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Conceptual Dictionary: Make internal functions private #25

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76 changes: 38 additions & 38 deletions pyiron_rdm/concept_dict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@

def process_general_job(job):
method_dict = {}
add_simulation_software(job, method_dict)
get_simulation_folder(job, method_dict)
_add_simulation_software(job, method_dict)
_get_simulation_folder(job, method_dict)
file_name = job.path + "_concept_dict.json"
with open(file_name, "w") as f:
json.dump(method_dict, f, indent=2)
Expand All @@ -33,12 +33,12 @@ def process_general_job(job):

def process_lammps_job(job):
method_dict = {}
add_lammps_contexts(method_dict)
_add_lammps_contexts(method_dict)
# get_structures(job, method_dict)
identify_lammps_method(job, method_dict)
extract_lammps_calculated_quantities(job, method_dict)
add_simulation_software(job, method_dict)
get_simulation_folder(job, method_dict)
_identify_lammps_method(job, method_dict)
_extract_lammps_calculated_quantities(job, method_dict)
_add_simulation_software(job, method_dict)
_get_simulation_folder(job, method_dict)
file_name = job.path + "_concept_dict.json"
with open(file_name, "w") as f:
json.dump(method_dict, f, indent=2)
Expand All @@ -54,11 +54,11 @@ def process_structure_crystal(
options=None,
):
sample_dict = {}
add_structure_contexts(sample_dict)
get_chemical_species(structure, sample_dict)
identify_structure_parameters(structure_parameters, sample_dict)
get_simulation_cell(structure, sample_dict)
add_structure_software(pr, structure_name, sample_dict)
_add_structure_contexts(sample_dict)
_get_chemical_species(structure, sample_dict)
_identify_structure_parameters(structure_parameters, sample_dict)
_get_simulation_cell(structure, sample_dict)
_add_structure_software(pr, structure_name, sample_dict)
sample_dict["path"] = structure_path
if options.get("defects"):
sample_dict["defects"] = options["defects"]
Expand All @@ -72,11 +72,11 @@ def process_structure_crystal(

def process_murnaghan_job(job):
method_dict = {}
add_murnaghan_contexts(method_dict)
identify_murnaghan_method(job, method_dict)
extract_murnaghan_calculated_quantities(job, method_dict)
add_simulation_software(job, method_dict)
get_simulation_folder(job, method_dict)
_add_murnaghan_contexts(method_dict)
_identify_murnaghan_method(job, method_dict)
_extract_murnaghan_calculated_quantities(job, method_dict)
_add_simulation_software(job, method_dict)
_get_simulation_folder(job, method_dict)
file_name = job.path + "_concept_dict.json"
with open(file_name, "w") as f:
json.dump(method_dict, f, indent=2)
Expand All @@ -85,18 +85,18 @@ def process_murnaghan_job(job):

def process_vasp_job(job):
method_dict = {}
add_vasp_contexts(method_dict)
identify_vasp_method(job, method_dict)
extract_vasp_calculated_quantities(job, method_dict)
add_simulation_software(job, method_dict)
get_simulation_folder(job, method_dict)
_add_vasp_contexts(method_dict)
_identify_vasp_method(job, method_dict)
_extract_vasp_calculated_quantities(job, method_dict)
_add_simulation_software(job, method_dict)
_get_simulation_folder(job, method_dict)
file_name = job.path + "_concept_dict.json"
with open(file_name, "w") as f:
json.dump(method_dict, f, indent=2)
return method_dict


def add_lammps_contexts(method_dict):
def _add_lammps_contexts(method_dict):
method_dict["@context"] = {}
method_dict["@context"][
"sample"
Expand Down Expand Up @@ -203,7 +203,7 @@ def get_structures(job, method_dict):
}


def identify_lammps_method(job, method_dict):
def _identify_lammps_method(job, method_dict):
job_dict = job.input.to_dict()
input_dict = {
job_dict["control_inp/data_dict"]["Parameter"][x]: job_dict[
Expand Down Expand Up @@ -407,7 +407,7 @@ def identify_lammps_method(job, method_dict):
method_dict[md_method]["potential"]["url"] = url


def extract_lammps_calculated_quantities(job, method_dict):
def _extract_lammps_calculated_quantities(job, method_dict):
"""
Extracts calculated quantities from a job.

Expand Down Expand Up @@ -514,7 +514,7 @@ def extract_lammps_calculated_quantities(job, method_dict):
method_dict["outputs"] = outputs


def add_simulation_software(job, method_dict):
def _add_simulation_software(job, method_dict):
method_dict["workflow_manager"] = {}
import platform
import subprocess
Expand Down Expand Up @@ -692,11 +692,11 @@ def add_simulation_software(job, method_dict):
method_dict["job_details"] = pyiron_job_details


def get_simulation_folder(job, method_dict):
def _get_simulation_folder(job, method_dict):
method_dict["path"] = job.path


def add_murnaghan_contexts(method_dict):
def _add_murnaghan_contexts(method_dict):
method_dict["@context"] = {}
method_dict["@context"][
"sample"
Expand Down Expand Up @@ -741,7 +741,7 @@ def add_murnaghan_contexts(method_dict):
] = "http://purls.helmholtz-metadaten.de/asmo/Volume"


def identify_murnaghan_method(job, method_dict):
def _identify_murnaghan_method(job, method_dict):

if job.input["fit_type"] == "birchmurnaghan":
method_dict["equation_of_state_fit"] = (
Expand Down Expand Up @@ -794,7 +794,7 @@ def identify_murnaghan_method(job, method_dict):
method_dict["inputs"] = inputs


def extract_murnaghan_calculated_quantities(job, method_dict):
def _extract_murnaghan_calculated_quantities(job, method_dict):
outputs = []
outputs.append(
{
Expand Down Expand Up @@ -909,7 +909,7 @@ def get_unit_cell_parameters(structure):
return structure_parameters


def add_structure_contexts(sample_dict):
def _add_structure_contexts(sample_dict):
sample_dict["@context"] = {}
sample_dict["@context"]["path"] = "http://purls.helmholtz-metadaten.de/cmso/hasPath"
sample_dict["@context"][
Expand Down Expand Up @@ -976,7 +976,7 @@ def add_structure_contexts(sample_dict):
] = "http://purls.helmholtz-metadaten.de/cmso/hasAngle"


def identify_structure_parameters(structure_parameters, sample_dict):
def _identify_structure_parameters(structure_parameters, sample_dict):
if not structure_parameters:
return
else:
Expand Down Expand Up @@ -1052,7 +1052,7 @@ def identify_structure_parameters(structure_parameters, sample_dict):
sample_dict["unit_cell"] = unit_cell_details


def get_chemical_species(structure, sample_dict):
def _get_chemical_species(structure, sample_dict):
structure = structure
natoms = structure.get_number_of_atoms()
species_dict = dict(structure.get_number_species_atoms())
Expand All @@ -1068,7 +1068,7 @@ def get_chemical_species(structure, sample_dict):
sample_dict["atoms"] = atoms_list


def get_simulation_cell(structure, sample_dict):
def _get_simulation_cell(structure, sample_dict):
structure = structure
cell_lengths = str(
[
Expand Down Expand Up @@ -1123,7 +1123,7 @@ def get_simulation_cell(structure, sample_dict):
sample_dict["simulation_cell"] = simulation_cell_details


def add_structure_software(pr, structure_name, sample_dict):
def _add_structure_software(pr, structure_name, sample_dict):
sample_dict["workflow_manager"] = {}
import platform
import subprocess
Expand Down Expand Up @@ -1227,7 +1227,7 @@ def add_structure_software(pr, structure_name, sample_dict):
sample_dict["job_details"] = pyiron_job_details


def add_vasp_contexts(method_dict):
def _add_vasp_contexts(method_dict):
# TODO: check, expand on
method_dict["@context"] = {}
method_dict["@context"][
Expand Down Expand Up @@ -1318,7 +1318,7 @@ def add_vasp_contexts(method_dict):
] = "http://purls.helmholtz-metadaten.de/asmo/NumberOfIonicSteps"


def identify_vasp_method(job, method_dict):
def _identify_vasp_method(job, method_dict):
# copy-pasted from pyiron-conceptual-dictionary
indf = job.input.incar.to_dict()
params = indf["data_dict"]["Parameter"]
Expand Down Expand Up @@ -1453,7 +1453,7 @@ def identify_vasp_method(job, method_dict):
method_dict["xc_functional"] = xc


def extract_vasp_calculated_quantities(job, method_dict):
def _extract_vasp_calculated_quantities(job, method_dict):
"""
Extracts calculated quantities from a job.

Expand Down
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