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Comparing trunk/src/brains/Snapshot.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

#	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
46	–	* @time 10:56am
47		* @version 1.0
48		*/
49
#	Line 51 | Line 51
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 RealType 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	<	RealType fortranHmat[9];
65	<	RealType 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.reciprocalPotential = 0.0;
74	>	frameData.excludedPotentials = potVec(0.0);
75	>	frameData.restraintPotential = 0.0;
76	>	frameData.rawPotential = 0.0;
77	>	frameData.xyArea = 0.0;
78	>	frameData.volume = 0.0;
79	>	frameData.thermostat = make_pair(0.0, 0.0);
80	>	frameData.electronicThermostat = make_pair(0.0, 0.0);
81	>	frameData.barostat = Mat3x3d(0.0);
82	>	frameData.stressTensor = Mat3x3d(0.0);
83	>	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
84
85	+	clearDerivedProperties();
86	+	}
87	+
88	+	Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
89	+	int storageLayout) :
90	+	atomData(nAtoms, storageLayout),
91	+	rigidbodyData(nRigidbodies, storageLayout),
92	+	cgData(nCutoffGroups, DataStorage::dslPosition),
93	+	orthoTolerance_(1e-6) {
94	+
95	+	frameData.id = -1;
96	+	frameData.currentTime = 0;
97	+	frameData.hmat = Mat3x3d(0.0);
98	+	frameData.invHmat = Mat3x3d(0.0);
99	+	frameData.bBox = Mat3x3d(0.0);
100	+	frameData.invBbox = Mat3x3d(0.0);
101	+	frameData.orthoRhombic = false;
102	+	frameData.bondPotential = 0.0;
103	+	frameData.bendPotential = 0.0;
104	+	frameData.torsionPotential = 0.0;
105	+	frameData.inversionPotential = 0.0;
106	+	frameData.lrPotentials = potVec(0.0);
107	+	frameData.reciprocalPotential = 0.0;
108	+	frameData.excludedPotentials = potVec(0.0);
109	+	frameData.restraintPotential = 0.0;
110	+	frameData.rawPotential = 0.0;
111	+	frameData.xyArea = 0.0;
112	+	frameData.volume = 0.0;
113	+	frameData.thermostat = make_pair(0.0, 0.0);
114	+	frameData.electronicThermostat = make_pair(0.0, 0.0);
115	+	frameData.barostat = Mat3x3d(0.0);
116	+	frameData.stressTensor = Mat3x3d(0.0);
117	+	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
118	+
119	+	clearDerivedProperties();
120	+	}
121	+
122	+	void Snapshot::clearDerivedProperties() {
123	+	frameData.totalEnergy = 0.0;
124	+	frameData.translationalKinetic = 0.0;
125	+	frameData.rotationalKinetic = 0.0;
126	+	frameData.kineticEnergy = 0.0;
127	+	frameData.potentialEnergy = 0.0;
128	+	frameData.shortRangePotential = 0.0;
129	+	frameData.longRangePotential = 0.0;
130	+	frameData.pressure = 0.0;
131	+	frameData.temperature = 0.0;
132	+	frameData.pressureTensor = Mat3x3d(0.0);
133	+	frameData.systemDipole = Vector3d(0.0);
134	+	frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
135	+	frameData.electronicTemperature = 0.0;
136	+	frameData.COM = V3Zero;
137	+	frameData.COMvel = V3Zero;
138	+	frameData.COMw = V3Zero;
139	+
140	+	hasTotalEnergy = false;
141	+	hasTranslationalKineticEnergy = false;
142	+	hasRotationalKineticEnergy = false;
143	+	hasKineticEnergy = false;
144	+	hasShortRangePotential = false;
145	+	hasLongRangePotential = false;
146	+	hasPotentialEnergy = false;
147	+	hasXYarea = false;
148	+	hasVolume = false;
149	+	hasPressure = false;
150	+	hasTemperature = false;
151	+	hasElectronicTemperature = false;
152	+	hasCOM = false;
153	+	hasCOMvel = false;
154	+	hasCOMw = false;
155	+	hasPressureTensor = false;
156	+	hasSystemDipole = false;
157	+	hasConvectiveHeatFlux = false;
158	+	hasInertiaTensor = false;
159	+	hasGyrationalVolume = false;
160	+	hasHullVolume = false;
161	+	hasConservedQuantity = false;
162	+	hasBoundingBox = false;
163	+	}
164	+
165	+	/** Returns the id of this Snapshot */
166	+	int Snapshot::getID() {
167	+	return frameData.id;
168	+	}
169	+
170	+	/** Sets the id of this Snapshot */
171	+	void Snapshot::setID(int id) {
172	+	frameData.id = id;
173	+	}
174	+
175	+	int Snapshot::getSize() {
176	+	return atomData.getSize() + rigidbodyData.getSize();
177	+	}
178	+
179	+	/** Returns the number of atoms */
180	+	int Snapshot::getNumberOfAtoms() {
181	+	return atomData.getSize();
182	+	}
183	+
184	+	/** Returns the number of rigid bodies */
185	+	int Snapshot::getNumberOfRigidBodies() {
186	+	return rigidbodyData.getSize();
187	+	}
188	+
189	+	/** Returns the number of rigid bodies */
190	+	int Snapshot::getNumberOfCutoffGroups() {
191	+	return cgData.getSize();
192	+	}
193	+
194	+	/** Returns the H-Matrix */
195	+	Mat3x3d Snapshot::getHmat() {
196	+	return frameData.hmat;
197	+	}
198	+
199	+	/** Sets the H-Matrix */
200	+	void Snapshot::setHmat(const Mat3x3d& m) {
201	+	hasVolume = false;
202	+	frameData.hmat = m;
203	+	frameData.invHmat = frameData.hmat.inverse();
204	+
205		//determine whether the box is orthoTolerance or not
206	<	int oldOrthoRhombic = orthoRhombic_;
206	>	bool oldOrthoRhombic = frameData.orthoRhombic;
207
208	<	RealType smallDiag = fabs(hmat_(0, 0));
209	<	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
210	<	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
211	<	RealType tol = smallDiag * orthoTolerance;
208	>	RealType smallDiag = fabs(frameData.hmat(0, 0));
209	>	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
210	>	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
211	>	RealType tol = smallDiag * orthoTolerance_;
212
213	<	orthoRhombic_ = 1;
213	>	frameData.orthoRhombic = true;
214
215		for (int i = 0; i < 3; i++ ) {
216		for (int j = 0 ; j < 3; j++) {
217		if (i != j) {
218	<	if (orthoRhombic_) {
219	<	if ( fabs(hmat_(i, j)) >= tol)
220	<	orthoRhombic_ = 0;
218	>	if (frameData.orthoRhombic) {
219	>	if ( fabs(frameData.hmat(i, j)) >= tol)
220	>	frameData.orthoRhombic = false;
221		}
222		}
223		}
224		}
225	+
226	+	if( oldOrthoRhombic != frameData.orthoRhombic){
227	+
228	+	// It is finally time to suppress these warnings once and for
229	+	// all.  They were annoying and not very informative.
230
231	<	if( oldOrthoRhombic != orthoRhombic_ ){
232	<
233	<	if( orthoRhombic_ ) {
234	<	sprintf( painCave.errMsg,
235	<	"OOPSE is switching from the default Non-Orthorhombic\n"
236	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
237	<	"\tThis is usually a good thing, but if you want the\n"
238	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
239	<	"\tvariable ( currently set to %G ) smaller.\n",
240	<	orthoTolerance);
241	<	painCave.severity = OOPSE_INFO;
242	<	simError();
243	<	}
244	<	else {
245	<	sprintf( painCave.errMsg,
246	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
247	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
248	<	"\tThis is usually because the box has deformed under\n"
249	<	"\tNPTf integration. If you want to live on the edge with\n"
250	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
251	<	"\tvariable ( currently set to %G ) larger.\n",
252	<	orthoTolerance);
253	<	painCave.severity = OOPSE_WARNING;
111	<	simError();
112	<	}
231	>	// if( frameData.orthoRhombic ) {
232	>	//   sprintf( painCave.errMsg,
233	>	//         "OpenMD is switching from the default Non-Orthorhombic\n"
234	>	//         "\tto the faster Orthorhombic periodic boundary computations.\n"
235	>	//         "\tThis is usually a good thing, but if you want the\n"
236	>	//         "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
237	>	//         "\tvariable ( currently set to %G ) smaller.\n",
238	>	//         orthoTolerance_);
239	>	//   painCave.severity = OPENMD_INFO;
240	>	//   simError();
241	>	// }
242	>	// else {
243	>	//   sprintf( painCave.errMsg,
244	>	//         "OpenMD is switching from the faster Orthorhombic to the more\n"
245	>	//         "\tflexible Non-Orthorhombic periodic boundary computations.\n"
246	>	//         "\tThis is usually because the box has deformed under\n"
247	>	//         "\tNPTf integration. If you want to live on the edge with\n"
248	>	//         "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
249	>	//         "\tvariable ( currently set to %G ) larger.\n",
250	>	//         orthoTolerance_);
251	>	//   painCave.severity = OPENMD_WARNING;
252	>	//   simError();
253	>	// }
254		}
255	+	}
256	+
257	+	/** Returns the inverse H-Matrix */
258	+	Mat3x3d Snapshot::getInvHmat() {
259	+	return frameData.invHmat;
260	+	}
261
262	<	//notify fortran simulation box has changed
263	<	setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
262	>	/** Returns the Bounding Box */
263	>	Mat3x3d Snapshot::getBoundingBox() {
264	>	return frameData.bBox;
265		}
266
267	+	/** Sets the Bounding Box */
268	+	void Snapshot::setBoundingBox(const Mat3x3d& m) {
269	+	frameData.bBox = m;
270	+	frameData.invBbox = frameData.bBox.inverse();
271	+	hasBoundingBox = true;
272	+	}
273
274	<	void Snapshot::wrapVector(Vector3d& pos) {
274	>	/** Returns the inverse Bounding Box */
275	>	Mat3x3d Snapshot::getInvBoundingBox() {
276	>	return frameData.invBbox;
277	>	}
278
279	<	int i;
280	<	Vector3d scaled;
279	>	RealType Snapshot::getXYarea() {
280	>	if (!hasXYarea) {
281	>	Vector3d x = frameData.hmat.getColumn(0);
282	>	Vector3d y = frameData.hmat.getColumn(1);
283	>	frameData.xyArea = cross(x,y).length();
284	>	hasXYarea = true;
285	>	}
286	>	return frameData.xyArea;
287	>	}
288
289	<	if( !orthoRhombic_ ){
289	>	RealType Snapshot::getVolume() {
290	>	if (!hasVolume) {
291	>	frameData.volume = frameData.hmat.determinant();
292	>	hasVolume = true;
293	>	}
294	>	return frameData.volume;
295	>	}
296
297	<	// calc the scaled coordinates.
298	<	scaled = invHmat_* pos;
297	>	void Snapshot::setVolume(RealType vol) {
298	>	hasVolume = true;
299	>	frameData.volume = vol;
300	>	}
301
130	–	// wrap the scaled coordinates
131	–	for (i = 0; i < 3; ++i) {
132	–	scaled[i] -= roundMe(scaled[i]);
133	–	}
302
303	+	/** Wrap a vector according to periodic boundary conditions */
304	+	void Snapshot::wrapVector(Vector3d& pos) {
305	+
306	+	if( !frameData.orthoRhombic ) {
307	+	Vector3d scaled = frameData.invHmat * pos;
308	+	for (int i = 0; i < 3; i++) {
309	+	scaled[i] -= roundMe( scaled[i] );
310	+	}
311		// calc the wrapped real coordinates from the wrapped scaled coordinates
312	<	pos = hmat_ * scaled;
312	>	pos = frameData.hmat * scaled;
313	>	} else {
314	>	RealType scaled;
315	>	for (int i=0; i<3; i++) {
316	>	scaled = pos[i] * frameData.invHmat(i,i);
317	>	scaled -= roundMe( scaled );
318	>	pos[i] = scaled * frameData.hmat(i,i);
319	>	}
320	>	}
321	>	}
322
323	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
323	>	/** Scaling a vector to multiples of the periodic box */
324	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
325
326	+	Vector3d scaled;
327	+
328	+	if( !frameData.orthoRhombic )
329	+	scaled = frameData.invHmat * pos;
330	+	else {
331		// calc the scaled coordinates.
332	<	for (i=0; i<3; i++) {
333	<	scaled[i] = pos[i] * invHmat_(i, i);
334	<	}
144	<
145	<	// wrap the scaled coordinates
146	<	for (i = 0; i < 3; ++i) {
147	<	scaled[i] -= roundMe(scaled[i]);
148	<	}
332	>	for (int i=0; i<3; i++)
333	>	scaled[i] = pos[i] * frameData.invHmat(i, i);
334	>	}
335
336	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
337	<	for (i=0; i<3; i++) {
338	<	pos[i] = scaled[i] * hmat_(i, i);
336	>	return scaled;
337	>	}
338	>
339	>	void Snapshot::setCOM(const Vector3d& com) {
340	>	frameData.COM = com;
341	>	hasCOM = true;
342	>	}
343	>
344	>	void Snapshot::setCOMvel(const Vector3d& comVel) {
345	>	frameData.COMvel = comVel;
346	>	hasCOMvel = true;
347	>	}
348	>
349	>	void Snapshot::setCOMw(const Vector3d& comw) {
350	>	frameData.COMw = comw;
351	>	hasCOMw = true;
352	>	}
353	>
354	>	Vector3d Snapshot::getCOM() {
355	>	return frameData.COM;
356	>	}
357	>
358	>	Vector3d Snapshot::getCOMvel() {
359	>	return frameData.COMvel;
360	>	}
361	>
362	>	Vector3d Snapshot::getCOMw() {
363	>	return frameData.COMw;
364	>	}
365	>
366	>	RealType Snapshot::getTime() {
367	>	return frameData.currentTime;
368	>	}
369	>
370	>	void Snapshot::increaseTime(RealType dt) {
371	>	setTime(getTime() + dt);
372	>	}
373	>
374	>	void Snapshot::setTime(RealType time) {
375	>	frameData.currentTime = time;
376	>	}
377	>
378	>	void Snapshot::setBondPotential(RealType bp) {
379	>	frameData.bondPotential = bp;
380	>	}
381	>
382	>	void Snapshot::setBendPotential(RealType bp) {
383	>	frameData.bendPotential = bp;
384	>	}
385	>
386	>	void Snapshot::setTorsionPotential(RealType tp) {
387	>	frameData.torsionPotential = tp;
388	>	}
389	>
390	>	void Snapshot::setInversionPotential(RealType ip) {
391	>	frameData.inversionPotential = ip;
392	>	}
393	>
394	>
395	>	RealType Snapshot::getBondPotential() {
396	>	return frameData.bondPotential;
397	>	}
398	>	RealType Snapshot::getBendPotential() {
399	>	return frameData.bendPotential;
400	>	}
401	>	RealType Snapshot::getTorsionPotential() {
402	>	return frameData.torsionPotential;
403	>	}
404	>	RealType Snapshot::getInversionPotential() {
405	>	return frameData.inversionPotential;
406	>	}
407	>
408	>	RealType Snapshot::getShortRangePotential() {
409	>	if (!hasShortRangePotential) {
410	>	frameData.shortRangePotential = frameData.bondPotential;
411	>	frameData.shortRangePotential += frameData.bendPotential;
412	>	frameData.shortRangePotential += frameData.torsionPotential;
413	>	frameData.shortRangePotential += frameData.inversionPotential;
414	>	hasShortRangePotential = true;
415	>	}
416	>	return frameData.shortRangePotential;
417	>	}
418	>
419	>	void Snapshot::setReciprocalPotential(RealType rp){
420	>	frameData.reciprocalPotential = rp;
421	>	}
422	>
423	>	RealType Snapshot::getReciprocalPotential() {
424	>	return frameData.reciprocalPotential;
425	>	}
426	>
427	>	void Snapshot::setLongRangePotential(potVec lrPot) {
428	>	frameData.lrPotentials = lrPot;
429	>	}
430	>
431	>	RealType Snapshot::getLongRangePotential() {
432	>	if (!hasLongRangePotential) {
433	>	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
434	>	frameData.longRangePotential += frameData.lrPotentials[i];
435		}
436	<
436	>	frameData.longRangePotential += frameData.reciprocalPotential;
437	>	hasLongRangePotential = true;
438	>	}
439	>	return frameData.longRangePotential;
440	>	}
441	>
442	>	potVec Snapshot::getLongRangePotentials() {
443	>	return frameData.lrPotentials;
444	>	}
445	>
446	>	RealType Snapshot::getPotentialEnergy() {
447	>	if (!hasPotentialEnergy) {
448	>	frameData.potentialEnergy = this->getLongRangePotential();
449	>	frameData.potentialEnergy += this->getShortRangePotential();
450	>	hasPotentialEnergy = true;
451		}
452	+	return frameData.potentialEnergy;
453	+	}
454	+
455	+	void Snapshot::setExcludedPotentials(potVec exPot) {
456	+	frameData.excludedPotentials = exPot;
457	+	}
458
459	+	potVec Snapshot::getExcludedPotentials() {
460	+	return frameData.excludedPotentials;
461		}
462	+
463	+	void Snapshot::setRestraintPotential(RealType rp) {
464	+	frameData.restraintPotential = rp;
465	+	}
466	+
467	+	RealType Snapshot::getRestraintPotential() {
468	+	return frameData.restraintPotential;
469	+	}
470	+
471	+	void Snapshot::setRawPotential(RealType rp) {
472	+	frameData.rawPotential = rp;
473	+	}
474	+
475	+	RealType Snapshot::getRawPotential() {
476	+	return frameData.rawPotential;
477	+	}
478
479	<	}
479	>	RealType Snapshot::getTranslationalKineticEnergy() {
480	>	return frameData.translationalKinetic;
481	>	}
482	>
483	>	RealType Snapshot::getRotationalKineticEnergy() {
484	>	return frameData.rotationalKinetic;
485	>	}
486	>
487	>	RealType Snapshot::getKineticEnergy() {
488	>	return frameData.kineticEnergy;
489	>	}
490	>
491	>	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
492	>	hasTranslationalKineticEnergy = true;
493	>	frameData.translationalKinetic = tke;
494	>	}
495	>
496	>	void Snapshot::setRotationalKineticEnergy(RealType rke) {
497	>	hasRotationalKineticEnergy = true;
498	>	frameData.rotationalKinetic = rke;
499	>	}
500	>
501	>	void Snapshot::setKineticEnergy(RealType ke) {
502	>	hasKineticEnergy = true;
503	>	frameData.kineticEnergy = ke;
504	>	}
505	>
506	>	RealType Snapshot::getTotalEnergy() {
507	>	return frameData.totalEnergy;
508	>	}
509	>
510	>	void Snapshot::setTotalEnergy(RealType te) {
511	>	hasTotalEnergy = true;
512	>	frameData.totalEnergy = te;
513	>	}
514	>
515	>	RealType Snapshot::getConservedQuantity() {
516	>	return frameData.conservedQuantity;
517	>	}
518	>
519	>	void Snapshot::setConservedQuantity(RealType cq) {
520	>	hasConservedQuantity = true;
521	>	frameData.conservedQuantity = cq;
522	>	}
523	>
524	>	RealType Snapshot::getTemperature() {
525	>	return frameData.temperature;
526	>	}
527	>
528	>	void Snapshot::setTemperature(RealType temp) {
529	>	hasTemperature = true;
530	>	frameData.temperature = temp;
531	>	}
532	>
533	>	RealType Snapshot::getElectronicTemperature() {
534	>	return frameData.electronicTemperature;
535	>	}
536	>
537	>	void Snapshot::setElectronicTemperature(RealType eTemp) {
538	>	hasElectronicTemperature = true;
539	>	frameData.electronicTemperature = eTemp;
540	>	}
541	>
542	>	RealType Snapshot::getPressure() {
543	>	return frameData.pressure;
544	>	}
545	>
546	>	void Snapshot::setPressure(RealType pressure) {
547	>	hasPressure = true;
548	>	frameData.pressure = pressure;
549	>	}
550	>
551	>	Mat3x3d Snapshot::getPressureTensor() {
552	>	return frameData.pressureTensor;
553	>	}
554	>
555	>
556	>	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
557	>	hasPressureTensor = true;
558	>	frameData.pressureTensor = pressureTensor;
559	>	}
560	>
561	>	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
562	>	frameData.stressTensor = stressTensor;
563	>	}
564	>
565	>	Mat3x3d  Snapshot::getStressTensor() {
566	>	return frameData.stressTensor;
567	>	}
568	>
569	>	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
570	>	frameData.conductiveHeatFlux = chf;
571	>	}
572	>
573	>	Vector3d Snapshot::getConductiveHeatFlux() {
574	>	return frameData.conductiveHeatFlux;
575	>	}
576
577	+	Vector3d Snapshot::getConvectiveHeatFlux() {
578	+	return frameData.convectiveHeatFlux;
579	+	}
580	+
581	+	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
582	+	hasConvectiveHeatFlux = true;
583	+	frameData.convectiveHeatFlux = chf;
584	+	}
585	+
586	+	Vector3d Snapshot::getHeatFlux() {
587	+	// BE CAREFUL WITH UNITS
588	+	return getConductiveHeatFlux() + getConvectiveHeatFlux();
589	+	}
590	+
591	+	Vector3d Snapshot::getSystemDipole() {
592	+	return frameData.systemDipole;
593	+	}
594	+
595	+	void Snapshot::setSystemDipole(const Vector3d& bd) {
596	+	hasSystemDipole = true;
597	+	frameData.systemDipole = bd;
598	+	}
599	+
600	+	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
601	+	frameData.thermostat = thermostat;
602	+	}
603	+
604	+	pair<RealType, RealType> Snapshot::getThermostat() {
605	+	return frameData.thermostat;
606	+	}
607	+
608	+	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
609	+	frameData.electronicThermostat = eTherm;
610	+	}
611	+
612	+	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
613	+	return frameData.electronicThermostat;
614	+	}
615	+
616	+	void Snapshot::setBarostat(const Mat3x3d& barostat) {
617	+	frameData.barostat = barostat;
618	+	}
619	+
620	+	Mat3x3d Snapshot::getBarostat() {
621	+	return frameData.barostat;
622	+	}
623	+
624	+	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
625	+	frameData.inertiaTensor = inertiaTensor;
626	+	hasInertiaTensor = true;
627	+	}
628	+
629	+	Mat3x3d Snapshot::getInertiaTensor() {
630	+	return frameData.inertiaTensor;
631	+	}
632	+
633	+	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
634	+	frameData.gyrationalVolume = gyrationalVolume;
635	+	hasGyrationalVolume = true;
636	+	}
637	+
638	+	RealType Snapshot::getGyrationalVolume() {
639	+	return frameData.gyrationalVolume;
640	+	}
641	+
642	+	void Snapshot::setHullVolume(const RealType hullVolume) {
643	+	frameData.hullVolume = hullVolume;
644	+	hasHullVolume = true;
645	+	}
646	+
647	+	RealType Snapshot::getHullVolume() {
648	+	return frameData.hullVolume;
649	+	}
650	+
651	+	void Snapshot::setOrthoTolerance(RealType ot) {
652	+	orthoTolerance_ = ot;
653	+	}
654	+	}

Comparing trunk/src/brains/Snapshot.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

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