Increase output parsing#269
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avmarchenko merged 30 commits intoexa-analytics:mainfrom Jan 18, 2023
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… ALASKA/SLAPAF/MCKINLEY
Added hessian parsers to the standard output and formatted checkpoint files from Gaussian. Also, added a keyword for the atom parser as both the gradient and hessian matrix are printed from the input orientation as opposed to the standard orientation. Unit tests still need to be added.
Changed while loop terminating condition to an error when trying to convert a string to a float. This is necessary because initial tests had a different string terminating the hessian block. Added unit tests for the parser in the Output and Fchk classes.
Removed the frequency_ext dataframe and parser as it was going through the same parsing logic as the frequency parser. The data is now added to the frequency dataframe as new columns.
Added parsers for the electric dipole and quadrupole moment, and magnetic dipole moment. The electric dipole parser can read the data in the length or velocity formalism with a keyword. Also added a parser for all spectral properties including, rotatory and dipole strengths in the length and velocity formalisms. Added relevant unit tests.
avmarchenko
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Nov 13, 2022
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Thanks for this work. I think we can simplify parse_atom by making the kwarg accept values of atom ordering rather than be a boolean.
Changed atom table parsing input keyword to be a string. Will verify that the tables exist and warn the users if it is not available and default to the 'Input orientation'.
Added parsing for several spin-free and spin-orbit properties from RASSI in OpenMolcas. Added first set of tests.
Added python 3.9 and 3.10 to CI/CD matrix. Fixed a deprecation warning in editor.py file due to np.int.
Added comments and updated docstrings in the Molcas output parser. Increased code coverage for the new parser methods.
… molcas-parser
Fixed the parsing methods for the gradient and frequency parsing methods. Added unit tests for coverage of new methods.
Addressed comments and added clause to test for raising an exception when the value of orientation is not what is expected.
Added parsing methods for the SS/MS-PT2 energies from a Molcas calculation with the CASPT2 module. Also added parsing method for the orbital occupations calculated by RASSCF. Added unit tests with new files to account for changes and edge cases.
…into output-parsing
Added some print statements to make the user aware that the parsing methods have to use the input orientation of the atom table. Fixed a possible bug and minor changes.
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Jan 16, 2023
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Thank you for these changes.
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Ready to be merged |
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Here I want to increase the properties that we can parse with exatomic.
It is a WIP and will push updates when I complete parsers for a quantum chemistry code.
Added/Modified:
frequencydata frame with data from the oldfrequency_extdata frameRemoved:
frequency_extdata frame