Descriptor
These functions are used to read initial atomic structures saved as extxyz files and create descriptors
- atomdnn.descriptor.create_descriptors(elements, xyzfiles, descriptor, format='extxyz', descriptors_path=None, descriptor_filename='dump_fp.*', der_filename='dump_der.*', start_file_id=1, image_num=None, skip=0, keep_lmpfiles=False, create_data=True, verbose=False, silent=False, **kwargs)[source]
Read extxyz files as inputs and create descriptors and their derivatives w.r.t. atom coordinates.
- Parameters:
elements – a list of elements, e.g. [‘C’,’O’,’H’], make sure the sequence is consistant
xyzfiles – a serials of extxyz files of input atomic structures, wildcard * is used for files numerically ordered
descritpor (dictionary) – the parameter dictionary of the descriptor
format – ‘lammp-data’,’extxyz’,’vasp’ etc. See complete list on https://wiki.fysik.dtu.dk/ase/ase/io/io.html#ase.io.read. ‘extxyz’ is recommanded.
descriptors_path – a new directory where descirptors will be generated, default is ‘./descriptors’
descriptor_filename – default is ‘dump_fp.*’, numerically ordered
der_filename – default is ‘dump_der.*’, numerically ordered
start_file_id (int) – starting id for descriptor and derivative files
image_num – number of images that will be used, if it’s None then read all files specified by xyzfile_name
skip (int) – skip some images
keep_lmpfiles (bool) – set to True if want to keep the lammps input and datafiles used for creating descriptors
create_data (bool) – set to True if want to create Data object using the generated descriptors
verbose (bool) – set to True if want to print out the extxyz file names used for creating descriptors
kwargs – used to pass optional file styles