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

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trunk/src/brains/Snapshot.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.cpp (file contents), Revision 1838 by gezelter, Tue Jan 22 16:20:11 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, 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
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.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	+	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	+	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	+	clearDerivedProperties();
116	+	}
117	+
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	+	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	+	/** 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	+	/** 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	<	int oldOrthoRhombic = orthoRhombic_;
201	>	bool oldOrthoRhombic = frameData.orthoRhombic;
202
203	<	RealType smallDiag = fabs(hmat_(0, 0));
204	<	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
205	<	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
206	<	RealType tol = smallDiag * orthoTolerance;
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	<	orthoRhombic_ = 1;
208	>	frameData.orthoRhombic = true;
209
210		for (int i = 0; i < 3; i++ ) {
211		for (int j = 0 ; j < 3; j++) {
212		if (i != j) {
213	<	if (orthoRhombic_) {
214	<	if ( fabs(hmat_(i, j)) >= tol)
215	<	orthoRhombic_ = 0;
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	<	if( oldOrthoRhombic != orthoRhombic_ ){
227	<
228	<	if( orthoRhombic_ ) {
229	<	sprintf( painCave.errMsg,
230	<	"OOPSE is switching from the default Non-Orthorhombic\n"
231	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
232	<	"\tThis is usually a good thing, but if you want the\n"
233	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
234	<	"\tvariable ( currently set to %G ) smaller.\n",
235	<	orthoTolerance);
236	<	painCave.severity = OOPSE_INFO;
237	<	simError();
238	<	}
239	<	else {
240	<	sprintf( painCave.errMsg,
241	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
242	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
243	<	"\tThis is usually because the box has deformed under\n"
244	<	"\tNPTf integration. If you want to live on the edge with\n"
245	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
246	<	"\tvariable ( currently set to %G ) larger.\n",
247	<	orthoTolerance);
248	<	painCave.severity = OOPSE_WARNING;
111	<	simError();
112	<	}
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	<	//notify fortran simulation box has changed
258	<	setFortranBox(fortranHmat, fortranInvHmat, &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	+	RealType Snapshot::getVolume() {
268	+	if (!hasVolume) {
269	+	frameData.volume = frameData.hmat.determinant();
270	+	hasVolume = true;
271	+	}
272	+	return frameData.volume;
273	+	}
274
275	+	void Snapshot::setVolume(RealType vol) {
276	+	hasVolume = true;
277	+	frameData.volume = vol;
278	+	}
279	+
280	+	/** Wrap a vector according to periodic boundary conditions */
281		void Snapshot::wrapVector(Vector3d& pos) {
282	+
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	<	int i;
299	>	/** Scaling a vector to multiples of the periodic box */
300	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
301	>
302		Vector3d scaled;
303
304	<	if( !orthoRhombic_ ){
305	<
304	>	if( !frameData.orthoRhombic )
305	>	scaled = frameData.invHmat * pos;
306	>	else {
307		// calc the scaled coordinates.
308	<	scaled = invHmat_* pos;
308	>	for (int i=0; i<3; i++)
309	>	scaled[i] = pos[i] * frameData.invHmat(i, i);
310	>	}
311
312	<	// wrap the scaled coordinates
313	<	for (i = 0; i < 3; ++i) {
132	<	scaled[i] -= roundMe(scaled[i]);
133	<	}
312	>	return scaled;
313	>	}
314
315	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
316	<	pos = hmat_ * scaled;
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	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
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	<	// calc the scaled coordinates.
400	<	for (i=0; i<3; i++) {
401	<	scaled[i] = pos[i] * invHmat_(i, i);
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	<
405	<	// wrap the scaled coordinates
406	<	for (i = 0; i < 3; ++i) {
407	<	scaled[i] -= roundMe(scaled[i]);
148	<	}
404	>	hasLongRangePotential = true;
405	>	}
406	>	return frameData.longRangePotential;
407	>	}
408
409	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
410	<	for (i=0; i<3; i++) {
411	<	pos[i] = scaled[i] * hmat_(i, i);
412	<	}
413	<
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	<	}
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 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.cpp (property svn:keywords), Revision 1838 by gezelter, Tue Jan 22 16:20:11 2013 UTC

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