Descriptor
These functions are used to read initial atomic structures saved as extxyz files and create descriptors
- atomdnn.descriptor.create_descriptors(lmpexe, elements, xyzfile_path, xyzfile_name, descriptors_path, descriptor, descriptor_filename='dump_fp.*', der_filename='dump_der.*', start_file_id=1, image_num=None, skip=0, keep_lmpfiles=False, verbose=False)[source]
Read extxyz files as inputs and create descriptors and their derivatives w.r.t. atom coordinates.
- Parameters
lmpexe – lammps executable
xyzfile_path – directory contains a serials of extxyz files of input atomic structures
xyzfile_name – extxyz filename, wildcard * is used for files numerically ordered
descriptors_path – a new directory where descirptors will be generated
descritpor (dictionary) – the parameter dictionary of the descriptor
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
verbose (bool) – set to True if want to print out the extxyz file names used for creating descriptors