronicTemperature = true;
506	+	frameData.electronicTemperature = eTemp;
507	+	}
508	+
509	+	RealType Snapshot::getPressure() {
510	+	return frameData.pressure;
511	+	}
512	+
513	+	void Snapshot::setPressure(RealType pressure) {
514	+	hasPressure = true;
515	+	frameData.pressure = pressure;
516	+	}
517	+
518	+	Mat3x3d Snapshot::getPressureTensor() {
519	+	return frameData.pressureTensor;
520	+	}
521	+
522	+
523	+	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
524	+	hasPressureTensor = true;
525	+	frameData.pressureTensor = pressureTensor;
526	+	}
527	+
528	+	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
529	+	frameData.stressTensor = stressTensor;
530	+	}
531	+
532	+	Mat3x3d  Snapshot::getStressTensor() {
533	+	return frameData.stressTensor;
534	+	}
535	+
536	+	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
537	+	frameData.conductiveHeatFlux = chf;
538	+	}
539	+
540	+	Vector3d Snapshot::getConductiveHeatFlux() {
541	+	return frameData.conductiveHeatFlux;
542	+	}
543	+
544	+	Vector3d Snapshot::getConvectiveHeatFlux() {
545	+	return frameData.convectiveHeatFlux;
546	+	}
547	+
548	+	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
549	+	hasConvectiveHeatFlux = true;
550	+	frameData.convectiveHeatFlux = chf;
551	+	}
552	+
553	+	Vector3d Snapshot::getHeatFlux() {
554	+	// BE CAREFUL WITH UNITS
555	+	return getConductiveHeatFlux() + getConvectiveHeatFlux();
556	+	}
557	+
558	+	Vector3d Snapshot::getSystemDipole() {
559	+	return frameData.systemDipole;
560	+	}
561	+
562	+	void Snapshot::setSystemDipole(const Vector3d& bd) {
563	+	hasSystemDipole = true;
564	+	frameData.systemDipole = bd;
565	+	}
566	+
567	+	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
568	+	frameData.thermostat = thermostat;
569	+	}
570	+
571	+	pair<RealType, RealType> Snapshot::getThermostat() {
572	+	return frameData.thermostat;
573	+	}
574	+
575	+	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
576	+	frameData.electronicThermostat = eTherm;
577	+	}
578	+
579	+	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
580	+	return frameData.electronicThermostat;
581	+	}
582	+
583	+	void Snapshot::setBarostat(const Mat3x3d& barostat) {
584	+	frameData.barostat = barostat;
585	+	}
586	+
587	+	Mat3x3d Snapshot::getBarostat() {
588	+	return frameData.barostat;
589	+	}
590	+
591	+	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
592	+	frameData.inertiaTensor = inertiaTensor;
593	+	hasInertiaTensor = true;
594	+	}
595	+
596	+	Mat3x3d Snapshot::getInertiaTensor() {
597	+	return frameData.inertiaTensor;
598	+	}
599	+
600	+	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
601	+	frameData.gyrationalVolume = gyrationalVolume;
602	+	hasGyrationalVolume = true;
603	+	}
604	+
605	+	RealType Snapshot::getGyrationalVolume() {
606	+	return frameData.gyrationalVolume;
607	+	}
608	+
609	+	void Snapshot::setHullVolume(const RealType hullVolume) {
610	+	frameData.hullVolume = hullVolume;
611	+	hasHullVolume = true;
612	+	}
613	+
614	+	RealType Snapshot::getHullVolume() {
615	+	return frameData.hullVolume;
616	+	}
617	+
618	+	void Snapshot::setOrthoTolerance(RealType ot) {
619	+	orthoTolerance_ = ot;
620	+	}
621	+	}

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 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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