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

atomdnn.descriptor.create_lmp_input(descriptor, descriptors_path)[source]

Creates a lammps input file for computing descriptors and derivatives

Parameters

descritpor (dictionary) – the parameter dictionary of the descriptor

atomdnn.descriptor.get_filenames(file_path, file_name)[source]

Get the names of a set of files that match the patten given by file_name. Return the filenames having the format of ‘string1*string2’, in which string1 and string2 can be any strings amd * must be an integer.