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

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trunk/src/brains/Snapshot.cpp (file contents), Revision 890 by gezelter, Thu Feb 16 22:05:48 2006 UTC vs.
branches/development/src/brains/Snapshot.cpp (file contents), Revision 1858 by gezelter, Wed Apr 3 21:32:13 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 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	+	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.bBox = Mat3x3d(0.0);
99	+	frameData.invBbox = Mat3x3d(0.0);
100	+	frameData.orthoRhombic = false;
101	+	frameData.bondPotential = 0.0;
102	+	frameData.bendPotential = 0.0;
103	+	frameData.torsionPotential = 0.0;
104	+	frameData.inversionPotential = 0.0;
105	+	frameData.lrPotentials = potVec(0.0);
106	+	frameData.excludedPotentials = potVec(0.0);
107	+	frameData.restraintPotential = 0.0;
108	+	frameData.rawPotential = 0.0;
109	+	frameData.xyArea = 0.0;
110	+	frameData.volume = 0.0;
111	+	frameData.thermostat = make_pair(0.0, 0.0);
112	+	frameData.electronicThermostat = make_pair(0.0, 0.0);
113	+	frameData.barostat = Mat3x3d(0.0);
114	+	frameData.stressTensor = Mat3x3d(0.0);
115	+	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
116	+
117	+	clearDerivedProperties();
118	+	}
119	+
120	+	void Snapshot::clearDerivedProperties() {
121	+	frameData.totalEnergy = 0.0;
122	+	frameData.translationalKinetic = 0.0;
123	+	frameData.rotationalKinetic = 0.0;
124	+	frameData.kineticEnergy = 0.0;
125	+	frameData.potentialEnergy = 0.0;
126	+	frameData.shortRangePotential = 0.0;
127	+	frameData.longRangePotential = 0.0;
128	+	frameData.pressure = 0.0;
129	+	frameData.temperature = 0.0;
130	+	frameData.pressureTensor = Mat3x3d(0.0);
131	+	frameData.systemDipole = Vector3d(0.0);
132	+	frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
133	+	frameData.electronicTemperature = 0.0;
134	+	frameData.COM = V3Zero;
135	+	frameData.COMvel = V3Zero;
136	+	frameData.COMw = V3Zero;
137	+
138	+	hasTotalEnergy = false;
139	+	hasTranslationalKineticEnergy = false;
140	+	hasRotationalKineticEnergy = false;
141	+	hasKineticEnergy = false;
142	+	hasShortRangePotential = false;
143	+	hasLongRangePotential = false;
144	+	hasPotentialEnergy = false;
145	+	hasXYarea = false;
146	+	hasVolume = false;
147	+	hasPressure = false;
148	+	hasTemperature = false;
149	+	hasElectronicTemperature = false;
150	+	hasCOM = false;
151	+	hasCOMvel = false;
152	+	hasCOMw = false;
153	+	hasPressureTensor = false;
154	+	hasSystemDipole = false;
155	+	hasConvectiveHeatFlux = false;
156	+	hasInertiaTensor = false;
157	+	hasGyrationalVolume = false;
158	+	hasHullVolume = false;
159	+	hasConservedQuantity = false;
160	+	}
161	+
162	+	/** Returns the id of this Snapshot */
163	+	int Snapshot::getID() {
164	+	return frameData.id;
165	+	}
166	+
167	+	/** Sets the id of this Snapshot */
168	+	void Snapshot::setID(int id) {
169	+	frameData.id = id;
170	+	}
171	+
172	+	int Snapshot::getSize() {
173	+	return atomData.getSize() + rigidbodyData.getSize();
174	+	}
175	+
176	+	/** Returns the number of atoms */
177	+	int Snapshot::getNumberOfAtoms() {
178	+	return atomData.getSize();
179	+	}
180	+
181	+	/** Returns the number of rigid bodies */
182	+	int Snapshot::getNumberOfRigidBodies() {
183	+	return rigidbodyData.getSize();
184	+	}
185	+
186	+	/** Returns the number of rigid bodies */
187	+	int Snapshot::getNumberOfCutoffGroups() {
188	+	return cgData.getSize();
189	+	}
190	+
191	+	/** Returns the H-Matrix */
192	+	Mat3x3d Snapshot::getHmat() {
193	+	return frameData.hmat;
194	+	}
195	+
196	+	/** Sets the H-Matrix */
197	+	void Snapshot::setHmat(const Mat3x3d& m) {
198	+	hasVolume = false;
199	+	frameData.hmat = m;
200	+	frameData.invHmat = frameData.hmat.inverse();
201	+
202		//determine whether the box is orthoTolerance or not
203	<	int oldOrthoRhombic = orthoRhombic_;
203	>	bool oldOrthoRhombic = frameData.orthoRhombic;
204
205	<	double smallDiag = fabs(hmat_(0, 0));
206	<	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
207	<	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
208	<	double tol = smallDiag * orthoTolerance;
205	>	RealType smallDiag = fabs(frameData.hmat(0, 0));
206	>	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
207	>	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
208	>	RealType tol = smallDiag * orthoTolerance_;
209
210	<	orthoRhombic_ = 1;
210	>	frameData.orthoRhombic = true;
211
212		for (int i = 0; i < 3; i++ ) {
213		for (int j = 0 ; j < 3; j++) {
214		if (i != j) {
215	<	if (orthoRhombic_) {
216	<	if ( fabs(hmat_(i, j)) >= tol)
217	<	orthoRhombic_ = 0;
215	>	if (frameData.orthoRhombic) {
216	>	if ( fabs(frameData.hmat(i, j)) >= tol)
217	>	frameData.orthoRhombic = false;
218		}
219		}
220		}
221		}
222	+
223	+	if( oldOrthoRhombic != frameData.orthoRhombic){
224	+
225	+	// It is finally time to suppress these warnings once and for
226	+	// all.  They were annoying and not very informative.
227
228	<	if( oldOrthoRhombic != orthoRhombic_ ){
229	<
230	<	if( orthoRhombic_ ) {
231	<	sprintf( painCave.errMsg,
232	<	"OOPSE is switching from the default Non-Orthorhombic\n"
233	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
234	<	"\tThis is usually a good thing, but if you want the\n"
235	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
236	<	"\tvariable ( currently set to %G ) smaller.\n",
237	<	orthoTolerance);
238	<	painCave.severity = OOPSE_INFO;
239	<	simError();
240	<	}
241	<	else {
242	<	sprintf( painCave.errMsg,
243	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
244	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
245	<	"\tThis is usually because the box has deformed under\n"
246	<	"\tNPTf integration. If you want to live on the edge with\n"
247	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
248	<	"\tvariable ( currently set to %G ) larger.\n",
249	<	orthoTolerance);
250	<	painCave.severity = OOPSE_WARNING;
111	<	simError();
112	<	}
228	>	// if( frameData.orthoRhombic ) {
229	>	//   sprintf( painCave.errMsg,
230	>	//         "OpenMD 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 = OPENMD_INFO;
237	>	//   simError();
238	>	// }
239	>	// else {
240	>	//   sprintf( painCave.errMsg,
241	>	//         "OpenMD 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 = OPENMD_WARNING;
249	>	//   simError();
250	>	// }
251		}
252	+	}
253	+
254	+	/** Returns the inverse H-Matrix */
255	+	Mat3x3d Snapshot::getInvHmat() {
256	+	return frameData.invHmat;
257	+	}
258
259	<	//notify fortran simulation box has changed
260	<	setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
259	>	/** Returns the Bounding Box */
260	>	Mat3x3d Snapshot::getBoundingBox() {
261	>	return frameData.bBox;
262		}
263
264	+	/** Sets the Bounding Box */
265	+	void Snapshot::setBoundingBox(const Mat3x3d& m) {
266	+	frameData.bBox = m;
267	+	frameData.invBbox = frameData.bBox.inverse();
268	+	}
269
270	<	void Snapshot::wrapVector(Vector3d& pos) {
270	>	/** Returns the inverse Bounding Box */
271	>	Mat3x3d Snapshot::getInvBoundingBox() {
272	>	return frameData.invBbox;
273	>	}
274
275	<	int i;
276	<	Vector3d scaled;
275	>	RealType Snapshot::getXYarea() {
276	>	if (!hasXYarea) {
277	>	Vector3d x = frameData.hmat.getColumn(0);
278	>	Vector3d y = frameData.hmat.getColumn(1);
279	>	frameData.xyArea = cross(x,y).length();
280	>	hasXYarea = true;
281	>	}
282	>	return frameData.xyArea;
283	>	}
284
285	<	if( !orthoRhombic_ ){
285	>	RealType Snapshot::getVolume() {
286	>	if (!hasVolume) {
287	>	frameData.volume = frameData.hmat.determinant();
288	>	hasVolume = true;
289	>	}
290	>	return frameData.volume;
291	>	}
292
293	<	// calc the scaled coordinates.
294	<	scaled = invHmat_* pos;
293	>	void Snapshot::setVolume(RealType vol) {
294	>	hasVolume = true;
295	>	frameData.volume = vol;
296	>	}
297
298	<	// wrap the scaled coordinates
299	<	for (i = 0; i < 3; ++i) {
300	<	scaled[i] -= roundMe(scaled[i]);
301	<	}
302	<
298	>	/** Wrap a vector according to periodic boundary conditions */
299	>	void Snapshot::wrapVector(Vector3d& pos) {
300	>
301	>	Vector3d scaled = scaleVector(pos);
302	>
303	>	for (int i = 0; i < 3; i++)
304	>	scaled[i] -= roundMe(scaled[i]);
305	>
306	>	if( !frameData.orthoRhombic )
307	>	pos = frameData.hmat * scaled;
308	>	else {
309	>
310		// calc the wrapped real coordinates from the wrapped scaled coordinates
311	<	pos = hmat_ * scaled;
311	>	for (int i=0; i<3; i++) {
312	>	pos[i] = scaled[i] * frameData.hmat(i, i);
313	>	}
314	>	}
315	>	}
316
317	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
317	>	/** Scaling a vector to multiples of the periodic box */
318	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
319
320	+	Vector3d scaled;
321	+
322	+	if( !frameData.orthoRhombic )
323	+	scaled = frameData.invHmat * pos;
324	+	else {
325		// calc the scaled coordinates.
326	<	for (i=0; i<3; i++) {
327	<	scaled[i] = pos[i] * invHmat_(i, i);
328	<	}
144	<
145	<	// wrap the scaled coordinates
146	<	for (i = 0; i < 3; ++i) {
147	<	scaled[i] -= roundMe(scaled[i]);
148	<	}
326	>	for (int i=0; i<3; i++)
327	>	scaled[i] = pos[i] * frameData.invHmat(i, i);
328	>	}
329
330	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
331	<	for (i=0; i<3; i++) {
332	<	pos[i] = scaled[i] * hmat_(i, i);
330	>	return scaled;
331	>	}
332	>
333	>	void Snapshot::setCOM(const Vector3d& com) {
334	>	frameData.COM = com;
335	>	hasCOM = true;
336	>	}
337	>
338	>	void Snapshot::setCOMvel(const Vector3d& comVel) {
339	>	frameData.COMvel = comVel;
340	>	hasCOMvel = true;
341	>	}
342	>
343	>	void Snapshot::setCOMw(const Vector3d& comw) {
344	>	frameData.COMw = comw;
345	>	hasCOMw = true;
346	>	}
347	>
348	>	Vector3d Snapshot::getCOM() {
349	>	return frameData.COM;
350	>	}
351	>
352	>	Vector3d Snapshot::getCOMvel() {
353	>	return frameData.COMvel;
354	>	}
355	>
356	>	Vector3d Snapshot::getCOMw() {
357	>	return frameData.COMw;
358	>	}
359	>
360	>	RealType Snapshot::getTime() {
361	>	return frameData.currentTime;
362	>	}
363	>
364	>	void Snapshot::increaseTime(RealType dt) {
365	>	setTime(getTime() + dt);
366	>	}
367	>
368	>	void Snapshot::setTime(RealType time) {
369	>	frameData.currentTime = time;
370	>	}
371	>
372	>	void Snapshot::setBondPotential(RealType bp) {
373	>	frameData.bondPotential = bp;
374	>	}
375	>
376	>	void Snapshot::setBendPotential(RealType bp) {
377	>	frameData.bendPotential = bp;
378	>	}
379	>
380	>	void Snapshot::setTorsionPotential(RealType tp) {
381	>	frameData.torsionPotential = tp;
382	>	}
383	>
384	>	void Snapshot::setInversionPotential(RealType ip) {
385	>	frameData.inversionPotential = ip;
386	>	}
387	>
388	>
389	>	RealType Snapshot::getBondPotential() {
390	>	return frameData.bondPotential;
391	>	}
392	>	RealType Snapshot::getBendPotential() {
393	>	return frameData.bendPotential;
394	>	}
395	>	RealType Snapshot::getTorsionPotential() {
396	>	return frameData.torsionPotential;
397	>	}
398	>	RealType Snapshot::getInversionPotential() {
399	>	return frameData.inversionPotential;
400	>	}
401	>
402	>	RealType Snapshot::getShortRangePotential() {
403	>	if (!hasShortRangePotential) {
404	>	frameData.shortRangePotential = frameData.bondPotential;
405	>	frameData.shortRangePotential += frameData.bendPotential;
406	>	frameData.shortRangePotential += frameData.torsionPotential;
407	>	frameData.shortRangePotential += frameData.inversionPotential;
408	>	hasShortRangePotential = true;
409	>	}
410	>	return frameData.shortRangePotential;
411	>	}
412	>
413	>	void Snapshot::setLongRangePotential(potVec lrPot) {
414	>	frameData.lrPotentials = lrPot;
415	>	}
416	>
417	>	RealType Snapshot::getLongRangePotential() {
418	>	if (!hasLongRangePotential) {
419	>	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
420	>	frameData.longRangePotential += frameData.lrPotentials[i];
421		}
422	<
422	>	hasLongRangePotential = true;
423	>	}
424	>	return frameData.longRangePotential;
425	>	}
426	>
427	>	potVec Snapshot::getLongRangePotentials() {
428	>	return frameData.lrPotentials;
429	>	}
430	>
431	>	RealType Snapshot::getPotentialEnergy() {
432	>	if (!hasPotentialEnergy) {
433	>	frameData.potentialEnergy = this->getLongRangePotential();
434	>	frameData.potentialEnergy += this->getShortRangePotential();
435	>	hasPotentialEnergy = true;
436		}
437	+	return frameData.potentialEnergy;
438	+	}
439	+
440	+	void Snapshot::setExcludedPotentials(potVec exPot) {
441	+	frameData.excludedPotentials = exPot;
442	+	}
443
444	+	potVec Snapshot::getExcludedPotentials() {
445	+	return frameData.excludedPotentials;
446		}
447	+
448	+	void Snapshot::setRestraintPotential(RealType rp) {
449	+	frameData.restraintPotential = rp;
450	+	}
451	+
452	+	RealType Snapshot::getRestraintPotential() {
453	+	return frameData.restraintPotential;
454	+	}
455	+
456	+	void Snapshot::setRawPotential(RealType rp) {
457	+	frameData.rawPotential = rp;
458	+	}
459	+
460	+	RealType Snapshot::getRawPotential() {
461	+	return frameData.rawPotential;
462	+	}
463
464	<	}
464	>	RealType Snapshot::getTranslationalKineticEnergy() {
465	>	return frameData.translationalKinetic;
466	>	}
467	>
468	>	RealType Snapshot::getRotationalKineticEnergy() {
469	>	return frameData.rotationalKinetic;
470	>	}
471	>
472	>	RealType Snapshot::getKineticEnergy() {
473	>	return frameData.kineticEnergy;
474	>	}
475	>
476	>	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
477	>	hasTranslationalKineticEnergy = true;
478	>	frameData.translationalKinetic = tke;
479	>	}
480	>
481	>	void Snapshot::setRotationalKineticEnergy(RealType rke) {
482	>	hasRotationalKineticEnergy = true;
483	>	frameData.rotationalKinetic = rke;
484	>	}
485	>
486	>	void Snapshot::setKineticEnergy(RealType ke) {
487	>	hasKineticEnergy = true;
488	>	frameData.kineticEnergy = ke;
489	>	}
490	>
491	>	RealType Snapshot::getTotalEnergy() {
492	>	return frameData.totalEnergy;
493	>	}
494	>
495	>	void Snapshot::setTotalEnergy(RealType te) {
496	>	hasTotalEnergy = true;
497	>	frameData.totalEnergy = te;
498	>	}
499	>
500	>	RealType Snapshot::getConservedQuantity() {
501	>	return frameData.conservedQuantity;
502	>	}
503	>
504	>	void Snapshot::setConservedQuantity(RealType cq) {
505	>	hasConservedQuantity = true;
506	>	frameData.conservedQuantity = cq;
507	>	}
508	>
509	>	RealType Snapshot::getTemperature() {
510	>	return frameData.temperature;
511	>	}
512	>
513	>	void Snapshot::setTemperature(RealType temp) {
514	>	hasTemperature = true;
515	>	frameData.temperature = temp;
516	>	}
517	>
518	>	RealType Snapshot::getElectronicTemperature() {
519	>	return frameData.electronicTemperature;
520	>	}
521	>
522	>	void Snapshot::setElectronicTemperature(RealType eTemp) {
523	>	hasElectronicTemperature = true;
524	>	frameData.electronicTemperature = eTemp;
525	>	}
526	>
527	>	RealType Snapshot::getPressure() {
528	>	return frameData.pressure;
529	>	}
530	>
531	>	void Snapshot::setPressure(RealType pressure) {
532	>	hasPressure = true;
533	>	frameData.pressure = pressure;
534	>	}
535	>
536	>	Mat3x3d Snapshot::getPressureTensor() {
537	>	return frameData.pressureTensor;
538	>	}
539	>
540	>
541	>	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
542	>	hasPressureTensor = true;
543	>	frameData.pressureTensor = pressureTensor;
544	>	}
545	>
546	>	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
547	>	frameData.stressTensor = stressTensor;
548	>	}
549	>
550	>	Mat3x3d  Snapshot::getStressTensor() {
551	>	return frameData.stressTensor;
552	>	}
553	>
554	>	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
555	>	frameData.conductiveHeatFlux = chf;
556	>	}
557	>
558	>	Vector3d Snapshot::getConductiveHeatFlux() {
559	>	return frameData.conductiveHeatFlux;
560	>	}
561
562	+	Vector3d Snapshot::getConvectiveHeatFlux() {
563	+	return frameData.convectiveHeatFlux;
564	+	}
565	+
566	+	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
567	+	hasConvectiveHeatFlux = true;
568	+	frameData.convectiveHeatFlux = chf;
569	+	}
570	+
571	+	Vector3d Snapshot::getHeatFlux() {
572	+	// BE CAREFUL WITH UNITS
573	+	return getConductiveHeatFlux() + getConvectiveHeatFlux();
574	+	}
575	+
576	+	Vector3d Snapshot::getSystemDipole() {
577	+	return frameData.systemDipole;
578	+	}
579	+
580	+	void Snapshot::setSystemDipole(const Vector3d& bd) {
581	+	hasSystemDipole = true;
582	+	frameData.systemDipole = bd;
583	+	}
584	+
585	+	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
586	+	frameData.thermostat = thermostat;
587	+	}
588	+
589	+	pair<RealType, RealType> Snapshot::getThermostat() {
590	+	return frameData.thermostat;
591	+	}
592	+
593	+	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
594	+	frameData.electronicThermostat = eTherm;
595	+	}
596	+
597	+	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
598	+	return frameData.electronicThermostat;
599	+	}
600	+
601	+	void Snapshot::setBarostat(const Mat3x3d& barostat) {
602	+	frameData.barostat = barostat;
603	+	}
604	+
605	+	Mat3x3d Snapshot::getBarostat() {
606	+	return frameData.barostat;
607	+	}
608	+
609	+	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
610	+	frameData.inertiaTensor = inertiaTensor;
611	+	hasInertiaTensor = true;
612	+	}
613	+
614	+	Mat3x3d Snapshot::getInertiaTensor() {
615	+	return frameData.inertiaTensor;
616	+	}
617	+
618	+	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
619	+	frameData.gyrationalVolume = gyrationalVolume;
620	+	hasGyrationalVolume = true;
621	+	}
622	+
623	+	RealType Snapshot::getGyrationalVolume() {
624	+	return frameData.gyrationalVolume;
625	+	}
626	+
627	+	void Snapshot::setHullVolume(const RealType hullVolume) {
628	+	frameData.hullVolume = hullVolume;
629	+	hasHullVolume = true;
630	+	}
631	+
632	+	RealType Snapshot::getHullVolume() {
633	+	return frameData.hullVolume;
634	+	}
635	+
636	+	void Snapshot::setOrthoTolerance(RealType ot) {
637	+	orthoTolerance_ = ot;
638	+	}
639	+	}

Comparing:
trunk/src/brains/Snapshot.cpp (property svn:keywords), Revision 890 by gezelter, Thu Feb 16 22:05:48 2006 UTC vs.
branches/development/src/brains/Snapshot.cpp (property svn:keywords), Revision 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

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