| 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). |
| 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 |
|
*/ |
| 44 |
|
* @file Snapshot.cpp |
| 45 |
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* @author tlin |
| 46 |
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* @date 11/11/2004 |
| 47 |
– |
* @time 10:56am |
| 47 |
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* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 72 |
|
frameData.lrPotentials = potVec(0.0); |
| 73 |
|
frameData.excludedPotentials = potVec(0.0); |
| 74 |
|
frameData.restraintPotential = 0.0; |
| 75 |
< |
frameData.rawPotential = 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); |
| 94 |
|
frameData.id = -1; |
| 95 |
|
frameData.currentTime = 0; |
| 96 |
|
frameData.hmat = Mat3x3d(0.0); |
| 97 |
< |
frameData.invHmat = 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; |
| 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); |
| 133 |
|
frameData.electronicTemperature = 0.0; |
| 134 |
|
frameData.COM = V3Zero; |
| 135 |
|
frameData.COMvel = V3Zero; |
| 136 |
< |
frameData.COMw = V3Zero; |
| 136 |
> |
frameData.COMw = V3Zero; |
| 137 |
|
|
| 138 |
|
hasTotalEnergy = false; |
| 139 |
|
hasTranslationalKineticEnergy = false; |
| 141 |
|
hasKineticEnergy = false; |
| 142 |
|
hasShortRangePotential = false; |
| 143 |
|
hasLongRangePotential = false; |
| 144 |
< |
hasPotentialEnergy = false; |
| 144 |
> |
hasPotentialEnergy = false; |
| 145 |
> |
hasXYarea = false; |
| 146 |
|
hasVolume = false; |
| 147 |
|
hasPressure = false; |
| 148 |
|
hasTemperature = false; |
| 222 |
|
|
| 223 |
|
if( oldOrthoRhombic != frameData.orthoRhombic){ |
| 224 |
|
|
| 225 |
< |
if( frameData.orthoRhombic ) { |
| 226 |
< |
sprintf( painCave.errMsg, |
| 227 |
< |
"OpenMD is switching from the default Non-Orthorhombic\n" |
| 228 |
< |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 229 |
< |
"\tThis is usually a good thing, but if you want the\n" |
| 230 |
< |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 231 |
< |
"\tvariable ( currently set to %G ) smaller.\n", |
| 232 |
< |
orthoTolerance_); |
| 233 |
< |
painCave.severity = OPENMD_INFO; |
| 234 |
< |
simError(); |
| 235 |
< |
} |
| 236 |
< |
else { |
| 237 |
< |
sprintf( painCave.errMsg, |
| 238 |
< |
"OpenMD is switching from the faster Orthorhombic to the more\n" |
| 239 |
< |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 240 |
< |
"\tThis is usually because the box has deformed under\n" |
| 241 |
< |
"\tNPTf integration. If you want to live on the edge with\n" |
| 242 |
< |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 243 |
< |
"\tvariable ( currently set to %G ) larger.\n", |
| 244 |
< |
orthoTolerance_); |
| 245 |
< |
painCave.severity = OPENMD_WARNING; |
| 246 |
< |
simError(); |
| 247 |
< |
} |
| 225 |
> |
// It is finally time to suppress these warnings once and for |
| 226 |
> |
// all. They were annoying and not very informative. |
| 227 |
> |
|
| 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 |
|
|
| 256 |
|
return frameData.invHmat; |
| 257 |
|
} |
| 258 |
|
|
| 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 |
+ |
/** Returns the inverse Bounding Box */ |
| 271 |
+ |
Mat3x3d Snapshot::getInvBoundingBox() { |
| 272 |
+ |
return frameData.invBbox; |
| 273 |
+ |
} |
| 274 |
+ |
|
| 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 |
|
RealType Snapshot::getVolume() { |
| 286 |
|
if (!hasVolume) { |
| 287 |
|
frameData.volume = frameData.hmat.determinant(); |
