bool AmberNetcdf::parseFrame() {
if (_current_frame >= _nframes)
return(false);
readRawFrame(_current_frame);
return(true);
}
QByteArray StandardSerialPortBackend::readDataFrame(uint size, bool verbose)
{
// qDebug() << "!d" << tr("DBG -- Serial Port readDataFrame...");
QByteArray data = readRawFrame(size + 1, verbose);
if (data.isEmpty()) {
return data;
}
quint8 expected = (quint8)data.at(size);
quint8 got = sioChecksum(data, size);
if (expected == got) {
data.resize(size);
return data;
} else {
if (verbose) {
qWarning() << "!w" << tr("Data frame checksum error, expected: %1, got: %2. (%3)")
.arg(expected)
.arg(got)
.arg(QString(data.toHex()));
}
data.clear();
return data;
}
}
void AmberNetcdf::init(const char* name, const uint natoms) {
int retval;
retval = nc_open(name, NC_NOWRITE, &_ncid);
if (retval)
throw(FileOpenError(name, "", retval)); // May want to preserve code here in the future...
// Read and validate global attributes...
readGlobalAttributes();
if (_conventions.empty() || _conventionVersion.empty())
throw(FileOpenError(name, "Unable to find convention global attributes. Is this really an Amber NetCDF trajectory?"));
if (_conventions.find("AMBER") == std::string::npos)
throw(FileOpenError(name, "Cannot find AMBER tag in global attribues. Is this really an Amber NetCDF trajectory?"));
if (_conventionVersion != std::string("1.0"))
throw(FileOpenError(name, "Convention version is '" + _conventionVersion + "', but only 1.0 is supported for Amber NetCDF trajectories."));
// Verify # of atoms match...
int atom_id;
retval = nc_inq_dimid(_ncid, "atom", &atom_id);
if (retval)
throw(FileOpenError(name, "Cannot read atom id"), retval);
retval = nc_inq_dimlen(_ncid, atom_id, &_natoms);
if (retval)
throw(FileOpenError(name, "Cannot read atom length", retval));
if (_natoms != natoms)
throw(FileOpenError(name, "AmberNetcdf has different number of atoms than expected"));
// Get nframes
int frame_id;
retval = nc_inq_dimid(_ncid, "frame", &frame_id);
if (retval)
throw(FileOpenError(name, "Cannot read frame information", retval));
retval = nc_inq_dimlen(_ncid, frame_id, &_nframes);
// Check for periodic cells...
retval = nc_inq_varid(_ncid, "cell_lengths", &_cell_lengths_id);
_periodic = !retval;
// Any additional validation should go here...
// Get coord-id for later use...
retval = nc_inq_varid(_ncid, "coordinates", &_coord_id);
if (retval)
throw(FileOpenError(name, "Cannot get id for coordinates", retval));
// Attempt to determine timestep by looking at dT between frames 1 & 2
if (_nframes >= 2) {
int time_id;
retval = nc_inq_varid(_ncid, "time", &time_id);
if (!retval) {
float t0, t1;
size_t idx[1];
idx[0] = 0;
retval = nc_get_var1_float(_ncid, time_id, idx, &t0);
if (retval)
throw(FileOpenError(name, "Cannot get first time point", retval));
idx[0] = 1;
retval = nc_get_var1_float(_ncid, time_id, idx, &t1);
if (retval)
throw(FileOpenError(name, "Cannot get second time point", retval));
// Assume units are in picoseconds
_timestep = (t1-t0)*1e-12;
}
}
// Now cache the first frame...
readRawFrame(0);
cached_first = true;
}
