Input parsing cleaning and PhysConsts from QCelemental#404

Merged

stigrj merged 75 commits intoMRChemSoft:masterfrom Brakjen:molecule-class-cleanup-input-parser

Apr 27, 2022

+1,396-458

Commits on Mar 24, 2022

Added predicate for ensuring positive spin multiplicities
Anders Brakestad
committed
Moved the molecule validation out of the api file, to make the structure cleaner.
Anders Brakestad
committed
Simplified write_molecule function
Anders Brakestad
committed
Removed method for writing to program syntax. might as well do this in api.py to keep the code consistent there
Anders Brakestad
committed
Removed import of weird package that was sneaked in somehow
Anders Brakestad
committed

Commits on Mar 25, 2022

Cleanup and doc
Anders Brakestad
committed
Not use walrus operator to avoid having to change python version requirement.
Anders Brakestad
committed
fix comment typo
Brakjen
authored
Removed unnecessary todo
Anders Brakestad
committed
Removed __init__ file in input parsing plumbing
Anders Brakestad
committed
Cleaned up the imports, moved constants to separate file temporarily to
Anders Brakestad
committed

Commits on Mar 28, 2022

Converted test input to json
Anders Brakestad
committed
Removed duplicated cavity sphere in ref input and reran test. The test now passes.
Anders Brakestad
committed
Added short docstring
Anders Brakestad
committed

Commits on Mar 30, 2022

Sketched the handling of physical constants to use qcelemental on the python side.
Anders Brakestad
committed

Commits on Mar 31, 2022

Write constants to program.json
Anders Brakestad
committed
Singleton class providing access to the constants.
Anders Brakestad
committed
clang format
Anders Brakestad
committed
clang format
Anders Brakestad
committed
clanga format
Anders Brakestad
committed

Commits on Apr 1, 2022

Added default constants to constructor. will be accessed if no data has been set, so that unit tests can pass.
Anders Brakestad
committed
Added qcelemental as python dep
Anders Brakestad
committed

Commits on Apr 4, 2022

Now only a subset of the constants relevant for MRChem are added to the program input.
Anders Brakestad
committed
Added qcelemental to let tests run via github actions pass.
Anders Brakestad
committed
Fixed bug in the case of constants name. all constants passed to cpp are lower_case
Anders Brakestad
committed
Added qcelemental to make codecoverage pass
Anders Brakestad
committed
Minor style fixes.
Anders Brakestad
committed
Removed unused import.
Anders Brakestad
committed
Comment docs
Anders Brakestad
committed

Commits on Apr 5, 2022

Redesigned MRChemConstants. No longer inherits from qcelemental, but instantiates a PhysicalConstantsContext in __init__. This cleans up the class namespace a bit.
Anders Brakestad
committed
Fixed indendation
Anders Brakestad
committed
Added qcelemental to dev packages
Anders Brakestad
committed
Updated singleton design, and the calls for fetching constants.
Anders Brakestad
committed
Updated call to MRChemConstants
Anders Brakestad
committed

Commits on Apr 6, 2022

Fix symbols not found error during linking.
Anders Brakestad
committed
Remove explicitly defined constants. will fix unit tests later
Anders Brakestad
committed
clang format
Anders Brakestad
committed
Script that can update the constants section in template.yml, execute parselglossy to update the input parser, and copy the new user ref to doc/users/
Anders Brakestad
committed
Added description to CLI interface
Anders Brakestad
committed
Update to match name for light speed constant
Anders Brakestad
committed
Minor style changes
Anders Brakestad
committed
Small bug fixes
Anders Brakestad
committed
Now fetch constants from user_dict
Anders Brakestad
committed
Added instructions for updating constants and the input parser with the new script.
Anders Brakestad
committed
Updated template and input parser to allow the user to overwrite constant defaults
Anders Brakestad
committed
Updated README
Anders Brakestad
committed
Added dryrun option to CLI
Anders Brakestad
committed
Store constants explicitly in cpp to make unit tests pass.
Anders Brakestad
committed
Remove qcelemental dependency from input parsing.
Anders Brakestad
committed

Commits on Apr 7, 2022

Clarify instructions on updating the input parser
Brakjen
authored
Updated the way constants are defined. Removed unused constants. Added a try-catch clause when getting constants, to help debugging when using incorrect constant names. Added more detailed docstrin…
Anders Brakestad
committed
Updated constant docstrings plus some minor cleanups
Anders Brakestad
committed
Removed sqrt(pi) as a separate constant
Anders Brakestad
committed
Removed light_speed keyword from ZORA input section. This is taken care of in the new Constants input section
Anders Brakestad
committed
Removed light_speed keyword from ZORA input section. This is taken care of in the new Constants input section
Anders Brakestad
committed
Added a print function to PhysicalConstants. Prints at printlevel 0.
Anders Brakestad
committed
Bug fixes related to the light speed keyword being moved from ZORA to Constants
Anders Brakestad
committed
Removed pi from mrchem constants. Now mrcpp::pi is used for all calls to pi.
Anders Brakestad
committed

Commits on Apr 8, 2022

Added constants section to input schema
Anders Brakestad
committed
Made constants being printed at printlevel 1 and above
Anders Brakestad
committed

Commits on Apr 11, 2022

Commits on Apr 12, 2022

Merge branch 'master' into molecule-class-cleanup-input-parser
stigrj
authored

Commits on Apr 21, 2022

Minor cleanups
Anders Brakestad
committed
Increased distance to colon to allow for printing longer strings
Anders Brakestad
committed

Commits on Apr 25, 2022

Ensure the indentation scheme in the input template.
Anders Brakestad
committed
Added json print helper method to print_utils. Use this to print physical constants. Removed print precision option, now print constants exactly as given.
Anders Brakestad
committed
Undo modification to print widths.
Anders Brakestad
committed
Removed unused parameters.
Anders Brakestad
committed
Added ruamel.yaml to dev packages
Anders Brakestad
committed

Commits on Apr 26, 2022

Updated json printer to newest version.
Anders Brakestad
committed

Commits on Apr 27, 2022

Fix colon shift
Stig Rune Jensen
committed
Add cavity input section only when used
Stig Rune Jensen
committed
Update input schema with cavity changes
stigrj
committed