//==============================================================================
/// Parse a single base dimension definition.
///
/// \param [in] dim The YAML map node for the dimension.
///
void DefinitionParser::ParseBaseDimension( const YAML::Node& dim )
{
QString name;
dim["name"] >> name;
QString unit_name;
dim["unit"] >> unit_name;
DimensionId id;
id[unit_name] = 1;
(void)DefineDimension( dim.GetMark(), name, id, unit_name );
}
//==============================================================================
/// Parse a single derived dimension definition.
///
/// \param [in] dim The YAML map node for the dimension.
///
void DefinitionParser::ParseDerivedDimension( const YAML::Node& dim )
{
QString name;
dim["name"] >> name;
QString unit_name;
dim["unit"] >> unit_name;
QString derivation;
dim["derivation"] >> derivation;
DimensionId id = ParseDerivation( derivation );
(void)DefineDimension( dim.GetMark(), name, id, unit_name );
}
bool CNetCDFTraj::WriteHeader(CAmberTopology* p_top)
{
if( p_top == NULL ){
INVALID_ARGUMENT("p_top == NULL");
}
if( NCID < 0 ) {
ES_ERROR("file is not opened");
return(false);
}
int dimensionID[NC_MAX_VAR_DIMS];
NumOfTopologyAtoms = p_top->AtomList.GetNumberOfAtoms();
ActualAtoms = NumOfTopologyAtoms;
CurrentSnapshot = 0;
TotalSnapshots = 0;
if( Coordinates != NULL ) {
delete Coordinates;
}
Coordinates = new float[ActualAtoms*3];
// global dimmensions
DefineDimension(AMBER_NETCDF_FRAME, NC_UNLIMITED, &TimeDID);
DefineDimension(AMBER_NETCDF_SPATIAL, 3, &SpatialDID);
DefineDimension(AMBER_NETCDF_ATOM, ActualAtoms, &CoordinateDID);
DefineDimension(AMBER_NETCDF_LABEL, AMBER_NETCDF_LABELLEN, &LabelDID);
DefineDimension(AMBER_NETCDF_CELL_SPATIAL, 3, &CellSpatialDID);
DefineDimension(AMBER_NETCDF_CELL_ANGULAR, 3, &CellAngularDID);
// put global attributes
Conventions = "AMBER";
ConventionVersion = "1.0";
PutAttributeText(NC_GLOBAL, "title", Title);
PutAttributeText(NC_GLOBAL, "application", Application);
PutAttributeText(NC_GLOBAL, "program", Program);
PutAttributeText(NC_GLOBAL, "programVersion", Version);
PutAttributeText(NC_GLOBAL, "Conventions", Conventions);
PutAttributeText(NC_GLOBAL, "ConventionVersion", ConventionVersion);
// handle definition of non-optional variables
dimensionID[0] = SpatialDID;
DefineVariable(AMBER_NETCDF_SPATIAL, NC_CHAR, 1, dimensionID, &SpatialVID);
dimensionID[0] = TimeDID;
DefineVariable(AMBER_NETCDF_TIME, NC_FLOAT, 1, dimensionID, &TimeVID);
PutAttributeText(TimeVID, "units", "picosecond");
dimensionID[0] = TimeDID;
dimensionID[1] = CoordinateDID;
dimensionID[2] = SpatialDID;
DefineVariable(AMBER_NETCDF_COORDS, NC_FLOAT, 3, dimensionID, &CoordinateVID);
PutAttributeText(CoordinateVID, "units", "angstrom");
dimensionID[0] = CellSpatialDID;
DefineVariable(AMBER_NETCDF_CELL_SPATIAL, NC_CHAR, 1, dimensionID, &CellSpatialVID);
dimensionID[0] = CellAngularDID;
dimensionID[1] = LabelDID;
DefineVariable(AMBER_NETCDF_CELL_ANGULAR, NC_CHAR, 2, dimensionID, &CellAngularVID);
// set up box coords
HasBox = p_top->BoxInfo.GetType() != AMBER_BOX_NONE;
if( HasBox ) {
dimensionID[0] = TimeDID;
dimensionID[1] = CellSpatialDID;
DefineVariable("cell_lengths", NC_DOUBLE, 2, dimensionID, &CellLengthVID);
PutAttributeText(CellLengthVID, "units", "angstrom");
dimensionID[1] = CellAngularDID;
DefineVariable("cell_angles", NC_DOUBLE, 2, dimensionID, &CellAngleVID);
PutAttributeText(CellAngleVID, "units", "degree");
}
int err,oldMode;
// set fill mode
err = nc_set_fill(NCID, NC_NOFILL, &oldMode);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set fill value (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
// end definition
err = nc_enddef(NCID);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to end definitions (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
size_t start[3];
size_t count[3];
char xyz[3];
char abc[15] = { 'a', 'l', 'p', 'h', 'a',
'b', 'e', 't', 'a', ' ',
'g', 'a', 'm', 'm', 'a' };
// setup labels
start[0] = 0;
count[0] = 3;
xyz[0] = 'x';
xyz[1] = 'y';
xyz[2] = 'z';
err = nc_put_vara_text(NCID, SpatialVID, start, count, xyz);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set spatial VID 'x', 'y' and 'z' (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
start[0] = 0;
count[0] = 3;
xyz[0] = 'a';
xyz[1] = 'b';
xyz[2] = 'c';
err = nc_put_vara_text(NCID, CellSpatialVID, start, count, xyz);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set spatial cell VID 'a', 'b' and 'c' (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
start[0] = 0;
start[1] = 0;
count[0] = 3;
count[1] = 5;
err = nc_put_vara_text(NCID, CellAngularVID, start, count, abc);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set angular cell VID 'alpha', 'beta ' and 'gamma' (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
return(true);
}
