| 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(); |
| 169 |
|
if (currentSnapshot_->getTime() >= currSample) { |
| 170 |
|
dumpWriter->writeDumpAndEor(); |
| 171 |
|
|
| 177 |
– |
if (simParams->getUseSolidThermInt()) |
| 178 |
– |
restWriter->writeZAngFile(); |
| 179 |
– |
|
| 172 |
|
currSample += sampleTime; |
| 173 |
|
} |
| 174 |
|
|
| 197 |
|
void VelocityVerletIntegrator::finalize() { |
| 198 |
|
dumpWriter->writeEor(); |
| 199 |
|
|
| 208 |
– |
if (simParams->getUseSolidThermInt()) { |
| 209 |
– |
restWriter->writeZAngFile(); |
| 210 |
– |
delete restWriter; |
| 211 |
– |
restWriter = NULL; |
| 212 |
– |
} |
| 213 |
– |
|
| 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 |
|
|
| 273 |
|
return new StatWriter(info_->getStatFileName(), mask); |
| 274 |
|
} |
| 275 |
|
|
| 283 |
– |
RestWriter* VelocityVerletIntegrator::createRestWriter(){ |
| 284 |
– |
return new RestWriter(info_); |
| 285 |
– |
} |
| 276 |
|
|
| 287 |
– |
|
| 277 |
|
} //end namespace oopse |
