| 67 |
|
|
| 68 |
|
forceMan_->init(); |
| 69 |
|
|
| 70 |
< |
// remove center of mass drift velocity (in case we passed in a configuration |
| 71 |
< |
// that was drifting |
| 70 |
> |
// remove center of mass drift velocity (in case we passed in a |
| 71 |
> |
// configuration that was drifting) |
| 72 |
|
velocitizer_->removeComDrift(); |
| 73 |
|
|
| 74 |
|
// initialize the forces before the first step |
| 75 |
|
calcForce(true, true); |
| 76 |
|
|
| 77 |
< |
//execute constraint algorithm to make sure at the very beginning the system is constrained |
| 77 |
> |
// execute the constraint algorithm to make sure that the system is |
| 78 |
> |
// constrained at the very beginning |
| 79 |
|
if (info_->getNGlobalConstraints() > 0) { |
| 80 |
|
rattle->constraintA(); |
| 81 |
|
calcForce(true, true); |
| 82 |
< |
rattle->constraintB(); |
| 83 |
< |
info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot |
| 82 |
> |
rattle->constraintB(); |
| 83 |
> |
//copy the current snapshot to previous snapshot |
| 84 |
> |
info_->getSnapshotManager()->advance(); |
| 85 |
|
} |
| 86 |
|
|
| 87 |
|
if (needVelocityScaling) { |
| 91 |
|
dumpWriter = createDumpWriter(); |
| 92 |
|
|
| 93 |
|
statWriter = createStatWriter(); |
| 94 |
< |
|
| 94 |
> |
|
| 95 |
> |
dumpWriter->writeDumpAndEor(); |
| 96 |
> |
|
| 97 |
|
if (simParams->getUseSolidThermInt()) { |
| 98 |
|
restWriter = createRestWriter(); |
| 99 |
< |
restWriter->writeZangle(); |
| 99 |
> |
restWriter->writeZAngFile(); |
| 100 |
|
} |
| 101 |
|
|
| 98 |
– |
dumpWriter->writeDumpAndEor(); |
| 99 |
– |
|
| 100 |
– |
|
| 102 |
|
//save statistics, before writeStat, we must save statistics |
| 103 |
|
thermo.saveStat(); |
| 104 |
|
saveConservedQuantity(); |
| 151 |
|
|
| 152 |
|
//increase time |
| 153 |
|
currentSnapshot_->increaseTime(dt); |
| 154 |
< |
|
| 154 |
> |
|
| 155 |
|
if (needVelocityScaling) { |
| 156 |
|
if (currentSnapshot_->getTime() >= currThermal) { |
| 157 |
|
velocitizer_->velocitize(targetScalingTemp); |
| 158 |
|
currThermal += thermalTime; |
| 159 |
|
} |
| 160 |
|
} |
| 161 |
< |
|
| 161 |
> |
|
| 162 |
|
if (currentSnapshot_->getTime() >= currSample) { |
| 163 |
|
dumpWriter->writeDumpAndEor(); |
| 164 |
< |
|
| 164 |
> |
|
| 165 |
|
if (simParams->getUseSolidThermInt()) |
| 166 |
< |
restWriter->writeZangle(); |
| 166 |
> |
restWriter->writeZAngFile(); |
| 167 |
|
|
| 168 |
|
currSample += sampleTime; |
| 169 |
|
} |
| 170 |
< |
|
| 170 |
> |
|
| 171 |
|
if (currentSnapshot_->getTime() >= currStatus) { |
| 172 |
|
//save statistics, before writeStat, we must save statistics |
| 173 |
|
thermo.saveStat(); |
| 191 |
|
dumpWriter->writeEor(); |
| 192 |
|
|
| 193 |
|
if (simParams->getUseSolidThermInt()) { |
| 194 |
< |
restWriter->writeZangle(); |
| 194 |
> |
// restWriter->writeZAngFile(); |
| 195 |
|
delete restWriter; |
| 196 |
|
restWriter = NULL; |
| 197 |
|
} |
| 232 |
|
mask.set(Stats::VHARM); |
| 233 |
|
} |
| 234 |
|
|
| 235 |
< |
if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){ |
| 235 |
> |
if (simParams->havePrintPressureTensor() && |
| 236 |
> |
simParams->getPrintPressureTensor()){ |
| 237 |
|
mask.set(Stats::PRESSURE_TENSOR_X); |
| 238 |
|
mask.set(Stats::PRESSURE_TENSOR_Y); |
| 239 |
|
mask.set(Stats::PRESSURE_TENSOR_Z); |
