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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 1879 by gezelter, Sun Jun 16 15:15:42 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.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	+	hasBoundingBox = false;
161	+	}
162	+
163	+	/** Returns the id of this Snapshot */
164	+	int Snapshot::getID() {
165	+	return frameData.id;
166	+	}
167	+
168	+	/** Sets the id of this Snapshot */
169	+	void Snapshot::setID(int id) {
170	+	frameData.id = id;
171	+	}
172	+
173	+	int Snapshot::getSize() {
174	+	return atomData.getSize() + rigidbodyData.getSize();
175	+	}
176	+
177	+	/** Returns the number of atoms */
178	+	int Snapshot::getNumberOfAtoms() {
179	+	return atomData.getSize();
180	+	}
181	+
182	+	/** Returns the number of rigid bodies */
183	+	int Snapshot::getNumberOfRigidBodies() {
184	+	return rigidbodyData.getSize();
185	+	}
186	+
187	+	/** Returns the number of rigid bodies */
188	+	int Snapshot::getNumberOfCutoffGroups() {
189	+	return cgData.getSize();
190	+	}
191	+
192	+	/** Returns the H-Matrix */
193	+	Mat3x3d Snapshot::getHmat() {
194	+	return frameData.hmat;
195	+	}
196	+
197	+	/** Sets the H-Matrix */
198	+	void Snapshot::setHmat(const Mat3x3d& m) {
199	+	hasVolume = false;
200	+	frameData.hmat = m;
201	+	frameData.invHmat = frameData.hmat.inverse();
202	+
203		//determine whether the box is orthoTolerance or not
204	<	int oldOrthoRhombic = orthoRhombic_;
204	>	bool oldOrthoRhombic = frameData.orthoRhombic;
205
206	<	RealType smallDiag = fabs(hmat_(0, 0));
207	<	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
208	<	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
209	<	RealType tol = smallDiag * orthoTolerance;
206	>	RealType smallDiag = fabs(frameData.hmat(0, 0));
207	>	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
208	>	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
209	>	RealType tol = smallDiag * orthoTolerance_;
210
211	<	orthoRhombic_ = 1;
211	>	frameData.orthoRhombic = true;
212
213		for (int i = 0; i < 3; i++ ) {
214		for (int j = 0 ; j < 3; j++) {
215		if (i != j) {
216	<	if (orthoRhombic_) {
217	<	if ( fabs(hmat_(i, j)) >= tol)
218	<	orthoRhombic_ = 0;
216	>	if (frameData.orthoRhombic) {
217	>	if ( fabs(frameData.hmat(i, j)) >= tol)
218	>	frameData.orthoRhombic = false;
219		}
220		}
221		}
222		}
223	+
224	+	if( oldOrthoRhombic != frameData.orthoRhombic){
225	+
226	+	// It is finally time to suppress these warnings once and for
227	+	// all.  They were annoying and not very informative.
228
229	<	if( oldOrthoRhombic != orthoRhombic_ ){
230	<
231	<	if( orthoRhombic_ ) {
232	<	sprintf( painCave.errMsg,
233	<	"OOPSE 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 = OOPSE_INFO;
240	<	simError();
241	<	}
242	<	else {
243	<	sprintf( painCave.errMsg,
244	<	"OOPSE 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 = OOPSE_WARNING;
111	<	simError();
112	<	}
229	>	// if( frameData.orthoRhombic ) {
230	>	//   sprintf( painCave.errMsg,
231	>	//         "OpenMD is switching from the default Non-Orthorhombic\n"
232	>	//         "\tto the faster Orthorhombic periodic boundary computations.\n"
233	>	//         "\tThis is usually a good thing, but if you want the\n"
234	>	//         "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
235	>	//         "\tvariable ( currently set to %G ) smaller.\n",
236	>	//         orthoTolerance_);
237	>	//   painCave.severity = OPENMD_INFO;
238	>	//   simError();
239	>	// }
240	>	// else {
241	>	//   sprintf( painCave.errMsg,
242	>	//         "OpenMD is switching from the faster Orthorhombic to the more\n"
243	>	//         "\tflexible Non-Orthorhombic periodic boundary computations.\n"
244	>	//         "\tThis is usually because the box has deformed under\n"
245	>	//         "\tNPTf integration. If you want to live on the edge with\n"
246	>	//         "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
247	>	//         "\tvariable ( currently set to %G ) larger.\n",
248	>	//         orthoTolerance_);
249	>	//   painCave.severity = OPENMD_WARNING;
250	>	//   simError();
251	>	// }
252		}
253	+	}
254	+
255	+	/** Returns the inverse H-Matrix */
256	+	Mat3x3d Snapshot::getInvHmat() {
257	+	return frameData.invHmat;
258	+	}
259
260	<	//notify fortran simulation box has changed
261	<	setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
260	>	/** Returns the Bounding Box */
261	>	Mat3x3d Snapshot::getBoundingBox() {
262	>	return frameData.bBox;
263		}
264
265	+	/** Sets the Bounding Box */
266	+	void Snapshot::setBoundingBox(const Mat3x3d& m) {
267	+	frameData.bBox = m;
268	+	frameData.invBbox = frameData.bBox.inverse();
269	+	hasBoundingBox = true;
270	+	}
271
272	<	void Snapshot::wrapVector(Vector3d& pos) {
272	>	/** Returns the inverse Bounding Box */
273	>	Mat3x3d Snapshot::getInvBoundingBox() {
274	>	return frameData.invBbox;
275	>	}
276
277	<	int i;
278	<	Vector3d scaled;
277	>	RealType Snapshot::getXYarea() {
278	>	if (!hasXYarea) {
279	>	Vector3d x = frameData.hmat.getColumn(0);
280	>	Vector3d y = frameData.hmat.getColumn(1);
281	>	frameData.xyArea = cross(x,y).length();
282	>	hasXYarea = true;
283	>	}
284	>	return frameData.xyArea;
285	>	}
286
287	<	if( !orthoRhombic_ ){
287	>	RealType Snapshot::getVolume() {
288	>	if (!hasVolume) {
289	>	frameData.volume = frameData.hmat.determinant();
290	>	hasVolume = true;
291	>	}
292	>	return frameData.volume;
293	>	}
294
295	<	// calc the scaled coordinates.
296	<	scaled = invHmat_* pos;
295	>	void Snapshot::setVolume(RealType vol) {
296	>	hasVolume = true;
297	>	frameData.volume = vol;
298	>	}
299
300	<	// wrap the scaled coordinates
301	<	for (i = 0; i < 3; ++i) {
302	<	scaled[i] -= roundMe(scaled[i]);
303	<	}
304	<
300	>	/** Wrap a vector according to periodic boundary conditions */
301	>	void Snapshot::wrapVector(Vector3d& pos) {
302	>
303	>	Vector3d scaled = scaleVector(pos);
304	>
305	>	for (int i = 0; i < 3; i++)
306	>	scaled[i] -= roundMe(scaled[i]);
307	>
308	>	if( !frameData.orthoRhombic )
309	>	pos = frameData.hmat * scaled;
310	>	else {
311	>
312		// calc the wrapped real coordinates from the wrapped scaled coordinates
313	<	pos = hmat_ * scaled;
313	>	for (int i=0; i<3; i++) {
314	>	pos[i] = scaled[i] * frameData.hmat(i, i);
315	>	}
316	>	}
317	>	}
318
319	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
319	>	/** Scaling a vector to multiples of the periodic box */
320	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
321
322	+	Vector3d scaled;
323	+
324	+	if( !frameData.orthoRhombic )
325	+	scaled = frameData.invHmat * pos;
326	+	else {
327		// calc the scaled coordinates.
328	<	for (i=0; i<3; i++) {
329	<	scaled[i] = pos[i] * invHmat_(i, i);
330	<	}
144	<
145	<	// wrap the scaled coordinates
146	<	for (i = 0; i < 3; ++i) {
147	<	scaled[i] -= roundMe(scaled[i]);
148	<	}
328	>	for (int i=0; i<3; i++)
329	>	scaled[i] = pos[i] * frameData.invHmat(i, i);
330	>	}
331
332	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
333	<	for (i=0; i<3; i++) {
334	<	pos[i] = scaled[i] * hmat_(i, i);
332	>	return scaled;
333	>	}
334	>
335	>	void Snapshot::setCOM(const Vector3d& com) {
336	>	frameData.COM = com;
337	>	hasCOM = true;
338	>	}
339	>
340	>	void Snapshot::setCOMvel(const Vector3d& comVel) {
341	>	frameData.COMvel = comVel;
342	>	hasCOMvel = true;
343	>	}
344	>
345	>	void Snapshot::setCOMw(const Vector3d& comw) {
346	>	frameData.COMw = comw;
347	>	hasCOMw = true;
348	>	}
349	>
350	>	Vector3d Snapshot::getCOM() {
351	>	return frameData.COM;
352	>	}
353	>
354	>	Vector3d Snapshot::getCOMvel() {
355	>	return frameData.COMvel;
356	>	}
357	>
358	>	Vector3d Snapshot::getCOMw() {
359	>	return frameData.COMw;
360	>	}
361	>
362	>	RealType Snapshot::getTime() {
363	>	return frameData.currentTime;
364	>	}
365	>
366	>	void Snapshot::increaseTime(RealType dt) {
367	>	setTime(getTime() + dt);
368	>	}
369	>
370	>	void Snapshot::setTime(RealType time) {
371	>	frameData.currentTime = time;
372	>	}
373	>
374	>	void Snapshot::setBondPotential(RealType bp) {
375	>	frameData.bondPotential = bp;
376	>	}
377	>
378	>	void Snapshot::setBendPotential(RealType bp) {
379	>	frameData.bendPotential = bp;
380	>	}
381	>
382	>	void Snapshot::setTorsionPotential(RealType tp) {
383	>	frameData.torsionPotential = tp;
384	>	}
385	>
386	>	void Snapshot::setInversionPotential(RealType ip) {
387	>	frameData.inversionPotential = ip;
388	>	}
389	>
390	>
391	>	RealType Snapshot::getBondPotential() {
392	>	return frameData.bondPotential;
393	>	}
394	>	RealType Snapshot::getBendPotential() {
395	>	return frameData.bendPotential;
396	>	}
397	>	RealType Snapshot::getTorsionPotential() {
398	>	return frameData.torsionPotential;
399	>	}
400	>	RealType Snapshot::getInversionPotential() {
401	>	return frameData.inversionPotential;
402	>	}
403	>
404	>	RealType Snapshot::getShortRangePotential() {
405	>	if (!hasShortRangePotential) {
406	>	frameData.shortRangePotential = frameData.bondPotential;
407	>	frameData.shortRangePotential += frameData.bendPotential;
408	>	frameData.shortRangePotential += frameData.torsionPotential;
409	>	frameData.shortRangePotential += frameData.inversionPotential;
410	>	hasShortRangePotential = true;
411	>	}
412	>	return frameData.shortRangePotential;
413	>	}
414	>
415	>	void Snapshot::setLongRangePotential(potVec lrPot) {
416	>	frameData.lrPotentials = lrPot;
417	>	}
418	>
419	>	RealType Snapshot::getLongRangePotential() {
420	>	if (!hasLongRangePotential) {
421	>	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
422	>	frameData.longRangePotential += frameData.lrPotentials[i];
423		}
424	<
424	>	hasLongRangePotential = true;
425	>	}
426	>	return frameData.longRangePotential;
427	>	}
428	>
429	>	potVec Snapshot::getLongRangePotentials() {
430	>	return frameData.lrPotentials;
431	>	}
432	>
433	>	RealType Snapshot::getPotentialEnergy() {
434	>	if (!hasPotentialEnergy) {
435	>	frameData.potentialEnergy = this->getLongRangePotential();
436	>	frameData.potentialEnergy += this->getShortRangePotential();
437	>	hasPotentialEnergy = true;
438		}
439	+	return frameData.potentialEnergy;
440	+	}
441	+
442	+	void Snapshot::setExcludedPotentials(potVec exPot) {
443	+	frameData.excludedPotentials = exPot;
444	+	}
445
446	+	potVec Snapshot::getExcludedPotentials() {
447	+	return frameData.excludedPotentials;
448		}
449	+
450	+	void Snapshot::setRestraintPotential(RealType rp) {
451	+	frameData.restraintPotential = rp;
452	+	}
453	+
454	+	RealType Snapshot::getRestraintPotential() {
455	+	return frameData.restraintPotential;
456	+	}
457	+
458	+	void Snapshot::setRawPotential(RealType rp) {
459	+	frameData.rawPotential = rp;
460	+	}
461	+
462	+	RealType Snapshot::getRawPotential() {
463	+	return frameData.rawPotential;
464	+	}
465
466	<	}
466	>	RealType Snapshot::getTranslationalKineticEnergy() {
467	>	return frameData.translationalKinetic;
468	>	}
469	>
470	>	RealType Snapshot::getRotationalKineticEnergy() {
471	>	return frameData.rotationalKinetic;
472	>	}
473	>
474	>	RealType Snapshot::getKineticEnergy() {
475	>	return frameData.kineticEnergy;
476	>	}
477	>
478	>	void Snapshot::setTranslationalKineticEnergy(RealType tke) {
479	>	hasTranslationalKineticEnergy = true;
480	>	frameData.translationalKinetic = tke;
481	>	}
482	>
483	>	void Snapshot::setRotationalKineticEnergy(RealType rke) {
484	>	hasRotationalKineticEnergy = true;
485	>	frameData.rotationalKinetic = rke;
486	>	}
487	>
488	>	void Snapshot::setKineticEnergy(RealType ke) {
489	>	hasKineticEnergy = true;
490	>	frameData.kineticEnergy = ke;
491	>	}
492	>
493	>	RealType Snapshot::getTotalEnergy() {
494	>	return frameData.totalEnergy;
495	>	}
496	>
497	>	void Snapshot::setTotalEnergy(RealType te) {
498	>	hasTotalEnergy = true;
499	>	frameData.totalEnergy = te;
500	>	}
501	>
502	>	RealType Snapshot::getConservedQuantity() {
503	>	return frameData.conservedQuantity;
504	>	}
505	>
506	>	void Snapshot::setConservedQuantity(RealType cq) {
507	>	hasConservedQuantity = true;
508	>	frameData.conservedQuantity = cq;
509	>	}
510	>
511	>	RealType Snapshot::getTemperature() {
512	>	return frameData.temperature;
513	>	}
514	>
515	>	void Snapshot::setTemperature(RealType temp) {
516	>	hasTemperature = true;
517	>	frameData.temperature = temp;
518	>	}
519	>
520	>	RealType Snapshot::getElectronicTemperature() {
521	>	return frameData.electronicTemperature;
522	>	}
523	>
524	>	void Snapshot::setElectronicTemperature(RealType eTemp) {
525	>	hasElectronicTemperature = true;
526	>	frameData.electronicTemperature = eTemp;
527	>	}
528	>
529	>	RealType Snapshot::getPressure() {
530	>	return frameData.pressure;
531	>	}
532	>
533	>	void Snapshot::setPressure(RealType pressure) {
534	>	hasPressure = true;
535	>	frameData.pressure = pressure;
536	>	}
537	>
538	>	Mat3x3d Snapshot::getPressureTensor() {
539	>	return frameData.pressureTensor;
540	>	}
541	>
542	>
543	>	void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) {
544	>	hasPressureTensor = true;
545	>	frameData.pressureTensor = pressureTensor;
546	>	}
547	>
548	>	void Snapshot::setStressTensor(const Mat3x3d& stressTensor) {
549	>	frameData.stressTensor = stressTensor;
550	>	}
551	>
552	>	Mat3x3d  Snapshot::getStressTensor() {
553	>	return frameData.stressTensor;
554	>	}
555	>
556	>	void Snapshot::setConductiveHeatFlux(const Vector3d& chf) {
557	>	frameData.conductiveHeatFlux = chf;
558	>	}
559	>
560	>	Vector3d Snapshot::getConductiveHeatFlux() {
561	>	return frameData.conductiveHeatFlux;
562	>	}
563
564	+	Vector3d Snapshot::getConvectiveHeatFlux() {
565	+	return frameData.convectiveHeatFlux;
566	+	}
567	+
568	+	void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) {
569	+	hasConvectiveHeatFlux = true;
570	+	frameData.convectiveHeatFlux = chf;
571	+	}
572	+
573	+	Vector3d Snapshot::getHeatFlux() {
574	+	// BE CAREFUL WITH UNITS
575	+	return getConductiveHeatFlux() + getConvectiveHeatFlux();
576	+	}
577	+
578	+	Vector3d Snapshot::getSystemDipole() {
579	+	return frameData.systemDipole;
580	+	}
581	+
582	+	void Snapshot::setSystemDipole(const Vector3d& bd) {
583	+	hasSystemDipole = true;
584	+	frameData.systemDipole = bd;
585	+	}
586	+
587	+	void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) {
588	+	frameData.thermostat = thermostat;
589	+	}
590	+
591	+	pair<RealType, RealType> Snapshot::getThermostat() {
592	+	return frameData.thermostat;
593	+	}
594	+
595	+	void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) {
596	+	frameData.electronicThermostat = eTherm;
597	+	}
598	+
599	+	pair<RealType, RealType> Snapshot::getElectronicThermostat() {
600	+	return frameData.electronicThermostat;
601	+	}
602	+
603	+	void Snapshot::setBarostat(const Mat3x3d& barostat) {
604	+	frameData.barostat = barostat;
605	+	}
606	+
607	+	Mat3x3d Snapshot::getBarostat() {
608	+	return frameData.barostat;
609	+	}
610	+
611	+	void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) {
612	+	frameData.inertiaTensor = inertiaTensor;
613	+	hasInertiaTensor = true;
614	+	}
615	+
616	+	Mat3x3d Snapshot::getInertiaTensor() {
617	+	return frameData.inertiaTensor;
618	+	}
619	+
620	+	void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) {
621	+	frameData.gyrationalVolume = gyrationalVolume;
622	+	hasGyrationalVolume = true;
623	+	}
624	+
625	+	RealType Snapshot::getGyrationalVolume() {
626	+	return frameData.gyrationalVolume;
627	+	}
628	+
629	+	void Snapshot::setHullVolume(const RealType hullVolume) {
630	+	frameData.hullVolume = hullVolume;
631	+	hasHullVolume = true;
632	+	}
633	+
634	+	RealType Snapshot::getHullVolume() {
635	+	return frameData.hullVolume;
636	+	}
637	+
638	+	void Snapshot::setOrthoTolerance(RealType ot) {
639	+	orthoTolerance_ = ot;
640	+	}
641	+	}

Comparing trunk/src/brains/Snapshot.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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