bool Cube::parseCoordinates(TextStream& textStream, unsigned nAtoms)
{
Data::Geometry* geometry(new Data::Geometry);
bool ok;
unsigned atomicNumber;
qglviewer::Vec position;
for (unsigned i = 0; i < nAtoms; ++i) {
QStringList tokens(textStream.nextLineAsTokens());
if (tokens.size() != 5) return false;
atomicNumber = tokens[0].toUInt(&ok); if (!ok) goto error;
position.x = tokens[2].toDouble(&ok); if (!ok) goto error;
position.y = tokens[3].toDouble(&ok); if (!ok) goto error;
position.z = tokens[4].toDouble(&ok); if (!ok) goto error;
geometry->append(atomicNumber, position);
}
geometry->scaleCoordinates(m_scale);
geometry->computeGasteigerCharges();
m_dataBank.append(geometry);
return true;
error:
QString msg("Incorrect format on line ");
msg += QString::number(textStream.lineNumber());
delete geometry;
return false;
}
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;
}
}
bool ExternalCharges::parse(TextStream& textStream)
{
int max(INT_MAX);
bool allOk(true), isDouble;
bool maxSet(false), invalidFormat(false);
double x, y, z, q;
QStringList tokens;
Data::PointChargeList* charges(new Data::PointChargeList);
while (!textStream.atEnd() && charges->size() < max) {
tokens = textStream.nextLineAsTokens();
if (tokens.size() >= 4) {
x = tokens[0].toDouble(&isDouble); allOk = allOk && isDouble;
y = tokens[1].toDouble(&isDouble); allOk = allOk && isDouble;
z = tokens[2].toDouble(&isDouble); allOk = allOk && isDouble;
q = tokens[3].toDouble(&isDouble); allOk = allOk && isDouble;
if (allOk) {
charges->append(new Data::PointCharge(q, qglviewer::Vec(x,y,z)));
}else {
invalidFormat = true;
break;
}
}else if (tokens.size() >= 1) {
if (tokens.first().contains("$end", Qt::CaseInsensitive) || maxSet) {
break;
}else {
max = tokens[0].toInt(&maxSet);
}
}
}
if (maxSet && charges->size() != max) {
if (invalidFormat) {
QString msg("Invalid format on line ");
m_errors.append(msg += QString::number(textStream.lineNumber()));
}else {
m_errors.append("End of stream encountered");
}
delete charges;
}else if (charges->isEmpty()) {
m_errors.append("No charges found");
delete charges;
}else {
m_dataBank.append(charges);
}
return m_errors.isEmpty();
}
bool Cube::parse(TextStream& textStream)
{
// Header information
textStream.skipLine(2);
int nAtoms(parseGridAxes(textStream));
if (nAtoms == 0) {
QString msg("Incorrect format on line ");
msg += QString::number(textStream.lineNumber());
msg += "\nExpected: <int> <double> <double> <double>";
m_errors.append(msg);
return false;
}
if (!parseCoordinates(textStream, nAtoms)) return false;
parseGridData(textStream);
return m_errors.isEmpty();
}
void QChemInput::readRemSection(TextStream& textStream)
{
QString line;
QStringList tokens;
bool finished(false);
Data::RemSection* rem = new Data::RemSection;
while (!textStream.atEnd() && !finished) {
line = textStream.nextLine();
line = line.replace('=', ' ');
tokens = TextStream::tokenize(line);
switch (tokens.size()) {
case 0:
// Ignore empty lines
break;
case 1:
if (tokens[0].contains("$end", Qt::CaseInsensitive)) {
finished = true;
}else if (tokens[0].contains("$rem", Qt::CaseInsensitive)) {
// carry on
}else {
m_errors.append("Invalid $rem format, line " +
QString::number(textStream.lineNumber()));
delete rem;
rem = 0;
finished = true;
}
break;
default:
rem->insert(tokens[0].toLower(), tokens[1].toLower());
break;
}
}
if (rem) m_dataBank.append(rem);
}
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);
}
}
// Note the grid data is read in as bohr, but converted to angstroms in the
// Grid constructor
bool QChemPlot::parse(TextStream& textStream)
{
QList<double> values;
QList<Data::SurfaceType> surfaceTypes(parseForProperties(textStream));
unsigned nProperties(surfaceTypes.size());
if (nProperties < 1) goto error;
values = textStream.nextLineAsDoubles();
if ((unsigned)values.size() != 3 + nProperties) goto error;
{/**/
double xMin(values[0]);
double yMin(values[1]);
double zMin(values[2]);
double xMax(xMin);
double yMax(yMin);
double zMax(zMin);
typedef QList<double> List;
List* data = new List[nProperties];
for (unsigned i = 0; i < nProperties; ++i) {
data[i].append(values[i+3]);
}
unsigned nx(1), ny(1), nz(1);
while (!textStream.atEnd()) {
if ((unsigned)values.size() == 3 + nProperties) {
if (values[0] > xMax) { xMax = values[0]; ++nx; }
if (values[1] > yMax) { yMax = values[1]; ++ny; }
if (values[2] > zMax) { zMax = values[2]; ++nz; }
for (unsigned i = 0; i < nProperties; ++i) {
data[i].append(values[i+3]);
}
}
values = textStream.nextLineAsDoubles();
}
qglviewer::Vec delta((xMax-xMin)/nx, (yMax-yMin)/ny, (zMax-zMin)/nz);
qglviewer::Vec origin(xMin, yMin, zMin);
Data::GridDataList* gridList(new Data::GridDataList);
try {
for (unsigned i = 0; i < nProperties; ++i) {
Data::GridSize size(origin, delta, nx, ny, nz);
gridList->append(new Data::GridData(size, surfaceTypes[i]));
}
m_dataBank.append(gridList);
} catch (...) {
m_errors.append("Problem creating QChem plot data");
delete gridList;
}
delete[] data;
}/**/
return m_errors.isEmpty();
error:
QString msg("Problem parsing QChem plot data, line ");
m_errors.append(msg += QString::number(textStream.lineNumber()));
return false;
}
