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Input parsing cleaning and PhysConsts from QCelemental #404

Merged
merged 75 commits into from
Apr 27, 2022
Merged

Input parsing cleaning and PhysConsts from QCelemental #404

merged 75 commits into from
Apr 27, 2022

Commits on Mar 24, 2022

  1. Added predicate for ensuring positive spin multiplicities

    Anders Brakestad committed Mar 24, 2022
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  2. Moved the molecule validation out of the api file, to make the struct… 

    …ure cleaner.
    Anders Brakestad committed Mar 24, 2022
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  3. Simplified write_molecule function

    Anders Brakestad committed Mar 24, 2022
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  4. Removed method for writing to program syntax. might as well do this i… 

    …n api.py to keep the code consistent there
    Anders Brakestad committed Mar 24, 2022
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  5. Removed import of weird package that was sneaked in somehow

    Anders Brakestad committed Mar 24, 2022
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Commits on Mar 25, 2022

  1. Cleanup and doc

    Anders Brakestad committed Mar 25, 2022
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  2. Not use walrus operator to avoid having to change python version requ… 

    …irement.
    Anders Brakestad committed Mar 25, 2022
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  3. fix comment typo

    @Brakjen
    Brakjen authored Mar 25, 2022
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  4. Removed unnecessary todo

    Anders Brakestad committed Mar 25, 2022
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  5. Removed __init__ file in input parsing plumbing

    Anders Brakestad committed Mar 25, 2022
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  6. Cleaned up the imports, moved constants to separate file temporarily to

    Anders Brakestad committed Mar 25, 2022
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Commits on Mar 28, 2022

  1. Converted test input to json

    Anders Brakestad committed Mar 28, 2022
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  2. Removed duplicated cavity sphere in ref input and reran test. The tes… 

    …t now passes.
    Anders Brakestad committed Mar 28, 2022
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  3. Added short docstring

    Anders Brakestad committed Mar 28, 2022
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Commits on Mar 30, 2022

  1. Sketched the handling of physical constants to use qcelemental on the… 

    … python side.
    Anders Brakestad committed Mar 30, 2022
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Commits on Mar 31, 2022

  1. Write constants to program.json

    Anders Brakestad committed Mar 31, 2022
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  2. Singleton class providing access to the constants.

    Anders Brakestad committed Mar 31, 2022
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  3. clang format

    Anders Brakestad committed Mar 31, 2022
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  4. clang format

    Anders Brakestad committed Mar 31, 2022
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  5. clanga format

    Anders Brakestad committed Mar 31, 2022
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Commits on Apr 1, 2022

  1. Added default constants to constructor. will be accessed if no data h… 

    …as been set, so that unit tests can pass.
    Anders Brakestad committed Apr 1, 2022
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  2. Added qcelemental as python dep

    Anders Brakestad committed Apr 1, 2022
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Commits on Apr 4, 2022

  1. Now only a subset of the constants relevant for MRChem are added to t… 

    …he program input.
    Anders Brakestad committed Apr 4, 2022
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  2. Added qcelemental to let tests run via github actions pass.

    Anders Brakestad committed Apr 4, 2022
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  3. Fixed bug in the case of constants name. all constants passed to cpp … 

    …are lower_case
    Anders Brakestad committed Apr 4, 2022
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  4. Added qcelemental to make codecoverage pass

    Anders Brakestad committed Apr 4, 2022
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  5. Minor style fixes.

    Anders Brakestad committed Apr 4, 2022
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  6. Removed unused import.

    Anders Brakestad committed Apr 4, 2022
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  7. Comment docs

    Anders Brakestad committed Apr 4, 2022
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Commits on Apr 5, 2022

  1. Redesigned MRChemConstants. No longer inherits from qcelemental, but … 

    …instantiates a PhysicalConstantsContext in __init__. This cleans up the class namespace a bit.
    Anders Brakestad committed Apr 5, 2022
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  2. Fixed indendation

    Anders Brakestad committed Apr 5, 2022
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  3. Added qcelemental to dev packages

    Anders Brakestad committed Apr 5, 2022
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  4. Updated singleton design, and the calls for fetching constants.

    Anders Brakestad committed Apr 5, 2022
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  5. Updated call to MRChemConstants

    Anders Brakestad committed Apr 5, 2022
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Commits on Apr 6, 2022

  1. Fix symbols not found error during linking.

    Anders Brakestad committed Apr 6, 2022
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  2. Remove explicitly defined constants. will fix unit tests later

    Anders Brakestad committed Apr 6, 2022
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  3. clang format

    Anders Brakestad committed Apr 6, 2022
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  4. 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 Apr 6, 2022
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  5. Added description to CLI interface

    Anders Brakestad committed Apr 6, 2022
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  6. Update to match name for light speed constant

    Anders Brakestad committed Apr 6, 2022
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  7. Minor style changes

    Anders Brakestad committed Apr 6, 2022
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  8. Small bug fixes

    Anders Brakestad committed Apr 6, 2022
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  9. Now fetch constants from user_dict

    Anders Brakestad committed Apr 6, 2022
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  10. Added instructions for updating constants and the input parser with t… 

    …he new script.
    Anders Brakestad committed Apr 6, 2022
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  11. Updated template and input parser to allow the user to overwrite cons… 

    …tant defaults
    Anders Brakestad committed Apr 6, 2022
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  12. Updated README

    Anders Brakestad committed Apr 6, 2022
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  13. Added dryrun option to CLI

    Anders Brakestad committed Apr 6, 2022
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  14. Store constants explicitly in cpp to make unit tests pass.

    Anders Brakestad committed Apr 6, 2022
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  15. Remove qcelemental dependency from input parsing.

    Anders Brakestad committed Apr 6, 2022
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Commits on Apr 7, 2022

  1. Clarify instructions on updating the input parser

    @Brakjen
    Brakjen authored Apr 7, 2022
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  2. Updated the way constants are defined. Removed unused constants. Adde… 

    …d a try-catch clause when getting constants, to help debugging when using incorrect constant names. Added more detailed docstrings to the constants, indicating areas of the code affected by changing the default of a constant.
    Anders Brakestad committed Apr 7, 2022
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  3. Updated constant docstrings plus some minor cleanups

    Anders Brakestad committed Apr 7, 2022
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  4. Removed sqrt(pi) as a separate constant

    Anders Brakestad committed Apr 7, 2022
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  5. Removed light_speed keyword from ZORA input section. This is taken ca… 

    …re of in the new Constants input section
    Anders Brakestad committed Apr 7, 2022
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  6. Removed light_speed keyword from ZORA input section. This is taken ca… 

    …re of in the new Constants input section
    Anders Brakestad committed Apr 7, 2022
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  7. Added a print function to PhysicalConstants. Prints at printlevel 0.

    Anders Brakestad committed Apr 7, 2022
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  8. Bug fixes related to the light speed keyword being moved from ZORA to… 

    … Constants
    Anders Brakestad committed Apr 7, 2022
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  9. Removed pi from mrchem constants. Now mrcpp::pi is used for all calls… 

    … to pi.
    Anders Brakestad committed Apr 7, 2022
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Commits on Apr 8, 2022

  1. Added constants section to input schema

    Anders Brakestad committed Apr 8, 2022
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  2. Made constants being printed at printlevel 1 and above

    Anders Brakestad committed Apr 8, 2022
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Commits on Apr 11, 2022

  1. Added keyword to printer so that the user can choose when to print th… 

    …e constants. Also made the spacing adaptive to the constant names.
    Anders Brakestad committed Apr 11, 2022
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  2. Merge branch 'master' into molecule-class-cleanup-input-parser

    @Brakjen
    Brakjen authored Apr 11, 2022
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  3. Fix error from conflic resolution

    Anders Brakestad committed Apr 11, 2022
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Commits on Apr 12, 2022

  1. Merge branch 'master' into molecule-class-cleanup-input-parser

    @stigrj
    stigrj authored Apr 12, 2022
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Commits on Apr 21, 2022

  1. Minor cleanups

    Anders Brakestad committed Apr 21, 2022
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  2. Increased distance to colon to allow for printing longer strings

    Anders Brakestad committed Apr 21, 2022
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Commits on Apr 25, 2022

  1. Ensure the indentation scheme in the input template.

    Anders Brakestad committed Apr 25, 2022
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  2. Added json print helper method to print_utils. Use this to print phys… 

    …ical constants. Removed print precision option, now print constants exactly as given.
    Anders Brakestad committed Apr 25, 2022
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  3. Undo modification to print widths.

    Anders Brakestad committed Apr 25, 2022
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  4. Removed unused parameters.

    Anders Brakestad committed Apr 25, 2022
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  5. Added ruamel.yaml to dev packages

    Anders Brakestad committed Apr 25, 2022
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Commits on Apr 26, 2022

  1. Updated json printer to newest version.

    Anders Brakestad committed Apr 26, 2022
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Commits on Apr 27, 2022

  1. Fix colon shift

    Stig Rune Jensen committed Apr 27, 2022
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  2. Add cavity input section only when used

    Stig Rune Jensen committed Apr 27, 2022
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  3. Update input schema with cavity changes

    @stigrj
    stigrj committed Apr 27, 2022
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