| 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 |
|
* @author tlin |
| 46 |
|
* @date 11/11/2004 |
| 47 |
– |
* @time 10:56am |
| 47 |
|
* @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); |
| 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); |
| 139 |
|
hasKineticEnergy = false; |
| 140 |
|
hasShortRangePotential = false; |
| 141 |
|
hasLongRangePotential = false; |
| 142 |
< |
hasPotentialEnergy = false; |
| 142 |
> |
hasPotentialEnergy = false; |
| 143 |
> |
hasXYarea = false; |
| 144 |
|
hasVolume = false; |
| 145 |
|
hasPressure = false; |
| 146 |
|
hasTemperature = false; |
| 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" |
| 227 |
< |
"\tThis is usually a good thing, but if you want the\n" |
| 228 |
< |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 229 |
< |
"\tvariable ( currently set to %G ) smaller.\n", |
| 230 |
< |
orthoTolerance_); |
| 231 |
< |
painCave.severity = OPENMD_INFO; |
| 232 |
< |
simError(); |
| 233 |
< |
} |
| 234 |
< |
else { |
| 235 |
< |
sprintf( painCave.errMsg, |
| 236 |
< |
"OpenMD is switching from the faster Orthorhombic to the more\n" |
| 237 |
< |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 238 |
< |
"\tThis is usually because the box has deformed under\n" |
| 239 |
< |
"\tNPTf integration. If you want to live on the edge with\n" |
| 240 |
< |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 241 |
< |
"\tvariable ( currently set to %G ) larger.\n", |
| 242 |
< |
orthoTolerance_); |
| 243 |
< |
painCave.severity = OPENMD_WARNING; |
| 244 |
< |
simError(); |
| 245 |
< |
} |
| 223 |
> |
// It is finally time to suppress these warnings once and for |
| 224 |
> |
// all. They were annoying and not very informative. |
| 225 |
> |
|
| 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 |
+ |
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() { |
