void QChemInput::readEfpFragmentSection(TextStream& textStream)
{
// Check for an existing list from the $molecule section
Data::EfpFragmentList* efps(0);
QList<Data::EfpFragmentList*> lists = m_dataBank.findData<Data::EfpFragmentList>();
if (lists.isEmpty()) {
efps = new Data::EfpFragmentList;
m_dataBank.append(efps);
}else {
efps = lists.last();
}
QString msg("Invalid $efp_fragments format on line ");
QStringList tokens;
bool ok, allOk;
int count(1);
while (!textStream.atEnd()) {
tokens = textStream.nextLineAsTokens();
if (tokens.size() == 1 && tokens[0].contains("$end", Qt::CaseInsensitive)) {
break;
}else if (tokens.size() < 7) {
Data::EfpFragment* efp(0);
if (count <= efps->size()) {
efp = efps->at(count-1);
}else {
efp = new Data::EfpFragment;
efps->append(efp);
}
efp->setName(tokens[0]);
}else {
allOk = true;
QString name(tokens[0]);
double x, y, z, a, b, c;
if (allOk) x = tokens[1].toDouble(&ok); allOk = allOk && ok;
if (allOk) y = tokens[2].toDouble(&ok); allOk = allOk && ok;
if (allOk) z = tokens[3].toDouble(&ok); allOk = allOk && ok;
if (allOk) a = tokens[4].toDouble(&ok); allOk = allOk && ok;
if (allOk) b = tokens[5].toDouble(&ok); allOk = allOk && ok;
if (allOk) c = tokens[6].toDouble(&ok); allOk = allOk && ok;
if (allOk) {
efps->append(new Data::EfpFragment(name, qglviewer::Vec(x,y,z), a, b, c));
}else {
m_errors.append(msg += QString::number(textStream.lineNumber()));
}
}
++count;
}
}
void QChemInput::readMoleculeSection(TextStream& textStream)
{
QString msg("Invalid $molecule format on line ");
int charge(0);
unsigned multiplicity(1);
bool ok;
// First line can only contain the charge and multiplicity or 'read'
QString line(textStream.nextLine());
line = line.replace(',', ' ');
QStringList tokens(TextStream::tokenize(line));
switch (tokens.size()) {
case 0: // Error
m_errors.append(msg + QString::number(textStream.lineNumber()));
return;
break;
case 1: // Could be reading in previous geometry
if (tokens[0].contains("read", Qt::CaseInsensitive)) {
if (m_geometryList->size() > 0) {
// copy previous geometry
Data::Geometry* geometry(new Data::Geometry(*(m_geometryList->last())));
m_geometryList->append(geometry);
}else {
// We assume we are reading an input section from
// an output file, so there is no new geometry.
}
}else {
m_errors.append(msg + QString::number(textStream.lineNumber()));
}
return;
break;
default:
charge = tokens[0].toInt(&ok);
if (ok) multiplicity = tokens[1].toUInt(&ok);
if (!ok) {
m_errors.append(msg + QString::number(textStream.lineNumber()));
return;
}
break;
}
// Second line could be a 'read' token or the first atom
line = textStream.nextLine();
// offset is passed to the CartesianCoordinates parser to give
// an accurate line number if an error occurs.
int offset(textStream.lineNumber()-1);
if (line.isEmpty()) {
m_errors.append(msg + QString::number(textStream.lineNumber()));
return;
}
// Special case: read previous geometry
if (line.contains("read", Qt::CaseInsensitive)) {
if (m_geometryList->size() > 0) {
// copy last geometry
Data::Geometry* geometry(new Data::Geometry(*(m_geometryList->last())));
geometry->setChargeAndMultiplicity(charge, multiplicity);
m_geometryList->append(geometry);
}else {
m_errors.append(msg + QString::number(textStream.lineNumber()));
}
return;
}
// Special case: EFP only fragments
if (line.contains("--")) {
// Check for an existing list which may have been created if the
// $efp_fragments section was parsed before $molecule.
Data::EfpFragmentList* efps(0);
QList<Data::EfpFragmentList*> lists = m_dataBank.findData<Data::EfpFragmentList>();
if (lists.isEmpty()) {
efps = new Data::EfpFragmentList;
m_dataBank.append(efps);
}else {
efps = lists.last();
}
int count(1);
while (!textStream.atEnd()) {
tokens = textStream.nextLineAsTokens();
if (tokens.size() == 1 && tokens[0].contains("$end", Qt::CaseInsensitive)) {
break;
}else if (tokens.size() == 6) {
bool allOk(true);
double x, y, z, a, b, c;
if (allOk) x = tokens[0].toDouble(&ok); allOk = allOk && ok;
if (allOk) y = tokens[1].toDouble(&ok); allOk = allOk && ok;
if (allOk) z = tokens[2].toDouble(&ok); allOk = allOk && ok;
if (allOk) a = tokens[3].toDouble(&ok); allOk = allOk && ok;
if (allOk) b = tokens[4].toDouble(&ok); allOk = allOk && ok;
if (allOk) c = tokens[5].toDouble(&ok); allOk = allOk && ok;
if (allOk) {
Data::EfpFragment* efp(0);
if (count <= efps->size()) {
efp = efps->at(count-1);
}else {
efp = new Data::EfpFragment;
efps->append(efp);
}
efp->setPosition(Vec(x,y,z));
efp->setEulerAngles(a,b,c);
}
++count;
}
}
return;
}
tokens = TextStream::tokenize(line);
bool zmat(tokens.size() == 1);
QStringList lines;
while (!textStream.atEnd() && !line.contains("$end", Qt::CaseInsensitive)) {
// Account for the possibility of a FSM job, which has two geometries
// separated by the **** token.
if (line.contains("****")) {
Data::Geometry* geom(parseGeometry(lines, offset, zmat));
if (geom) {
geom->setChargeAndMultiplicity(charge, multiplicity);
m_geometryList->append(geom);
}
offset = textStream.lineNumber();
lines.clear();
}else {
lines.append(line);
}
line = textStream.nextLine();
}
Data::Geometry* geom(parseGeometry(lines, offset, zmat));
if (geom) {
geom->setChargeAndMultiplicity(charge, multiplicity);
m_geometryList->append(geom);
}
}
Layer::List Factory::toLayers(Data::Base& data)
{
Layer::List layers;
//qDebug() << "Layer::Factory converting" << Data::Type::toString(data.typeID());
try {
switch (data.typeID()) {
case Data::Type::Bank: {
Data::Bank& bank(dynamic_cast<Data::Bank&>(data));
layers << convert(bank);
} break;
case Data::Type::GeometryList: {
Data::GeometryList& list(dynamic_cast<Data::GeometryList&>(data));
layers << convert(list);
} break;
case Data::Type::Geometry: {
Data::Geometry& geometry(dynamic_cast<Data::Geometry&>(data));
layers << convert(geometry);
} break;
case Data::Type::PointChargeList: {
Data::PointChargeList& charges(dynamic_cast<Data::PointChargeList&>(data));
layers << convert(charges);
} break;
case Data::Type::MolecularOrbitalsList: {
Data::MolecularOrbitalsList& list(dynamic_cast<Data::MolecularOrbitalsList&>(data));
layers << convert(list);
} break;
case Data::Type::MolecularOrbitals: {
Data::MolecularOrbitals&
molecularOrbitals(dynamic_cast<Data::MolecularOrbitals&>(data));
layers.append(new MolecularOrbitals(molecularOrbitals));
} break;
case Data::Type::ExcitedStates: {
Data::ExcitedStates&
states(dynamic_cast<Data::ExcitedStates&>(data));
layers.append(new ExcitedStates(states));
} break;
case Data::Type::Frequencies: {
Data::Frequencies&
frequencies(dynamic_cast<Data::Frequencies&>(data));
layers.append(new Frequencies(frequencies));
} break;
case Data::Type::FileList: {
Data::FileList& fileList(dynamic_cast<Data::FileList&>(data));
layers << convert(fileList);
} break;
case Data::Type::GridData: {
QLOG_WARN() << "Data::GridData passed to LayerFactory";
//Data::GridData& grid(dynamic_cast<Data::GridData&>(data));
//layers.append(new CubeData(grid));
} break;
case Data::Type::CubeData: {
Data::CubeData& cube(dynamic_cast<Data::CubeData&>(data));
layers.append(new CubeData(cube));
} break;
case Data::Type::EfpFragment: {
Data::EfpFragment& efp(dynamic_cast<Data::EfpFragment&>(data));
layers.append(new EfpFragment(efp));
} break;
case Data::Type::EfpFragmentList: {
Data::EfpFragmentList&
efpList(dynamic_cast<Data::EfpFragmentList&>(data));
layers << convert(efpList);
} break;
case Data::Type::Mesh: {
Data::Mesh& meshData(dynamic_cast<Data::Mesh&>(data));
Data::Surface surface(meshData);
Layer::Surface* surfaceLayer(new Surface(surface));
surfaceLayer->setCheckState(Qt::Checked);
layers.append(surfaceLayer);
} break;
case Data::Type::Surface: {
Data::Surface& surfaceData(dynamic_cast<Data::Surface&>(data));
Layer::Surface* surfaceLayer(new Surface(surfaceData));
surfaceLayer->setCheckState(surfaceData.isVisible() ? Qt::Checked : Qt::Unchecked);
layers.append(surfaceLayer);
} break;
case Data::Type::Nmr: {
Data::Nmr& nmrData(dynamic_cast<Data::Nmr&>(data));
Layer::Nmr* nmrLayer(new Nmr(nmrData));
layers.append(nmrLayer);
} break;
default:
QLOG_WARN() << "Unimplemented data type in Layer::Factory"
<< Data::Type::toString(data.typeID());
break;
}
} catch (const std::bad_cast& e) {
QLOG_ERROR() << "Data cast in Layer::Factory failed"
<< Data::Type::toString(data.typeID());
}
return layers;
}
