Lib

New, Refactored Mechdriver libs

Moldriver libs

mechlib.filesys.build_fs(run_prefix, save_prefix, end, rxn_locs=None, spc_locs=None, thy_locs=None, ts_locs=None, cnf_locs=None, tau_locs=None, instab_locs=None, zma_locs=None, scn_locs=None, cscn_locs=None)

Build the autofile filesystem objects for some specified fileystem layer using the root run/save and locs to build the full prefix path to the fileystem layer.

Parameters:

• run_prefix – root-path to the run-filesystem

• save_prefix – root-path to the save-filesystem

• end (str) – filesystem layer

• x_locs (locs fot REACTION layer) – locs used to construct prefix to end-layer

Type:

run_prefix: str

Type:

save_prefix: str

mechlib.filesys.prefix_fs(run_prefix, save_prefix)

Physically make the run/save filesys root given a prefix path :param str prefix: file path - /path/to/root/run

mechlib.filesys.reaction_fs(run_prefix, save_prefix, rxn_info)

Build reaction filesystem for a big list

mechlib.filesys.root_locs(spc_dct_i, saddle=False, name=None)

Set the root locatores for the species and TS

mechlib.filesys.rcts_cnf_fs(rct_infos, thy_info, run_prefix, save_prefix, hbond_cutoffs=None, nprocs=1)

set reactant filesystem stuff

Libs for handling calculating various pieces of a reaction channel

mechlib.reaction.split_unstable_full(pes_rlst, spc_rlst, spc_dct, spc_model_dct_i, save_prefix, nprocs=1)

Loop over the pes reaction list and break up the unstable species

mechlib.reaction.split_unstable_pes(rxn_lst, spc_dct, spc_model_dct_i, save_prefix, nprocs=1)

Build a new list of reactions for a given PES where all of the reactant and product species of the channels are assessed for instability and broken up.

Parameters:

• rxn_lst –

• spc_dct – species information dict[spc_name: spc_information]

• spc_mod_dct_i (dict[]) –

mechlib.reaction.reverse_ts_zmatrix(zrxn)

reverses a TS zma to be the other direction of reaction

mechlib.reaction.zmatrix_conversion_keys(gra_forw, gra_back)

returns the dictionary that transforms the forward graph into the backward graph

Libraries of functions that handle input-output for AutoMech

mechlib.amech_io.thermo_paths(spc_dct, spc_locs_dct, spc_mods, run_prefix, spc_grp_dct)

Set up the path for saving the pf input and output. Placed in a MESSPF, NASA dirs high in run filesys.

mechlib.amech_io.rate_paths(pes_dct, run_prefix)

Set up the path for saveing the input and output of MESSRATE calculations.

Creates paths for two different versions of mess

Run different types of directories (1 PES)

• fml-base: Standard base rate calculations (use idx)

• fml-wext: Well-Extended base calculations (use 10*idx)

mechlib.amech_io.output_path(dat, make_path=True, print_path=False, prefix=None)

Create the path for sub-directories locatted in the run directory where the MechDriver calculation was launched. These sub-directories are used to store various useful output from the MechDriver process.

Parameters:

• make_path (bool) – physically create directory for path during function

• print_path (bool) – print the created path to the screen

• prefix (str) – prefix for directory to be built

Return type:

str

mechlib.amech_io.job_path(prefix, prog, job, fml, locs_id=None, make_path=True, print_path=False)

Create the path for various types of calculations for a given species or PES.

Parameters:

• prefix (str) – root prefix to run/save filesyste,

• prog (str) – name of the program(s) called in the job

• fml – stoichiometry of the species/PES associate with job

• locs_id (int) – some identifier for leaf of the build filesys

• make_path (bool) – physically create directory for path during function

• print_path (bool) – print the created path to the screen

Fml type:

str

Return type:

str

Libraries of functions that parse the moldriver input files

mechlib.amech_io.parser.read_amech_input(job_path)

Reads all MechDriver input files provided by the user into strings. All whitespace and comment lines are stripped from the files.

Parameters:

job_path (str) – directory path where all input files exist

Return type:

dict[str:str]

Libraries of functions that handle input-output for AutoMech

mechlib.amech_io.printer.obj(key, prechar=None)

Print some standard object

mechlib.amech_io.printer.format_message(message, newline, indent)

Format a message string

mechlib.amech_io.printer.message(message_label, *args, newline=None, indent=None)

Print a general message to output.

mechlib.amech_io.printer.debug_message(message_label, *args, newline=None, indent=None, print_debug=True)

Print a debug message to output.

mechlib.amech_io.printer.info_message(message_label, *args, newline=None, indent=None)

Print an info message to output.

mechlib.amech_io.printer.error_message(message_label, *args, newline=None, indent=None)

Print an error message to output.

mechlib.amech_io.printer.warning_message(message_label, *args, newline=None, indent=None)

Print a warning message to output.

mechlib.amech_io.printer.runlst(run_inf, run_lst)

checks if run lst is a species lst

mechlib.amech_io.printer.program_header(driver)

print the header for a program

mechlib.amech_io.printer.program_exit(driver)

print the header for a program

mechlib.amech_io.printer.driver_tasks(run_es, write_messpf, run_messpf, run_nasa, write_messrate, run_messrate, run_fits, run_trans)

a

mechlib.amech_io.printer.random_cute_animal()

Print a picture of a fun, cute animal at random

mechlib.amech_io.printer.host_name()

print the host the calculation is running on

mechlib.amech_io.printer.energy(ene)

Print an energy value

mechlib.amech_io.printer.geometry(geom)

a

mechlib.amech_io.printer.gradient(grad)

a

mechlib.amech_io.printer.frequencies(freqs)

Print out the Harmonic frequencies and ZPVE

mechlib.amech_io.printer.molecular_properties(dmom, polar)

a

mechlib.amech_io.printer.constraint_dictionary(dct)

a

mechlib.amech_io.printer.existing_path(label, path)

a

mechlib.amech_io.printer.initial_geom_path(label, path)

a

mechlib.amech_io.printer.bad_conformer(reason)

a

mechlib.amech_io.printer.diverged_ts(param, ref_param, cnf_param)

a

mechlib.amech_io.printer.bad_equil_ts(cnf_dist, equi_bnd)

a

mechlib.amech_io.printer.save_conformer(cnf_save_path)

a

mechlib.amech_io.printer.save_conformer_energy(sp_save_path)

a

mechlib.amech_io.printer.save_symmetry(sym_save_path)

a

mechlib.amech_io.printer.already_running(task, path)

a

mechlib.amech_io.printer.save_reference(save_path)

a

mechlib.amech_io.printer.run_rotors(run_tors_names, const_names)

a

mechlib.amech_io.printer.save_irc(save_path)

a

mechlib.amech_io.printer.save_geo(save_path)

a

mechlib.amech_io.printer.save_energy(sp_save_path)

a

mechlib.amech_io.printer.save_anharmonicity(geo_save_path)

a

mechlib.amech_io.printer.save_frequencies(save_path)

a

mechlib.amech_io.printer.save_gradient(save_path)

a

mechlib.amech_io.printer.running(label=None, path=None, newline=False, indent=False)

Print a message that some task is running.

mechlib.amech_io.printer.results()

Print static results method.

mechlib.amech_io.printer.writing(label=None, path=None, newline=False, indent=False)

Print a message that some data is being written to a file.

mechlib.amech_io.printer.reading(label=None, path=None, newline=False, indent=False)

Print a message that a file is being read.

mechlib.amech_io.printer.saving(label=None, path=None, newline=False, indent=False)

Print a message that some data is being saved to a file.

mechlib.amech_io.printer.checking(label=None, path=None, newline=False, indent=False)

Print a message that a file/object is being checked..

mechlib.amech_io.printer.generating(label=None, path=None, newline=False, indent=False)

Print a message that a file/object is being generated.

mechlib.amech_io.printer.task_header(tsk, spc_name)

a

mechlib.amech_io.printer.task_footer()

a

mechlib.amech_io.printer.keyword_list(es_keyword_dct, thy_dct=None)

a

mechlib.amech_io.printer.output_task_header(tsk)

a

mechlib.amech_io.printer.output_keyword_list(es_keyword_dct, thy_dct=None)

a

mechlib.amech_io.printer.messpf(statement, path=None)

a

mechlib.amech_io.printer.nasa(statement, spc_name=None, path=None)

a

mechlib.amech_io.printer.pes(pes_idx, fml, sub_pes_idx)

a

mechlib.amech_io.printer.channel(chn_idx, reacs, prods)

a

mechlib.amech_io.printer.hrpotentials(tors_pots)

Check hr pot to see if a new mimnimum is needed

mechlib.amech_io.printer.lennard_jones_params(sigmas, epsilons)

Print Lennard-Jones parameters on individual lines.

Need to convert?

Parameters:

• sigmas (tuple(float)) – list of sigma values

• epsilons (tuple(float)) – list of epsilon values

mechlib.amech_io.printer.therm_paths_messpf_write_locations(spc_name, spc_locs_lst, spc_mods, thm_paths_dct)

prints out a table with the path that the messpf thermo input is written for each conformer and model

mechlib.amech_io.printer.therm_paths_messpf_run_locations(spc_name, spc_locs_lst, spc_mods, thm_paths_dct)

prints out a table with the path that the messpf thermo is calculated for each conformer and model

mechlib.amech_io.printer.print_thermo(spc_dct, ckin_nasa_str, spc_locs_dct, spc_locs_idx, spc_mod)

Generate and print thermo properties with the nasa polynomial string

mechlib.amech_io.printer.missing_input(prop)

Print a message saying that some required information is missing from an input file.

Libraries for writing output