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] Vardeman & Gezelter, in progress (2009). |
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 |
|
|
51 |
|
#include "utils/NumericConstant.hpp" |
52 |
|
#include "utils/simError.h" |
53 |
|
#include "utils/Utility.hpp" |
54 |
+ |
#include <cstdio> |
55 |
+ |
|
56 |
|
namespace OpenMD { |
57 |
|
|
58 |
< |
void Snapshot::setHmat(const Mat3x3d& m) { |
59 |
< |
hmat_ = m; |
60 |
< |
invHmat_ = hmat_.inverse(); |
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 |
+ |
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 |
< |
//prepare fortran Hmat |
85 |
< |
RealType fortranHmat[9]; |
86 |
< |
RealType fortranInvHmat[9]; |
87 |
< |
hmat_.getArray(fortranHmat); |
88 |
< |
invHmat_.getArray(fortranInvHmat); |
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)); |
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 != orthoRhombic_ ){ |
222 |
< |
|
223 |
< |
if( orthoRhombic_ ) { |
220 |
> |
|
221 |
> |
if( oldOrthoRhombic != frameData.orthoRhombic){ |
222 |
> |
|
223 |
> |
if( frameData.orthoRhombic ) { |
224 |
|
sprintf( painCave.errMsg, |
225 |
|
"OpenMD is switching from the default Non-Orthorhombic\n" |
226 |
|
"\tto the faster Orthorhombic periodic boundary computations.\n" |
244 |
|
simError(); |
245 |
|
} |
246 |
|
} |
247 |
+ |
} |
248 |
+ |
|
249 |
+ |
/** Returns the inverse H-Matrix */ |
250 |
+ |
Mat3x3d Snapshot::getInvHmat() { |
251 |
+ |
return frameData.invHmat; |
252 |
+ |
} |
253 |
|
|
254 |
< |
//notify fortran simulation box has changed |
255 |
< |
setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); |
254 |
> |
RealType Snapshot::getXYarea() { |
255 |
> |
if (!hasXYarea) { |
256 |
> |
Vector3d x = frameData.hmat.getColumn(0); |
257 |
> |
Vector3d y = frameData.hmat.getColumn(1); |
258 |
> |
frameData.xyArea = cross(x,y).length(); |
259 |
> |
hasXYarea = true; |
260 |
> |
} |
261 |
> |
return frameData.xyArea; |
262 |
|
} |
263 |
|
|
264 |
+ |
RealType Snapshot::getVolume() { |
265 |
+ |
if (!hasVolume) { |
266 |
+ |
frameData.volume = frameData.hmat.determinant(); |
267 |
+ |
hasVolume = true; |
268 |
+ |
} |
269 |
+ |
return frameData.volume; |
270 |
+ |
} |
271 |
|
|
272 |
< |
void Snapshot::wrapVector(Vector3d& pos) { |
272 |
> |
void Snapshot::setVolume(RealType vol) { |
273 |
> |
hasVolume = true; |
274 |
> |
frameData.volume = vol; |
275 |
> |
} |
276 |
|
|
277 |
< |
int i; |
278 |
< |
Vector3d scaled; |
279 |
< |
|
280 |
< |
if( !orthoRhombic_ ){ |
281 |
< |
|
282 |
< |
// calc the scaled coordinates. |
283 |
< |
scaled = invHmat_* pos; |
284 |
< |
|
285 |
< |
// wrap the scaled coordinates |
286 |
< |
for (i = 0; i < 3; ++i) { |
287 |
< |
scaled[i] -= roundMe(scaled[i]); |
288 |
< |
} |
134 |
< |
|
277 |
> |
/** Wrap a vector according to periodic boundary conditions */ |
278 |
> |
void Snapshot::wrapVector(Vector3d& pos) { |
279 |
> |
|
280 |
> |
Vector3d scaled = scaleVector(pos); |
281 |
> |
|
282 |
> |
for (int i = 0; i < 3; i++) |
283 |
> |
scaled[i] -= roundMe(scaled[i]); |
284 |
> |
|
285 |
> |
if( !frameData.orthoRhombic ) |
286 |
> |
pos = frameData.hmat * scaled; |
287 |
> |
else { |
288 |
> |
|
289 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
290 |
< |
pos = hmat_ * scaled; |
290 |
> |
for (int i=0; i<3; i++) { |
291 |
> |
pos[i] = scaled[i] * frameData.hmat(i, i); |
292 |
> |
} |
293 |
> |
} |
294 |
> |
} |
295 |
|
|
296 |
< |
} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element |
296 |
> |
/** Scaling a vector to multiples of the periodic box */ |
297 |
> |
inline Vector3d Snapshot::scaleVector(Vector3d& pos) { |
298 |
|
|
299 |
< |
// calc the scaled coordinates. |
141 |
< |
for (i=0; i<3; i++) { |
142 |
< |
scaled[i] = pos[i] * invHmat_(i, i); |
143 |
< |
} |
144 |
< |
|
145 |
< |
// wrap the scaled coordinates |
146 |
< |
for (i = 0; i < 3; ++i) { |
147 |
< |
scaled[i] -= roundMe(scaled[i]); |
148 |
< |
} |
299 |
> |
Vector3d scaled; |
300 |
|
|
301 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
302 |
< |
for (i=0; i<3; i++) { |
303 |
< |
pos[i] = scaled[i] * hmat_(i, i); |
304 |
< |
} |
305 |
< |
|
301 |
> |
if( !frameData.orthoRhombic ) |
302 |
> |
scaled = frameData.invHmat * pos; |
303 |
> |
else { |
304 |
> |
// calc the scaled coordinates. |
305 |
> |
for (int i=0; i<3; i++) |
306 |
> |
scaled[i] = pos[i] * frameData.invHmat(i, i); |
307 |
|
} |
308 |
|
|
309 |
+ |
return scaled; |
310 |
|
} |
311 |
|
|
312 |
+ |
void Snapshot::setCOM(const Vector3d& com) { |
313 |
+ |
frameData.COM = com; |
314 |
+ |
hasCOM = true; |
315 |
+ |
} |
316 |
+ |
|
317 |
+ |
void Snapshot::setCOMvel(const Vector3d& comVel) { |
318 |
+ |
frameData.COMvel = comVel; |
319 |
+ |
hasCOMvel = true; |
320 |
+ |
} |
321 |
+ |
|
322 |
+ |
void Snapshot::setCOMw(const Vector3d& comw) { |
323 |
+ |
frameData.COMw = comw; |
324 |
+ |
hasCOMw = true; |
325 |
+ |
} |
326 |
+ |
|
327 |
|
Vector3d Snapshot::getCOM() { |
328 |
< |
if( !hasCOM_ ) { |
161 |
< |
sprintf( painCave.errMsg, "COM was requested before COM was computed!\n"); |
162 |
< |
painCave.severity = OPENMD_ERROR; |
163 |
< |
simError(); |
164 |
< |
} |
165 |
< |
return COM_; |
328 |
> |
return frameData.COM; |
329 |
|
} |
330 |
|
|
331 |
|
Vector3d Snapshot::getCOMvel() { |
332 |
< |
if( !hasCOM_ ) { |
170 |
< |
sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n"); |
171 |
< |
painCave.severity = OPENMD_ERROR; |
172 |
< |
simError(); |
173 |
< |
} |
174 |
< |
return COMvel_; |
332 |
> |
return frameData.COMvel; |
333 |
|
} |
334 |
|
|
335 |
|
Vector3d Snapshot::getCOMw() { |
336 |
< |
if( !hasCOM_ ) { |
337 |
< |
sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n"); |
338 |
< |
painCave.severity = OPENMD_ERROR; |
339 |
< |
simError(); |
336 |
> |
return frameData.COMw; |
337 |
> |
} |
338 |
> |
|
339 |
> |
RealType Snapshot::getTime() { |
340 |
> |
return frameData.currentTime; |
341 |
> |
} |
342 |
> |
|
343 |
> |
void Snapshot::increaseTime(RealType dt) { |
344 |
> |
setTime(getTime() + dt); |
345 |
> |
} |
346 |
> |
|
347 |
> |
void Snapshot::setTime(RealType time) { |
348 |
> |
frameData.currentTime = time; |
349 |
> |
} |
350 |
> |
|
351 |
> |
void Snapshot::setBondPotential(RealType bp) { |
352 |
> |
frameData.bondPotential = bp; |
353 |
> |
} |
354 |
> |
|
355 |
> |
void Snapshot::setBendPotential(RealType bp) { |
356 |
> |
frameData.bendPotential = bp; |
357 |
> |
} |
358 |
> |
|
359 |
> |
void Snapshot::setTorsionPotential(RealType tp) { |
360 |
> |
frameData.torsionPotential = tp; |
361 |
> |
} |
362 |
> |
|
363 |
> |
void Snapshot::setInversionPotential(RealType ip) { |
364 |
> |
frameData.inversionPotential = ip; |
365 |
> |
} |
366 |
> |
|
367 |
> |
|
368 |
> |
RealType Snapshot::getBondPotential() { |
369 |
> |
return frameData.bondPotential; |
370 |
> |
} |
371 |
> |
RealType Snapshot::getBendPotential() { |
372 |
> |
return frameData.bendPotential; |
373 |
> |
} |
374 |
> |
RealType Snapshot::getTorsionPotential() { |
375 |
> |
return frameData.torsionPotential; |
376 |
> |
} |
377 |
> |
RealType Snapshot::getInversionPotential() { |
378 |
> |
return frameData.inversionPotential; |
379 |
> |
} |
380 |
> |
|
381 |
> |
RealType Snapshot::getShortRangePotential() { |
382 |
> |
if (!hasShortRangePotential) { |
383 |
> |
frameData.shortRangePotential = frameData.bondPotential; |
384 |
> |
frameData.shortRangePotential += frameData.bendPotential; |
385 |
> |
frameData.shortRangePotential += frameData.torsionPotential; |
386 |
> |
frameData.shortRangePotential += frameData.inversionPotential; |
387 |
> |
hasShortRangePotential = true; |
388 |
|
} |
389 |
< |
return COMw_; |
389 |
> |
return frameData.shortRangePotential; |
390 |
|
} |
391 |
+ |
|
392 |
+ |
void Snapshot::setLongRangePotential(potVec lrPot) { |
393 |
+ |
frameData.lrPotentials = lrPot; |
394 |
+ |
} |
395 |
+ |
|
396 |
+ |
RealType Snapshot::getLongRangePotential() { |
397 |
+ |
if (!hasLongRangePotential) { |
398 |
+ |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
399 |
+ |
frameData.longRangePotential += frameData.lrPotentials[i]; |
400 |
+ |
} |
401 |
+ |
hasLongRangePotential = true; |
402 |
+ |
} |
403 |
+ |
return frameData.longRangePotential; |
404 |
+ |
} |
405 |
+ |
|
406 |
+ |
potVec Snapshot::getLongRangePotentials() { |
407 |
+ |
return frameData.lrPotentials; |
408 |
+ |
} |
409 |
+ |
|
410 |
+ |
RealType Snapshot::getPotentialEnergy() { |
411 |
+ |
if (!hasPotentialEnergy) { |
412 |
+ |
frameData.potentialEnergy = this->getLongRangePotential(); |
413 |
+ |
frameData.potentialEnergy += this->getShortRangePotential(); |
414 |
+ |
hasPotentialEnergy = true; |
415 |
+ |
} |
416 |
+ |
return frameData.potentialEnergy; |
417 |
+ |
} |
418 |
+ |
|
419 |
+ |
void Snapshot::setExcludedPotentials(potVec exPot) { |
420 |
+ |
frameData.excludedPotentials = exPot; |
421 |
+ |
} |
422 |
+ |
|
423 |
+ |
potVec Snapshot::getExcludedPotentials() { |
424 |
+ |
return frameData.excludedPotentials; |
425 |
+ |
} |
426 |
+ |
|
427 |
+ |
void Snapshot::setRestraintPotential(RealType rp) { |
428 |
+ |
frameData.restraintPotential = rp; |
429 |
+ |
} |
430 |
+ |
|
431 |
+ |
RealType Snapshot::getRestraintPotential() { |
432 |
+ |
return frameData.restraintPotential; |
433 |
+ |
} |
434 |
+ |
|
435 |
+ |
void Snapshot::setRawPotential(RealType rp) { |
436 |
+ |
frameData.rawPotential = rp; |
437 |
+ |
} |
438 |
+ |
|
439 |
+ |
RealType Snapshot::getRawPotential() { |
440 |
+ |
return frameData.rawPotential; |
441 |
+ |
} |
442 |
+ |
|
443 |
+ |
RealType Snapshot::getTranslationalKineticEnergy() { |
444 |
+ |
return frameData.translationalKinetic; |
445 |
+ |
} |
446 |
+ |
|
447 |
+ |
RealType Snapshot::getRotationalKineticEnergy() { |
448 |
+ |
return frameData.rotationalKinetic; |
449 |
+ |
} |
450 |
+ |
|
451 |
+ |
RealType Snapshot::getKineticEnergy() { |
452 |
+ |
return frameData.kineticEnergy; |
453 |
+ |
} |
454 |
+ |
|
455 |
+ |
void Snapshot::setTranslationalKineticEnergy(RealType tke) { |
456 |
+ |
hasTranslationalKineticEnergy = true; |
457 |
+ |
frameData.translationalKinetic = tke; |
458 |
+ |
} |
459 |
+ |
|
460 |
+ |
void Snapshot::setRotationalKineticEnergy(RealType rke) { |
461 |
+ |
hasRotationalKineticEnergy = true; |
462 |
+ |
frameData.rotationalKinetic = rke; |
463 |
+ |
} |
464 |
+ |
|
465 |
+ |
void Snapshot::setKineticEnergy(RealType ke) { |
466 |
+ |
hasKineticEnergy = true; |
467 |
+ |
frameData.kineticEnergy = ke; |
468 |
+ |
} |
469 |
+ |
|
470 |
+ |
RealType Snapshot::getTotalEnergy() { |
471 |
+ |
return frameData.totalEnergy; |
472 |
+ |
} |
473 |
+ |
|
474 |
+ |
void Snapshot::setTotalEnergy(RealType te) { |
475 |
+ |
hasTotalEnergy = true; |
476 |
+ |
frameData.totalEnergy = te; |
477 |
+ |
} |
478 |
+ |
|
479 |
+ |
RealType Snapshot::getConservedQuantity() { |
480 |
+ |
return frameData.conservedQuantity; |
481 |
+ |
} |
482 |
+ |
|
483 |
+ |
void Snapshot::setConservedQuantity(RealType cq) { |
484 |
+ |
hasConservedQuantity = true; |
485 |
+ |
frameData.conservedQuantity = cq; |
486 |
+ |
} |
487 |
+ |
|
488 |
+ |
RealType Snapshot::getTemperature() { |
489 |
+ |
return frameData.temperature; |
490 |
+ |
} |
491 |
+ |
|
492 |
+ |
void Snapshot::setTemperature(RealType temp) { |
493 |
+ |
hasTemperature = true; |
494 |
+ |
frameData.temperature = temp; |
495 |
+ |
} |
496 |
+ |
|
497 |
+ |
RealType Snapshot::getElectronicTemperature() { |
498 |
+ |
return frameData.electronicTemperature; |
499 |
+ |
} |
500 |
+ |
|
501 |
+ |
void Snapshot::setElectronicTemperature(RealType eTemp) { |
502 |
+ |
hasElectronicTemperature = true; |
503 |
+ |
frameData.electronicTemperature = eTemp; |
504 |
+ |
} |
505 |
+ |
|
506 |
+ |
RealType Snapshot::getPressure() { |
507 |
+ |
return frameData.pressure; |
508 |
+ |
} |
509 |
+ |
|
510 |
+ |
void Snapshot::setPressure(RealType pressure) { |
511 |
+ |
hasPressure = true; |
512 |
+ |
frameData.pressure = pressure; |
513 |
+ |
} |
514 |
+ |
|
515 |
+ |
Mat3x3d Snapshot::getPressureTensor() { |
516 |
+ |
return frameData.pressureTensor; |
517 |
+ |
} |
518 |
+ |
|
519 |
+ |
|
520 |
+ |
void Snapshot::setPressureTensor(const Mat3x3d& pressureTensor) { |
521 |
+ |
hasPressureTensor = true; |
522 |
+ |
frameData.pressureTensor = pressureTensor; |
523 |
+ |
} |
524 |
+ |
|
525 |
+ |
void Snapshot::setStressTensor(const Mat3x3d& stressTensor) { |
526 |
+ |
frameData.stressTensor = stressTensor; |
527 |
+ |
} |
528 |
+ |
|
529 |
+ |
Mat3x3d Snapshot::getStressTensor() { |
530 |
+ |
return frameData.stressTensor; |
531 |
+ |
} |
532 |
+ |
|
533 |
+ |
void Snapshot::setConductiveHeatFlux(const Vector3d& chf) { |
534 |
+ |
frameData.conductiveHeatFlux = chf; |
535 |
+ |
} |
536 |
+ |
|
537 |
+ |
Vector3d Snapshot::getConductiveHeatFlux() { |
538 |
+ |
return frameData.conductiveHeatFlux; |
539 |
+ |
} |
540 |
+ |
|
541 |
+ |
Vector3d Snapshot::getConvectiveHeatFlux() { |
542 |
+ |
return frameData.convectiveHeatFlux; |
543 |
+ |
} |
544 |
+ |
|
545 |
+ |
void Snapshot::setConvectiveHeatFlux(const Vector3d& chf) { |
546 |
+ |
hasConvectiveHeatFlux = true; |
547 |
+ |
frameData.convectiveHeatFlux = chf; |
548 |
+ |
} |
549 |
+ |
|
550 |
+ |
Vector3d Snapshot::getHeatFlux() { |
551 |
+ |
// BE CAREFUL WITH UNITS |
552 |
+ |
return getConductiveHeatFlux() + getConvectiveHeatFlux(); |
553 |
+ |
} |
554 |
+ |
|
555 |
+ |
Vector3d Snapshot::getSystemDipole() { |
556 |
+ |
return frameData.systemDipole; |
557 |
+ |
} |
558 |
+ |
|
559 |
+ |
void Snapshot::setSystemDipole(const Vector3d& bd) { |
560 |
+ |
hasSystemDipole = true; |
561 |
+ |
frameData.systemDipole = bd; |
562 |
+ |
} |
563 |
+ |
|
564 |
+ |
void Snapshot::setThermostat(const pair<RealType, RealType>& thermostat) { |
565 |
+ |
frameData.thermostat = thermostat; |
566 |
+ |
} |
567 |
+ |
|
568 |
+ |
pair<RealType, RealType> Snapshot::getThermostat() { |
569 |
+ |
return frameData.thermostat; |
570 |
+ |
} |
571 |
+ |
|
572 |
+ |
void Snapshot::setElectronicThermostat(const pair<RealType, RealType>& eTherm) { |
573 |
+ |
frameData.electronicThermostat = eTherm; |
574 |
+ |
} |
575 |
+ |
|
576 |
+ |
pair<RealType, RealType> Snapshot::getElectronicThermostat() { |
577 |
+ |
return frameData.electronicThermostat; |
578 |
+ |
} |
579 |
|
|
580 |
+ |
void Snapshot::setBarostat(const Mat3x3d& barostat) { |
581 |
+ |
frameData.barostat = barostat; |
582 |
+ |
} |
583 |
+ |
|
584 |
+ |
Mat3x3d Snapshot::getBarostat() { |
585 |
+ |
return frameData.barostat; |
586 |
+ |
} |
587 |
+ |
|
588 |
+ |
void Snapshot::setInertiaTensor(const Mat3x3d& inertiaTensor) { |
589 |
+ |
frameData.inertiaTensor = inertiaTensor; |
590 |
+ |
hasInertiaTensor = true; |
591 |
+ |
} |
592 |
+ |
|
593 |
+ |
Mat3x3d Snapshot::getInertiaTensor() { |
594 |
+ |
return frameData.inertiaTensor; |
595 |
+ |
} |
596 |
+ |
|
597 |
+ |
void Snapshot::setGyrationalVolume(const RealType gyrationalVolume) { |
598 |
+ |
frameData.gyrationalVolume = gyrationalVolume; |
599 |
+ |
hasGyrationalVolume = true; |
600 |
+ |
} |
601 |
+ |
|
602 |
+ |
RealType Snapshot::getGyrationalVolume() { |
603 |
+ |
return frameData.gyrationalVolume; |
604 |
+ |
} |
605 |
+ |
|
606 |
+ |
void Snapshot::setHullVolume(const RealType hullVolume) { |
607 |
+ |
frameData.hullVolume = hullVolume; |
608 |
+ |
hasHullVolume = true; |
609 |
+ |
} |
610 |
+ |
|
611 |
+ |
RealType Snapshot::getHullVolume() { |
612 |
+ |
return frameData.hullVolume; |
613 |
+ |
} |
614 |
+ |
|
615 |
+ |
void Snapshot::setOrthoTolerance(RealType ot) { |
616 |
+ |
orthoTolerance_ = ot; |
617 |
+ |
} |
618 |
|
} |
187 |
– |
|