| 94 |
|
|
| 95 |
|
dumpWriter->writeDumpAndEor(); |
| 96 |
|
|
| 97 |
– |
if (simParams->getUseSolidThermInt()) { |
| 98 |
– |
restWriter = createRestWriter(); |
| 99 |
– |
restWriter->writeZAngFile(); |
| 100 |
– |
} |
| 101 |
– |
|
| 97 |
|
//save statistics, before writeStat, we must save statistics |
| 98 |
|
thermo.saveStat(); |
| 99 |
|
saveConservedQuantity(); |
| 100 |
+ |
if (simParams->getUseRNEMD()) |
| 101 |
+ |
rnemd_->getStatus(); |
| 102 |
+ |
|
| 103 |
|
statWriter->writeStat(currentSnapshot_->statData); |
| 104 |
|
|
| 105 |
|
currSample = sampleTime + currentSnapshot_->getTime(); |
| 106 |
< |
currStatus = statusTime + currentSnapshot_->getTime();; |
| 106 |
> |
currStatus = statusTime + currentSnapshot_->getTime(); |
| 107 |
|
currThermal = thermalTime + currentSnapshot_->getTime(); |
| 108 |
|
if (needReset) { |
| 109 |
|
currReset = resetTime + currentSnapshot_->getTime(); |
| 110 |
|
} |
| 111 |
+ |
if (simParams->getUseRNEMD()){ |
| 112 |
+ |
currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime(); |
| 113 |
+ |
} |
| 114 |
|
needPotential = false; |
| 115 |
|
needStress = false; |
| 116 |
|
|
| 159 |
|
currThermal += thermalTime; |
| 160 |
|
} |
| 161 |
|
} |
| 162 |
< |
|
| 162 |
> |
if (useRNEMD) { |
| 163 |
> |
if (currentSnapshot_->getTime() >= currRNEMD) { |
| 164 |
> |
rnemd_->doSwap(); |
| 165 |
> |
currRNEMD += RNEMD_swapTime; |
| 166 |
> |
} |
| 167 |
> |
} |
| 168 |
> |
|
| 169 |
|
if (currentSnapshot_->getTime() >= currSample) { |
| 170 |
|
dumpWriter->writeDumpAndEor(); |
| 171 |
< |
|
| 165 |
< |
if (simParams->getUseSolidThermInt()) |
| 166 |
< |
restWriter->writeZAngFile(); |
| 167 |
< |
|
| 171 |
> |
|
| 172 |
|
currSample += sampleTime; |
| 173 |
|
} |
| 174 |
< |
|
| 174 |
> |
|
| 175 |
|
if (currentSnapshot_->getTime() >= currStatus) { |
| 176 |
|
//save statistics, before writeStat, we must save statistics |
| 177 |
|
thermo.saveStat(); |
| 178 |
|
saveConservedQuantity(); |
| 179 |
+ |
|
| 180 |
+ |
if (simParams->getUseRNEMD()) |
| 181 |
+ |
rnemd_->getStatus(); |
| 182 |
+ |
|
| 183 |
|
statWriter->writeStat(currentSnapshot_->statData); |
| 184 |
< |
|
| 184 |
> |
|
| 185 |
|
needPotential = false; |
| 186 |
|
needStress = false; |
| 187 |
|
currStatus += statusTime; |
| 188 |
|
} |
| 189 |
< |
|
| 190 |
< |
if (needReset && currentSnapshot_->getTime() >= currReset) { |
| 191 |
< |
resetIntegrator(); |
| 192 |
< |
currReset += resetTime; |
| 193 |
< |
} |
| 186 |
< |
|
| 189 |
> |
|
| 190 |
> |
if (needReset && currentSnapshot_->getTime() >= currReset) { |
| 191 |
> |
resetIntegrator(); |
| 192 |
> |
currReset += resetTime; |
| 193 |
> |
} |
| 194 |
|
} |
| 195 |
|
|
| 196 |
|
|
| 197 |
|
void VelocityVerletIntegrator::finalize() { |
| 198 |
|
dumpWriter->writeEor(); |
| 199 |
|
|
| 193 |
– |
if (simParams->getUseSolidThermInt()) { |
| 194 |
– |
restWriter->writeZAngFile(); |
| 195 |
– |
delete restWriter; |
| 196 |
– |
restWriter = NULL; |
| 197 |
– |
} |
| 198 |
– |
|
| 200 |
|
delete dumpWriter; |
| 201 |
|
delete statWriter; |
| 202 |
|
|
| 226 |
|
|
| 227 |
|
std::string statFileFormatString = simParams->getStatFileFormat(); |
| 228 |
|
StatsBitSet mask = parseStatFileFormat(statFileFormatString); |
| 229 |
< |
|
| 230 |
< |
// if solidThermInt is true, add extra information to the statfile |
| 231 |
< |
if (simParams->getUseSolidThermInt()){ |
| 229 |
> |
|
| 230 |
> |
// if we're doing a thermodynamic integration, we'll want the raw |
| 231 |
> |
// potential as well as the full potential: |
| 232 |
> |
|
| 233 |
> |
|
| 234 |
> |
if (simParams->getUseThermodynamicIntegration()) |
| 235 |
|
mask.set(Stats::VRAW); |
| 236 |
+ |
|
| 237 |
+ |
// if we've got restraints turned on, we'll also want a report of the |
| 238 |
+ |
// total harmonic restraints |
| 239 |
+ |
if (simParams->getUseRestraints()){ |
| 240 |
|
mask.set(Stats::VHARM); |
| 241 |
|
} |
| 242 |
|
|
| 243 |
|
if (simParams->havePrintPressureTensor() && |
| 244 |
|
simParams->getPrintPressureTensor()){ |
| 245 |
< |
mask.set(Stats::PRESSURE_TENSOR_X); |
| 246 |
< |
mask.set(Stats::PRESSURE_TENSOR_Y); |
| 247 |
< |
mask.set(Stats::PRESSURE_TENSOR_Z); |
| 245 |
> |
mask.set(Stats::PRESSURE_TENSOR_XX); |
| 246 |
> |
mask.set(Stats::PRESSURE_TENSOR_XY); |
| 247 |
> |
mask.set(Stats::PRESSURE_TENSOR_XZ); |
| 248 |
> |
mask.set(Stats::PRESSURE_TENSOR_YX); |
| 249 |
> |
mask.set(Stats::PRESSURE_TENSOR_YY); |
| 250 |
> |
mask.set(Stats::PRESSURE_TENSOR_YZ); |
| 251 |
> |
mask.set(Stats::PRESSURE_TENSOR_ZX); |
| 252 |
> |
mask.set(Stats::PRESSURE_TENSOR_ZY); |
| 253 |
> |
mask.set(Stats::PRESSURE_TENSOR_ZZ); |
| 254 |
|
} |
| 255 |
|
|
| 256 |
|
if (simParams->getAccumulateBoxDipole()) { |
| 258 |
|
mask.set(Stats::BOX_DIPOLE_Y); |
| 259 |
|
mask.set(Stats::BOX_DIPOLE_Z); |
| 260 |
|
} |
| 261 |
+ |
|
| 262 |
+ |
if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) { |
| 263 |
+ |
if (simParams->getPrintTaggedPairDistance()) { |
| 264 |
+ |
mask.set(Stats::TAGGED_PAIR_DISTANCE); |
| 265 |
+ |
} |
| 266 |
+ |
} |
| 267 |
|
|
| 268 |
+ |
if (simParams->getUseRNEMD()) { |
| 269 |
+ |
mask.set(Stats::RNEMD_SWAP_TOTAL); |
| 270 |
+ |
} |
| 271 |
+ |
|
| 272 |
+ |
|
| 273 |
|
return new StatWriter(info_->getStatFileName(), mask); |
| 274 |
|
} |
| 275 |
|
|
| 251 |
– |
RestWriter* VelocityVerletIntegrator::createRestWriter(){ |
| 252 |
– |
return new RestWriter(info_); |
| 253 |
– |
} |
| 276 |
|
|
| 255 |
– |
|
| 277 |
|
} //end namespace oopse |
