Supported File Formats

The AtomsReaders and AtomsWriters dictionaries are used by the Atoms constructor, Atoms.write(), the AtomsList constructor and AtomsList.write() to work out how to read or write a particular file type, based on the filename extension.

The quippy native formats are Extended XYZ and NetCDF.

• Extended XYZ
• NetCDF

quippy.AtomsReaders

Supported file formats for reading Atoms objects from files.

File extension	Description
castep or castep_log	CASTEP output file
cell	CASTEP cell file
geom	CASTEP geom file
md	CASTEP MD file
nc	NetCDF file
pos	ASAP coordinate file
stdin	Read from stdin in extended XYZ format
string	Read from string in extended XYZ format
xyz	Extended XYZ format

quippy.AtomsWriters

Supported file formats for writing Atoms objects to files.

File extension	Description
cell	CASTEP cell file
nc	NetCDF file
pos	ASAP coordinate file
pov	POV-ray script
stdout	Write to stdout in extended XYZ format
string	Write to string in extended XYZ format
xyz	Extended XYZ format

Adding a new file type

To add support for a new file format, implement routines which read from or write to files following the templates below.

def sample_reader(filename):
    # insert code to open `filename` for reading

    while True:
       # determine if more frame are available
       if more_frames:
          # read next frame from `filename` into new Atoms object
          at = Atoms()
          yield at
       else:
          break


class sample_writer(object):
    def __init__(self, filename):
       # insert code to open `filename` for writing
       pass

    def write(self, at):
       # insert code to write `at` to `filename`
       pass

    def close(self):
       # insert code to close `filename`
       pass

sample_reader() is a generator which yields a succession of Atoms objects, raising StopIteration when there are no more available - for a file format which only permits one configuration per file, a simplified implementation template would be:

def sample_reader(filename):
   # insert code to open `filename` for reading
   # insert code to read from `filename` into new Atoms object
   yield at

To register the new file format, you just need to set entries in AtomsReaders and AtomsWriters:

from quippy import AtomsReaders, AtomsWriters
AtomsReaders['new_format'] = sample_reader
AtomsWriters['new_format'] = sameple_writer

For the case of reading, there is a generator atoms_reader() which can be used to simplify the registration process:

@atoms_reader('new_format')
def sample_reader(filename):
   ...

See the code in quippy.xyz_netcdf and quippy.castep for full examples.