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Commit b1acdfa1 authored by Mark Driver's avatar Mark Driver
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doc update.

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phasecalculator/io/phasecsvconverter.py
+ 32
− 32
View file @ b1acdfa1
...@@ -37,34 +37,34 @@ NAME_INCHIKEY_MAP = pureinf.get_name_inchikey_mapping() ...@@ -37,34 +37,34 @@ NAME_INCHIKEY_MAP = pureinf.get_name_inchikey_mapping()
INCHIKEY_SSIP_FILE_DICT = pureinf.get_ssip_file_dict() INCHIKEY_SSIP_FILE_DICT = pureinf.get_ssip_file_dict()
def convert_csv_file_to_phases(csv_filename): def convert_csv_file_to_phases(csv_filename):
""" """Read CSV file and convert contents to Phases.
Parameters Parameters
---------- ----------
csv_filename : TYPE csv_filename : str
DESCRIPTION. CSV filename.
Returns Returns
------- -------
TYPE Phases
DESCRIPTION. Phases object.
""" """
csv_file_contents = read_csv_file(csv_filename) csv_file_contents = read_csv_file(csv_filename)
return create_phases(csv_file_contents) return create_phases(csv_file_contents)
def read_csv_file(csv_filename): def read_csv_file(csv_filename):
""" """Read CSV file to list of rows.
Parameters Parameters
---------- ----------
csv_filename : TYPE csv_filename : str
DESCRIPTION. CSV filename.
Returns Returns
------- -------
list list
DESCRIPTION. list of rows.
""" """
with open(csv_filename, "r") as csv_file: with open(csv_filename, "r") as csv_file:
...@@ -72,17 +72,17 @@ def read_csv_file(csv_filename): ...@@ -72,17 +72,17 @@ def read_csv_file(csv_filename):
return [row for row in csv_reader] return [row for row in csv_reader]
def create_phases(csv_file_contents): def create_phases(csv_file_contents):
""" """Create Phases for csv file contents
Parameters Parameters
---------- ----------
csv_file_contents : TYPE csv_file_contents : list of lists
DESCRIPTION. List of CSV file lines.
Returns Returns
------- -------
TYPE Phases
DESCRIPTION. Phases object.
""" """
phase_list = [] phase_list = []
...@@ -93,18 +93,18 @@ def create_phases(csv_file_contents): ...@@ -93,18 +93,18 @@ def create_phases(csv_file_contents):
def create_phase(csv_file_line): def create_phase(csv_file_line):
""" """Create Phase from information list.
Parameters Parameters
---------- ----------
csv_file_line : TYPE csv_file_line : list of str
DESCRIPTION. line from CSV file.
Returns Returns
------- -------
TYPE Phase
DESCRIPTION. Phase object.
""" """
temperature = create_temperature(float(csv_file_line[0])) temperature = create_temperature(float(csv_file_line[0]))
...@@ -116,24 +116,24 @@ def create_phase(csv_file_line): ...@@ -116,24 +116,24 @@ def create_phase(csv_file_line):
return Phase(molecule_list, temperature) return Phase(molecule_list, temperature)
def create_molecule(name, molefraction): def create_molecule(name, molefraction):
""" """Create Molecule.
Parameters Parameters
---------- ----------
name : TYPE name : str
DESCRIPTION. Molecule name.
molefraction : TYPE molefraction : float
DESCRIPTION. mole fraction of molecule in phase.
Raises Raises
------ ------
keyerr keyerr
DESCRIPTION. Name does not match.
Returns Returns
------- -------
TYPE Molecule
DESCRIPTION. Molecule object.
""" """
try: try:
...@@ -145,17 +145,17 @@ def create_molecule(name, molefraction): ...@@ -145,17 +145,17 @@ def create_molecule(name, molefraction):
raise keyerr raise keyerr
def create_temperature(temperature_value): def create_temperature(temperature_value):
""" """Create Temperature.
Parameters Parameters
---------- ----------
temperature_value : TYPE temperature_value : float
DESCRIPTION. value in Kelvin.
Returns Returns
------- -------
TYPE Temperature
DESCRIPTION. Temperature object.
""" """
return Temperature(temperature_value, "KELVIN") return Temperature(temperature_value, "KELVIN")
\ No newline at end of file
phasecalculator/runners/phasexmlcreatorrunner.py
+ 76
− 59
View file @ b1acdfa1
...@@ -31,23 +31,28 @@ LOGGER.setLevel(logging.WARN) ...@@ -31,23 +31,28 @@ LOGGER.setLevel(logging.WARN)
def create_phase_and_solvent_files(system_info, filestem="system", **kwargs): def create_phase_and_solvent_files(system_info, filestem="system", **kwargs):
""" """Create solvent and phase files for given system.
Parameters Parameters
---------- ----------
system_info : TYPE system_info : System
DESCRIPTION. System object.
filestem : TYPE, optional filestem : str, optional
DESCRIPTION. The default is "system". filename stem. The default is "system".
**kwargs : TYPE solvent_info_filename : str, optional
DESCRIPTION. Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns Returns
------- -------
phase_file : TYPE phase_file : str
DESCRIPTION. Phase filename.
solvent_list : TYPE solvent_list : list of dict
DESCRIPTION. List of dictionaries containing solvent filename and temperature information.
""" """
create_scratch_dir(system_info) create_scratch_dir(system_info)
...@@ -60,21 +65,25 @@ def create_phase_and_solvent_files(system_info, filestem="system", **kwargs): ...@@ -60,21 +65,25 @@ def create_phase_and_solvent_files(system_info, filestem="system", **kwargs):
return phase_file, solvent_list return phase_file, solvent_list
def create_phase_file(system_info, filestem, **kwargs): def create_phase_file(system_info, filestem, **kwargs):
""" """Create phase file for input information.
Parameters Parameters
---------- ----------
system_info : TYPE system_info : System
DESCRIPTION. System object.
filestem : TYPE filestem : str
DESCRIPTION. filename stem.
**kwargs : TYPE solvent_info_filename : str, optional
DESCRIPTION. Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns Returns
------- -------
phase_filename : TYPE phase_filename : str
DESCRIPTION. phase filename.
""" """
phase_filename = create_phase_filename(system_info.runtime_information.scratch_dir, filestem) phase_filename = create_phase_filename(system_info.runtime_information.scratch_dir, filestem)
...@@ -83,21 +92,25 @@ def create_phase_file(system_info, filestem, **kwargs): ...@@ -83,21 +92,25 @@ def create_phase_file(system_info, filestem, **kwargs):
phasexmlcreate.create_phase_file(mole_fractions_by_temp_dict, phase_filename, ssip_filename_list=ssip_filename_list, **kwargs) phasexmlcreate.create_phase_file(mole_fractions_by_temp_dict, phase_filename, ssip_filename_list=ssip_filename_list, **kwargs)
return phase_filename return phase_filename
def create_solvent_files(system_info, filestem, **kwargs): def create_solvent_files(system_info, filestem, **kwargs):
""" """Create solvent files for input information.
Parameters Parameters
---------- ----------
system_info : TYPE system_info : System
DESCRIPTION. System object.
filestem : TYPE filestem : str
DESCRIPTION. filename stem.
**kwargs : TYPE solvent_info_filename : str, optional
DESCRIPTION. Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns Returns
------- -------
solvent_list : TYPE solvent_list : list of dict
DESCRIPTION. List of dictionaries containing solvent filename and temperature information.
""" """
mole_fractions_by_temp_dict = system_info.get_phase_compositions_by_temperature() mole_fractions_by_temp_dict = system_info.get_phase_compositions_by_temperature()
...@@ -113,27 +126,31 @@ def create_solvent_files(system_info, filestem, **kwargs): ...@@ -113,27 +126,31 @@ def create_solvent_files(system_info, filestem, **kwargs):
def create_solvent_file(mole_fraction_dict_list, ssip_filename_list, temp_info, filestem, scratch_dir, **kwargs): def create_solvent_file(mole_fraction_dict_list, ssip_filename_list, temp_info, filestem, scratch_dir, **kwargs):
""" """Create solvent file for input information.
Parameters Parameters
---------- ----------
mole_fraction_dict_list : TYPE mole_fraction_dict_list : list of dict
DESCRIPTION. Solvent compositions.
ssip_filename_list : TYPE ssip_filename_list : list of str
DESCRIPTION. SSIP filenames for molecules.
temp_info : TYPE temp_info : Temperature
DESCRIPTION. Temperature object.
filestem : TYPE filestem : str
DESCRIPTION. filename stem.
scratch_dir : TYPE scratch_dir : str
DESCRIPTION. scratch directory name.
**kwargs : TYPE solvent_info_filename : str, optional
DESCRIPTION. Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns Returns
------- -------
solvent_filename : TYPE solvent_filename : str
DESCRIPTION. filename path including scratch directory.
""" """
solvent_filename = create_solvent_filename(scratch_dir, temp_info, filestem) solvent_filename = create_solvent_filename(scratch_dir, temp_info, filestem)
...@@ -157,21 +174,21 @@ def create_scratch_dir(system_info): ...@@ -157,21 +174,21 @@ def create_scratch_dir(system_info):
scratch_path.mkdir(parents=True,exist_ok=True) scratch_path.mkdir(parents=True,exist_ok=True)
def create_solvent_filename(scratch_dir, temp_info, filestem): def create_solvent_filename(scratch_dir, temp_info, filestem):
""" """Create solvent filename.
Parameters Parameters
---------- ----------
scratch_dir : TYPE scratch_dir : str
DESCRIPTION. scratch directory name.
temp_info : TYPE temp_info : Temperature
DESCRIPTION. Temperature object.
filestem : TYPE filestem : str
DESCRIPTION. filename stem.
Returns Returns
------- -------
path : TYPE path : str
DESCRIPTION. filename path including scratch directory.
""" """
temp_string = create_temperaturestring(temp_info.temperature, temp_info.temperature_unit) temp_string = create_temperaturestring(temp_info.temperature, temp_info.temperature_unit)
...@@ -184,15 +201,15 @@ def create_phase_filename(scratch_dir, filestem): ...@@ -184,15 +201,15 @@ def create_phase_filename(scratch_dir, filestem):
Parameters Parameters
---------- ----------
scratch_dir : TYPE scratch_dir : str
DESCRIPTION. scratch directory name.
filestem : TYPE filestem : str
DESCRIPTION. filename stem.
Returns Returns
------- -------
path : TYPE path : str
DESCRIPTION. filename path including scratch directory.
""" """
filename = filestem + ".xml" filename = filestem + ".xml"
......
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