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Improved documentation
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@kmlefran
kmlefran committed Sep 13, 2023
1 parent a5432d9 commit 9f81ebf
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Showing 3 changed files with 44 additions and 42 deletions.
36 changes: 11 additions & 25 deletions aiida_aimall/calculations.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
"""
Calculations provided by aiida_aimall.
Register calculations via the "aiida.calculations" entry point in setup.json.
Upon pip install, AimqbCalculation is accessible in AiiDA.calculations plugins
Using the 'aimall' entry point
"""
from aiida.common import datastructures
from aiida.engine import CalcJob
Expand Down Expand Up @@ -33,7 +34,7 @@ def define(cls, spec):
"num_machines": 1,
"tot_num_mpiprocs": 2,
}
# commented out parser to see default folder structure

spec.inputs["metadata"]["options"]["parser_name"].default = "aimqb.base"
# new ports
# spec.input(
Expand All @@ -45,35 +46,19 @@ def define(cls, spec):
help="Command line parameters for aimqb",
)
spec.input(
"file", valid_type=SinglefileData, help="fchk, wfn, or wfx to run AimQB on"
"file",
valid_type=SinglefileData,
help="fchk, wfn, or wfx to run AimQB on",
)
# commented these to see

spec.output(
"output_parameters",
valid_type=Dict,
required=True,
help="The computed parameters of an AIMAll calculation",
)
# spec.output(
# "atomic_properties",
# valid_type=Dict,
# required=True,
# help="The result parameters of the calculation",
# )
# spec.output(
# "bcp_properties",
# valid_type=Dict,
# required=True,
# help="The properties of all BCPs in the molecule",
# )
# spec.output(
# "cc_properties",
# valid_type=Dict,
# required=False,
# help="The properties of VSCC in the molecule",
# )

# spec.default_output_node = "output_parameters"
spec.default_output_node = "output_parameters"
spec.outputs.dynamic = True

# would put error codes here
Expand All @@ -87,13 +72,14 @@ def prepare_for_submission(self, folder):
place all files needed by the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
# copy wfx file to input file
input_string = self.inputs.file.get_content()
with open(
folder.get_abs_path(self.INPUT_FILE), "w", encoding="utf-8"
) as out_file:
out_file.write(input_string)
codeinfo = datastructures.CodeInfo()
# probably modify the next line
# generate command line params
codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(
file_name=self.INPUT_FILE
)
Expand All @@ -103,7 +89,7 @@ def prepare_for_submission(self, folder):
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo] # list since can involve more than one

# Retrieve the sum file and the folder with atomic files
calcinfo.retrieve_list = [
self.OUTPUT_FILE.replace("out", "sum"),
self.OUTPUT_FILE.replace(".out", "_atomicfiles"),
Expand Down
27 changes: 15 additions & 12 deletions aiida_aimall/data/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
"""
Data types provided by plugin
Register data types via the "aiida.data" entry point in setup.json.
Upon pip install, AimqbParameters is accessible in AiiDA.data plugins
Using the 'aimall' entry point
"""
# You can directly use or subclass aiida.orm.data.Data
# or any other data type listed under 'verdi data'

from voluptuous import Optional, Schema

from aiida.orm import Dict

# AIMQB's command line options
# AIMQB's command line options and their expected type
cmdline_options = {
Optional("bim"): str,
Optional("iasmesh"): str,
Expand Down Expand Up @@ -51,14 +51,16 @@ class AimqbParameters(Dict): # pylint: disable=too-many-ancestors
This class represents a python dictionary used to
pass command line options to the executable.
The class takes a dictionary of parameters and validates
to ensure the aimqb command line parameters are correct
"""

schema = Schema(cmdline_options)

def __init__(self, parameter_dict=None, **kwargs):
"""Constructor for the data class
Usage: ``AimqbParameters(dict{'ignore-case': True})``
Usage: ``AimqbParameters(parameter_dict{'ignore-case': True})``
:param parameters_dict: dictionary with commandline parameters
:param type parameters_dict: dict
Expand All @@ -85,17 +87,18 @@ def cmdline_params(self, file_name):
e.g. [ '-atlaprhocps=True',...,'-nogui', 'filename']
:param file_name: Name of first file
:param file_name: Name of wfx/fchk/wfn file
:param type file_name: str
"""
parameters = []
# parameters = []

pm_dict = self.get_dict()
for key, value in pm_dict.items():
parameters += [f"-{key}={value}"]
parameters += ["-nogui"]
parameters += [file_name]
parameters = [f"-{key}={value}" for key, value in pm_dict.items()]
# for key, value in pm_dict.items():
# parameters += [f"-{key}={value}"]
parameters += ["-nogui"] # use no gui when running in aiida
parameters += [file_name] # input file

return [str(p) for p in parameters]

Expand All @@ -105,7 +108,7 @@ def __str__(self):
Append values of dictionary to usual representation. E.g.::
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}
{'atlaprhocps': True}
"""
string = super().__str__()
Expand Down
23 changes: 18 additions & 5 deletions aiida_aimall/parsers.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,15 +52,14 @@ def parse(self, **kwargs):
output_filename.replace(".out", "_atomicfiles"),
]
# Note: set(A) <= set(B) checks whether A is a subset of B

if not set(files_expected) <= set(files_retrieved):
self.logger.error(
f"Found files '{files_retrieved}', expected to find '{files_expected}'"
)
# return self.exit_codes.ERROR_MISSING_OUTPUT_FILES
return

# add output file
# parse output file
self.logger.info(f"Parsing '{output_filename}'")
OutFolderData = self.retrieved
with OutFolderData.open(output_filename.replace("out", "sum"), "rb") as handle:
Expand All @@ -70,20 +69,24 @@ def parse(self, **kwargs):
"atomic_properties": self._parse_atomic_props(sum_lines),
"bcp_properties": self._parse_bcp_props(sum_lines),
}
# if laprhocps were calculated, get cc_properties
if "-atlaprhocps=True" in input_parameters.cmdline_params("foo"):
out_dict["cc_properties"] = self._parse_cc_props(
out_dict["atomic_properties"]
)
# self.outputs.atomic_properties = self._parse_atomic_props(sum_lines)
# self.outputs.bcp_properties = self._parse_bcp_props(sum_lines)
# store in node
self.outputs.output_parameters = Dict(out_dict)
# self.outputs.output_parameters.cc_properties = self._parse_cc_props()

return # ExitCode(0)

def _parse_cc_props(self, atomic_properties):
"""Extract VSCC properties from output files
:param atomic_properties: dictionary of atomic properties from _parse_atomic_props
:param type atomic_properties: dict
"""
output_filename = self.node.process_class.OUTPUT_FILE
atom_list = list(atomic_properties.keys())
# for each atom, load the .agpviz file in the _atomicfiles folder and get cc props
cc_dict = {
x: qt.get_atom_vscc(
filename=self.retrieved.get_object_content(
Expand All @@ -102,8 +105,18 @@ def _parse_cc_props(self, atomic_properties):
return cc_dict

def _parse_atomic_props(self, sum_file_string):
"""Extracts atomic properties from .sum file
:param sum_file_string: lines of .sum output file
:param type sum_file_string: str
"""
return qt.get_atomic_props(sum_file_string.split("\n"))

def _parse_bcp_props(self, sum_file_string):
"""Extracts bcp properties from .sum file
:param sum_file_string: lines of .sum output file
:param type sum_file_string: str
"""
bcp_list = qt.find_all_connections(sum_file_string.split("\n"))
return qt.get_selected_bcps(sum_file_string.split("\n"), bcp_list)

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