Snapshot::Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) :
atomData(nAtoms), rigidbodyData(nRigidbodies),
cgData(nCutoffGroups, DataStorage::dslPosition),
orthoTolerance_(1e-6) {
frameData.id = -1;
frameData.currentTime = 0;
frameData.hmat = Mat3x3d(0.0);
frameData.invHmat = Mat3x3d(0.0);
frameData.orthoRhombic = false;
frameData.bondPotential = 0.0;
frameData.bendPotential = 0.0;
frameData.torsionPotential = 0.0;
frameData.inversionPotential = 0.0;
frameData.lrPotentials = potVec(0.0);
frameData.surfacePotential = 0.0;
frameData.reciprocalPotential = 0.0;
frameData.selfPotential = 0.0;
frameData.excludedPotentials = potVec(0.0);
frameData.restraintPotential = 0.0;
frameData.rawPotential = 0.0;
frameData.xyArea = 0.0;
frameData.volume = 0.0;
frameData.thermostat = make_pair(0.0, 0.0);
frameData.electronicThermostat = make_pair(0.0, 0.0);
frameData.barostat = Mat3x3d(0.0);
frameData.stressTensor = Mat3x3d(0.0);
frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
clearDerivedProperties();
}
NPT::NPT(SimInfo* info) :
VelocityVerletIntegrator(info), etaTolerance(1e-6), chiTolerance(1e-6),
maxIterNum_(4) {
Globals* simParams = info_->getSimParams();
if (!simParams->getUseIntialExtendedSystemState()) {
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
currSnapshot->setThermostat(make_pair(0.0, 0.0));
currSnapshot->setBarostat(Mat3x3d(0.0));
}
if (!simParams->haveTargetTemp()) {
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n");
painCave.isFatal = 1;
painCave.severity = OPENMD_ERROR;
simError();
} else {
targetTemp = simParams->getTargetTemp();
}
// We must set tauThermostat
if (!simParams->haveTauThermostat()) {
sprintf(painCave.errMsg, "If you use the constant temperature\n"
"\tintegrator, you must set tauThermostat.\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
} else {
tauThermostat = simParams->getTauThermostat();
}
if (!simParams->haveTargetPressure()) {
sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
" without a targetPressure!\n");
painCave.isFatal = 1;
simError();
} else {
targetPressure = simParams->getTargetPressure();
}
if (!simParams->haveTauBarostat()) {
sprintf(painCave.errMsg,
"If you use the NPT integrator, you must set tauBarostat.\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
} else {
tauBarostat = simParams->getTauBarostat();
}
tt2 = tauThermostat * tauThermostat;
tb2 = tauBarostat * tauBarostat;
updateSizes();
}
void Snapshot::clearDerivedProperties() {
frameData.totalEnergy = 0.0;
frameData.translationalKinetic = 0.0;
frameData.rotationalKinetic = 0.0;
frameData.kineticEnergy = 0.0;
frameData.potentialEnergy = 0.0;
frameData.shortRangePotential = 0.0;
frameData.longRangePotential = 0.0;
frameData.pressure = 0.0;
frameData.temperature = 0.0;
frameData.pressureTensor = Mat3x3d(0.0);
frameData.systemDipole = Vector3d(0.0);
frameData.systemQuadrupole = Mat3x3d(0.0);
frameData.convectiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
frameData.electronicTemperature = 0.0;
frameData.COM = V3Zero;
frameData.COMvel = V3Zero;
frameData.COMw = V3Zero;
hasTotalEnergy = false;
hasTranslationalKineticEnergy = false;
hasRotationalKineticEnergy = false;
hasKineticEnergy = false;
hasShortRangePotential = false;
hasLongRangePotential = false;
hasPotentialEnergy = false;
hasXYarea = false;
hasVolume = false;
hasPressure = false;
hasTemperature = false;
hasElectronicTemperature = false;
hasCOM = false;
hasCOMvel = false;
hasCOMw = false;
hasPressureTensor = false;
hasSystemDipole = false;
hasSystemQuadrupole = false;
hasConvectiveHeatFlux = false;
hasInertiaTensor = false;
hasGyrationalVolume = false;
hasHullVolume = false;
hasConservedQuantity = false;
hasBoundingBox = false;
}
void MomentumCorrFunc::preCorrelate() {
// Fill the histogram with empty 3x3 matrices:
std::fill(histogram_.begin(), histogram_.end(), Mat3x3d(0.0));
// count array set to zero
std::fill(count_.begin(), count_.end(), 0);
}
