Skip to content

Commit

Permalink
Resolving Issues #929 and #930 (#932)
Browse files Browse the repository at this point in the history 
* Adding qc_tasks and calculation.py

* big_commit for implementing the drone fucntionality of atomate(qchem) in emmet

* ran pre-commit locally and some minor changes

* writing_unit_tests_for_sp_and_opt

* ran pre-commit on test files

* corrected Union type error

* added numpy custom validators

* datetime import problem

* allowing arbitrary types

* further tests

* further tests

* change in io file convention

* checking qcinput

* checking qcinput

* Incorporating all the pydantic 2 changes

* changes in lot, task_type, calc_type

* removing circular dependency

* calc_doc issue

* Make more fields optional in accordance with pydantic 2

* Corrected the Input Doc problems

* CalcInput smx attribute issue

* correcting input to qcinput and qcoutput

* changes in the Optimization test doc for inputs

* molecule -> initial_molecule

* changes to the sp valid task_schema

* test_output breakdowns

* test_output breakdowns OutputDoc

* test_output breakdowns OutputDoc

* test_output breakdowns OutputDoc

* test_output breakdowns OutputDoc

* test_output breakdowns OutputDoc

* test_output breakdowns OutputDoc

* Changes to the TaskDoc

* Changes to the TaskDoc np.array

* Changes to the conftest

* Changes to the conftest arrays

* Changes to the conftest arrays

* Changes to test code

* Changes to test code

* Changes to test code

* Changes to test code

* Changes to test code

* Changes to test code

* Changes to test code

* Changes to test code

* Changes to test code

* Changes to test code

* fixing bug where solvent field was being accessed as a dict

* forgot pre-commit

* Changed the default args for initial_molecule and optimized_molecule to be Molecule not dict

* deleted the superfluous FW files

* making the TaskDoc.from_directory functionality for generalized to handle qchem calculaion directories not generated through atomate

* resolved the bugs with enthalpy, entropy and parsing frequencies
  • Loading branch information
@rdguha1995
rdguha1995 authored Feb 7, 2024
1 parent c54c6a9 commit 17b48ab
Show file tree
Hide file tree
Showing 2 changed files with 52 additions and 18 deletions.
24 changes: 17 additions & 7 deletions emmet-core/emmet/core/qc_tasks.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -76,9 +76,14 @@ class OutputDoc(BaseModel):
None, description="Natural Bonding Orbital (NBO) output"
)

frequencies: Optional[Union[Dict[str, Any], List]] = Field(
None,
description="The list of calculated frequencies if job type is freq (units: cm^-1)",
)

frequency_modes: Optional[Union[List, str]] = Field(
None,
description="The list of calculated frequency mode vectors if job type is freq (units: cm^-1)",
description="The list of calculated frequency mode vectors if job type is freq",
)

@classmethod
Expand Down Expand Up @@ -112,6 +117,7 @@ def from_qchem_calc_doc(cls, calc_doc: Calculation) -> "OutputDoc":
resp=calc_doc.output.resp,
nbo=calc_doc.output.nbo_data,
frequencies=calc_doc.output.frequencies,
frequency_modes=calc_doc.output.frequency_modes,
)


Expand Down Expand Up @@ -588,7 +594,9 @@ def _find_qchem_files(
)
in_task_name = in_task_name or "mol.qin"
if in_task_name == "orig":
task_files[in_task_name] = {"orig_input_file": file}
task_files[in_task_name] = {"orig_input_file": file.name}
elif in_task_name == "last":
continue
elif in_task_name == "mol.qin" or in_task_name == "mol.in":
if in_task_name == "mol.qin":
out_file = (
Expand All @@ -603,19 +611,21 @@ def _find_qchem_files(
else path / "mol.out"
)
task_files["standard"] = {
"qcinput_file": file,
"qcoutput_file": out_file,
"qcinput_file": file.name,
"qcoutput_file": out_file.name,
}
# This block will exist only if calcs were run through atomate
else:
try:
task_files[in_task_name] = {
"qcinput_file": file,
"qcoutput_file": Path("mol.qout." + in_task_name + ".gz"),
"qcinput_file": file.name,
"qcoutput_file": Path(
"mol.qout." + in_task_name + ".gz"
).name,
}
except FileNotFoundError:
task_files[in_task_name] = {
"qcinput_file": file,
"qcinput_file": file.name,
"qcoutput_file": "No qout files exist for this in file",
}

Expand Down
46 changes: 35 additions & 11 deletions emmet-core/emmet/core/qchem/calculation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -274,8 +274,8 @@ def from_qcoutput(cls, qcoutput: QCOutput) -> "CalculationOutput":
frequencies=qcoutput.data.get("frequencies", {}),
frequency_modes=qcoutput.data.get("frequency_mode_vectors", []),
final_energy=qcoutput.data.get("final_energy", None),
enthalpy=qcoutput.data.get("enthalpy", None),
entropy=qcoutput.data.get("entropy", None),
enthalpy=qcoutput.data.get("total_enthalpy", None),
entropy=qcoutput.data.get("total_entropy", None),
scan_energies=qcoutput.data.get("scan_energies", {}),
scan_geometries=qcoutput.data.get("optimized_geometries", {}),
scan_molecules=qcoutput.data.get("molecules_from_optimized_geometries", {}),
Expand Down Expand Up @@ -448,29 +448,53 @@ def _find_qchem_files(
path = Path(path)
task_files = OrderedDict()

in_file_pattern = re.compile(r"^(?P<in_task_name>mol\.qin(?:\..+)?)\.gz$")
in_file_pattern = re.compile(r"^(?P<in_task_name>mol\.(qin|in)(?:\..+)?)(\.gz)?$")

for file in path.iterdir():
if file.is_file():
in_match = in_file_pattern.match(file.name)

# This block is for generalizing outputs coming from both atomate and manual qchem calculations
if in_match:
in_task_name = in_match.group("in_task_name").replace("mol.qin.", "")
in_task_name = re.sub(
r"(\.gz|gz)$",
"",
in_match.group("in_task_name").replace("mol.qin.", ""),
)
in_task_name = in_task_name or "mol.qin"
if in_task_name == "orig":
task_files[in_task_name] = {"orig_input_file": file}
elif in_task_name == "mol.qin":
task_files[in_task_name] = {"orig_input_file": file.name}
elif in_task_name == "last":
continue
elif in_task_name == "mol.qin" or in_task_name == "mol.in":
if in_task_name == "mol.qin":
out_file = (
path / "mol.qout.gz"
if (path / "mol.qout.gz").exists()
else path / "mol.qout"
)
else:
out_file = (
path / "mol.out.gz"
if (path / "mol.out.gz").exists()
else path / "mol.out"
)
task_files["standard"] = {
"qcinput_file": file,
"qcoutput_file": Path("mol.qout.gz"),
"qcinput_file": file.name,
"qcoutput_file": out_file.name,
}
# This block will exist only if calcs were run through atomate
else:
try:
task_files[in_task_name] = {
"qcinput_file": file,
"qcoutput_file": Path("mol.qout." + in_task_name + ".gz"),
"qcinput_file": file.name,
"qcoutput_file": Path(
"mol.qout." + in_task_name + ".gz"
).name,
}
except FileNotFoundError:
task_files[in_task_name] = {
"qcinput_file": file,
"qcinput_file": file.name,
"qcoutput_file": "No qout files exist for this in file",
}

Expand Down

0 comments on commit 17b48ab

Please sign in to comment.