pymatgen.io.abinit.netcdf module

Wrapper for netCDF readers.

class ETSF_Reader(path)[source]

Bases: NetcdfReader

This object reads data from a file written according to the ETSF-IO specifications.

We assume that the netcdf file contains at least the crystallographic section.

Open the Netcdf file specified by path (read mode).

chemical_symbols()[source]: Chemical symbols char [number of atom species][symbol length].

read_abinit_hdr()[source]

Read the variables associated to the Abinit header.

Return AbinitHeader

read_abinit_xcfunc()[source]: Read ixc from an Abinit file. Return XcFunc object.

read_structure(cls=<class 'pymatgen.core.structure.Structure'>)[source]: Returns the crystalline structure stored in the rootgrp.

typeidx_from_symbol(symbol)[source]: Returns the type index from the chemical symbol. Note python convention.

class NO_DEFAULT[source]

Bases: object

Signal that read_value should raise an Error

class NetcdfReader(path)[source]

Bases: object

Wraps and extends netCDF4.Dataset. Read only mode. Supports with statements.

Additional documentation available at:: http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html

Open the Netcdf file specified by path (read mode).

read_dimvalue(dimname, path='/', default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]

Returns the value of a dimension.

Parameters:

dimname – Name of the variable
path – path to the group.
default – return default if dimname is not present and default is not NO_DEFAULT else raise self.Error.

read_keys(keys, dict_cls=<class 'monty.collections.AttrDict'>, path='/')[source]: Read a list of variables/dimensions from file. If a key is not present the corresponding entry in the output dictionary is set to None.

read_value(varname, path='/', cmode=None, default=<class 'pymatgen.io.abinit.netcdf.NO_DEFAULT'>)[source]

Returns the values of variable with name varname in the group specified by path.

Parameters:

varname – Name of the variable
path – path to the group.
cmode – if cmode==”c”, a complex ndarrays is constructed and returned (netcdf does not provide native support from complex datatype).
default – returns default if varname is not present. self.Error is raised if default is set to NO_DEFAULT

Returns:

numpy array if varname represents an array, scalar otherwise.

read_variable(varname, path='/')[source]: Returns the variable with name varname in the group specified by path.

read_varnames(path='/')[source]: List of variable names stored in the group specified by path.

walk_tree(top=None)[source]: Navigate all the groups in the file starting from top. If top is None, the root group is used.

as_etsfreader(file)[source]: Return an ETSF_Reader. Accepts filename or ETSF_Reader.

as_ncreader(file)[source]: Convert file into a NetcdfReader instance. Returns reader, closeit where closeit is set to True if we have to close the file before leaving the procedure.

structure_from_ncdata(ncdata, site_properties=None, cls=<class 'pymatgen.core.structure.Structure'>)[source]

Reads and returns a pymatgen structure from a NetCDF file containing crystallographic data in the ETSF-IO format.

Parameters: