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Commit 60e3ce79 authored by Mark Driver's avatar Mark Driver
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update documentation.

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phasecalculator/runners/phasecalculatorrunner.py
+ 88
− 54
View file @ 60e3ce79
......@@ -34,8 +34,23 @@ LOGGER.setLevel(logging.WARN)
def run_all_analysis(system_info, **kwargs):
# TODO Logging output of analysis
"""Generate required solvent and phase XML then run all relevant analysis.
Parameters
----------
system_info : System
System information.
output_filename : str, optional
output file location for similarity matrix. The default is
"similaritymatrix.csv".
memory_req : str, optional
Memory settings for jar executable. The default is None.
Returns
-------
None.
"""
phase_filename, solvent_list = create_phase_and_solvent_xml_files(system_info, **kwargs)
if system_info.calc_vle():
run_vle_analysis(system_info, phase_filename, **kwargs)
......@@ -45,21 +60,26 @@ def run_all_analysis(system_info, **kwargs):
run_similarity_analysis(system_info, solvent_list, **kwargs)
def run_fgip_analysis(system_info, solvent_filename_dict_list, **kwargs):
"""
"""Run FGIP analysis.
Parameters
----------
system_info : TYPE
DESCRIPTION.
solvent_filename_dict_list : TYPE
DESCRIPTION.
**kwargs : TYPE
DESCRIPTION.
system_info : System
System information.
solvent_filename_dict_list : dict
dictionary of solvent filenames with temperature information.
output_filename : str, optional
output file location for similarity matrix. The default is
"similaritymatrix.csv".
memory_req : str, optional
Memory settings for jar executable. The default is None.
Returns
-------
None.
combined_results : list
combined results of FGIP generation.
combined_latex_blocks : str
combined latex blocks for figures.
"""
# TODO: for each solvent file/temp combo in dict
......@@ -81,16 +101,19 @@ def run_fgip_analysis(system_info, solvent_filename_dict_list, **kwargs):
combined_latex_blocks += latex_blocks
return combined_results, combined_latex_blocks
def run_similarity_analysis(system_info, solvent_filename_dict, **kwargs):
"""
"""Run similarity analysis.
Parameters
----------
system_info : TYPE
DESCRIPTION.
solvent_filename_dict : TYPE
DESCRIPTION.
**kwargs : TYPE
DESCRIPTION.
system_info : System
System information.
solvent_filename_dict : dict
dictionary of solvent filenames with temperature information.
output_filename : str, optional
output file location for similarity matrix. The default is
"similaritymatrix.csv".
memory_req : str, optional
Memory settings for jar executable. The default is None.
Returns
-------
......@@ -115,25 +138,30 @@ def run_similarity_analysis(system_info, solvent_filename_dict, **kwargs):
output_type = system_info.output_information.similarity_output_type
out_res, poly_filename_list = simrun.extract_all_solvents_and_generate_polynomials(solvent_filename_dict_list,
output_dir)
simrun.run_similarity_analysis(poly_filename_list, output_type, output_dir)
#
simrun.run_similarity_analysis(poly_filename_list, output_type, output_dir, **kwargs)
def run_vle_analysis(system_info, phase_filename, **kwargs):
"""
"""Run VLE phase calculation.
Parameters
----------
system_info : TYPE
DESCRIPTION.
phase_filename : TYPE
DESCRIPTION.
**kwargs : TYPE
DESCRIPTION.
system_info : System
System information.
phase_filename : str
Filename for phase XML.
memory_req : str, optional
Memory settings for jar executable. The default is None.
Raises
------
FileNotFoundError
If jar file is not found.
Returns
-------
TYPE
DESCRIPTION.
CompletedProcess
result of system call.
"""
jar_path = system_info.runtime_information.phasetransfer_jar
......@@ -158,32 +186,32 @@ def create_output_dir(system_info):
return output_path.as_posix()
def create_free_energy_output_filename(solvent_filename):
"""
"""Create free energy filename for solvent file.
Parameters
----------
solvent_filename : TYPE
DESCRIPTION.
solvent_filename : str
Input solvent filename.
Returns
-------
TYPE
DESCRIPTION.
str
Output energy filename.
"""
return solvent_filename.replace(".xml","free.xml")
def create_binding_energy_output_filename(solvent_filename):
"""
"""Create binding energy filename for solvent file.
Parameters
----------
solvent_filename : TYPE
DESCRIPTION.
solvent_filename : str
Input solvent filename.
Returns
-------
TYPE
DESCRIPTION.
str
Output energy filename.
"""
return solvent_filename.replace(".xml", "binding.xml")
......@@ -192,35 +220,41 @@ def create_phase_output_filename(phase_filename):
Parameters
----------
phase_filename : TYPE
DESCRIPTION.
phase_filename : str
Input phase filename.
Returns
-------
TYPE
DESCRIPTION.
str
phase output filename.
"""
return phase_filename.replace(".xml", "calculated.xml")
def create_phase_and_solvent_xml_files(system_info, **kwargs):
"""
"""Create solvent and phase files for given system.
Parameters
----------
system_info : TYPE
DESCRIPTION.
filestem : TYPE, optional
DESCRIPTION. The default is "system".
**kwargs : TYPE
DESCRIPTION.
system_info : System
System object.
filestem : str, optional
filename stem. The default is "system".
solvent_info_filename : str, optional
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
-------
phase_file : TYPE
DESCRIPTION.
solvent_list : TYPE
DESCRIPTION.
phase_file : str
Phase filename.
solvent_list : list of dict
List of dictionaries containing solvent filename and temperature information.
"""
return phasexmlrun.create_phase_and_solvent_files(system_info, **kwargs)
\ No newline at end of file
phasecalculator/runners/similarityanalysisrunner.py
+ 21
− 20
View file @ 60e3ce79
......@@ -32,18 +32,19 @@ LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
def run_similarity_analysis(poly_filename_list, output_type, output_dir, output_filename="similaritymatrix.csv"):
"""
"""Run similarity analysis.
Parameters
----------
poly_filename_list : TYPE
DESCRIPTION.
output_type : TYPE
DESCRIPTION.
output_dir : TYPE
DESCRIPTION.
output_filename : TYPE, optional
DESCRIPTION. The default is "similaritymatrix.csv".
poly_filename_list : list of str
list of polynomial filenames.
output_type : str
Output type. Three options: "all", "mixturecomparison" or "purecomparison".
output_dir : str
output directory for results.
output_filename : str, optional
output file location for similarity matrix. The default is
"similaritymatrix.csv".
Returns
-------
......@@ -59,21 +60,21 @@ def run_similarity_analysis(poly_filename_list, output_type, output_dir, output_
def extract_all_solvents_and_generate_polynomials(solv_energy_dict_list, directory_base):
"""
"""Extract results for all solvents, and partition results based on temperature.
Parameters
----------
solv_energy_dict_list : TYPE
DESCRIPTION.
directory_base : TYPE
DESCRIPTION.
solv_energy_dict_list : list of dicts
Solvation energy files .
directory_base : str
Base output directory.
Returns
-------
combined_out_res : TYPE
DESCRIPTION.
combined_filename_list : TYPE
DESCRIPTION.
combined_out_res : list
List of polynomial generation results.
combined_filename_list : list of str
Polynomial filename list.
"""
combined_out_res = []
......@@ -120,8 +121,8 @@ def extract_solvents_and_generate_polynomials(solvent_filename, energy_xml_filen
----------
solvent_filename : str
filename for solvent XML.
energy_xml_filename : TYPE
DESCRIPTION.
energy_xml_filename : str
energy XML filename.
directory : str
Directory to put files.
......
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