asaplib.cli package

Submodules

asaplib.cli.cmd_asap module

Module containing the top level asap command

asaplib.cli.cmd_cli_options module

asaplib.cli.cmd_cli_options.atomic_to_global_desc_options(f)

Create common options for global descriptors constructed based on atomic fingerprints

asaplib.cli.cmd_cli_options.color_setup_options(f)

Create common options for handing color scales

asaplib.cli.cmd_cli_options.d_reduce_options(f)

Create common options for dimensionality reduction

asaplib.cli.cmd_cli_options.desc_options(f)

Create common options for computing descriptors

asaplib.cli.cmd_cli_options.dm_input_options(f)

common options for reading a design matrices, used for map, fit, kde, clustering, etc.

asaplib.cli.cmd_cli_options.file_input_format_options(f)

Create common options for I/O files

asaplib.cli.cmd_cli_options.file_input_options(f)

Create common options for I/O files

asaplib.cli.cmd_cli_options.file_output_options(f)

Create common options for I/O files

asaplib.cli.cmd_cli_options.fit_setup_options(f)

Create common options for making 2D maps of the data set

asaplib.cli.cmd_cli_options.kernel_options(f)

Create common options for compute kernel functions

asaplib.cli.cmd_cli_options.km_input_options(f)

common options for reading a kernel matrices, can be used for map, fit, kde, clustering, etc.

asaplib.cli.cmd_cli_options.map_io_options(f)

Create common options for making 2D maps of the data set

asaplib.cli.cmd_cli_options.map_setup_options(f)

Create common options for making 2D maps of the data set

asaplib.cli.cmd_cli_options.output_setup_options(f)

Create common options for output results from clustering/KDE analysis

asaplib.cli.cmd_cli_options.para_options(f)

Create common options for parallellization

asaplib.cli.cmd_cli_options.sparsification_options(f)

Create common options for sparsification

asaplib.cli.cmd_cli_options.state_input_options(f)

Create common options for I/O files

asaplib.cli.func_asap module

functions used in cmd_asap.py

asaplib.cli.func_asap.cluster_process(asapxyz, trainer, design_matrix, cluster_options)

handle clustering operations

asaplib.cli.func_asap.figure_style_setups(prefix, colorlabel, colorscale, colormap, style, aspect_ratio, adjusttext)

asaplib.cli.func_asap.kde_process(asapxyz, density_model, proj, kde_options)

handle kernel density estimation operations

asaplib.cli.func_asap.load_asapxyz(data_spec)

asaplib.cli.func_asap.load_in_file(in_file)

Here goes the routine to compute the descriptors according to the state file(s)

asaplib.cli.func_asap.map_plot(fig_spec, proj, proj_atomic, plotcolor, plotcolor_atomic, labels, annotate, axes)

Make plots

asaplib.cli.func_asap.map_process(obj, reduce_dict, axes, map_name)

process the dimensionality reduction command

asaplib.cli.func_asap.map_save(foutput, outmode, asapxyz, proj, proj_atomic, map_name, species_name)

Save the low-D projections

asaplib.cli.func_asap.output_desc(asapxyz, desc_spec, prefix, peratom=False, N_processes=8)

Compute and save the descriptors

asaplib.cli.func_asap.read_xyz_n_dm(fxyz, design_matrix, use_atomic_descriptors, only_use_species, peratom)

asaplib.cli.func_asap.set_reducer(reducer_type, element_wise, zeta)

setting up the reducer function that is used to convert atomic descriptors into global descriptors for a structure. At the moment only one single reducer function can be used.

Module contents

Command-line interface sub-package