Bug: Q-Chem's TaskDoc.from_directory does not properly parse enthalpy or entropy (or frequency modes)
#930
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Andrew-S-Rosen
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TaskDoc.from_directory does not properly parse enthalpy or entropyTaskDoc.from_directory does not properly parse enthalpy or entropy (or frequency modes)
munrojm
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Feb 7, 2024
* 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
Andrew-S-Rosen
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Feb 7, 2024
Use Emmet's Qchem TaskDoc. Closes #956. Requires: materialsproject/emmet#929, materialsproject/emmet#930 --------- Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
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Problem
Q-Chem's
TaskDoc.from_directory()function does not properly parse the enthalpy or entropy from a standard frequency calculation. This is true for Q-Chem 6.0 (i.e. is unrelated to the 6.1.1 problems).The "frequency_modes" are also not reported --- it is unclear to me if that is the same root cause or not.
freq.zip
Proposed Solution
N/A
Alternatives
CC @rdguha1995
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