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Orca Harness. #178

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Orca Harness. #178

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Commits on Nov 22, 2019

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Commits on Dec 3, 2019

  1. Merge branch 'master' into orca

    * master: (61 commits)
      Config: Changes new programs from job to task config
      Config: JobConfig -> TaskConfig
      Config: Adds nodes to config
      entos: Black reformat of entos.py and added @using_entos mark
      PR comments
      PR comments: TYPE_CHECKING, formatting, reduce redundant code
      entos: Added entos_policy to the input file
      entos: Updated commit for qcengine_records_commit
      hessparse and compute: Forgotten imports
      entos: Begun adding support for xtb in the entos Harness
      entos: Removed soon to be deprecated option
      entos: Added entos to the test_standard_suite_hf and did some minor cleanup in the entos Harness
      entos: Starting to add HF command to entos
      Fixed typo in error name
      Multiple changes based on review
      Gamess: replace print statements with logging
      Entos: add hessian and xtb support
      Parse named properties out of NWChem output
      Get more of the relevant fields from output
      Removed unncessary "pass" statement
      ...
    muammar committed Dec 3, 2019
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Commits on Dec 4, 2019

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Commits on Dec 5, 2019

  1. General improvements.

    - Total energy is returned when using DFT.
    - `commands` now contains the full PATH to the orca binary. That is
       important to run the binary in paralell mode.
    - Removal/commenting of unused stuff.
    muammar committed Dec 5, 2019
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  3. Removed commented files.

    muammar committed Dec 5, 2019
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Commits on Dec 9, 2019

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  3. Merge remote-tracking branch 'upstream/master' into orca

    * upstream/master:
      Qchem: SCF-> Total energy in the final basis set for correctly catching -D, etc.
      Qchem: PR comments
      Testing: Finishes up using conversion on several straglers
      Testing: Applies new using strategy to all files
      Testing: New using strategy
      Psi4: Fixes issue with HF3c execution
      PR comments
      PR comments: parse logfile for fields not available in QCSCR also, fix dipole parsing
      nwc: add hessian file; minor testing updates (MolSSI#177)
      PR comments: use qcel's NUMBER regex also, blacken and isort
      fix test until next qcel version
      PR comments: added ability to ingest logfile+QCSCR
      Blacken QCEngine
      PR comments: rename input, refactor NUMBER into regex snippet file
      Update QCENGINE_RECORDS_COMMIT
      Update QCENGINE_RECORDS_COMMIT
      Qchem: add tests for log parser for archival data
      Qchem: add log parser for archival data
    muammar committed Dec 9, 2019
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Commits on Dec 10, 2019

  1. General improvements

    - Cleaned up unneeded comments.
    - Added support for HF method.
    - Parallel computation support using %pal.
    - Black beautification.
    muammar committed Dec 10, 2019
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Commits on Dec 11, 2019

  1. Merge branch 'master' into orca

    * master: (21 commits)
      Docs: Changelog 0.13.0 extension
      Psi4: Ensures output data for psi4, fixes MolSSI#176
      Docs: Adds v0.13.0 changelog
      Lint: Fixes GHA routine
      Testing: Canonicalizes from testing, closes MolSSI#193
      Lint: Adds a GHA action to check for Black
      GitHub: Updates tempaltes to QCArchive standard
      Lint: Blackens code base
      Addresses MolSSI#186
      Improved MPI support
      Clarified documentation
      Improved documentation and type checking for node configuration
      Added ability to forward output from popen
      Documentation for configs needed for node-parallel tasks
      Removed unused import
      Bug fix: Use integer division not floating point
      Read from both stderr and stdout to prevent buffer deadlock
      Bug fix: Memory is per MPI rank
      Bug fix: Missing task configuration when making mpi command
      Improved warnings for when multi-node jobs are misconfigured
      ...
    muammar committed Dec 11, 2019
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Commits on Dec 18, 2019

  1. Merge branch 'master' into orca

    * master:
      NWCHEM: parse dispersion_correction output from psivar/ fix bug
      Read Dispersion Energy from nwchem output file and add it to psivar
      Update harvester.py
    muammar committed Dec 18, 2019
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Commits on Jan 9, 2020

  1. Remove unneeded code.

    muammar committed Jan 9, 2020
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  2. Merge branch 'master' into orca

    * master: (29 commits)
      CI for NWChem (MolSSI#212)
      Make sure input extras tags get to the output
      Added NWChem to the canonical harness tests
      Calls to rtdb must use all threads
      Remove assumption that NWChem uses original order of atoms
      Fixed test for cores_per_rank
      Correctly determine memory sizes, when MPI should be used
      Account for cores_per_rank when computing total ranks
      Added a more difficult test for the nwchem hessian
      Read hessian array in proper order
      Use pep8 variable names
      Rotate gradients and hessian to match input molecule
      Linted with black
      Added Hessian support and improved gradient accuracy
      Allow for methods that are combinations of several functionals
      psi4 windows version and outfile psiapi mode (MolSSI#201)
      NWCHEM:  added keyword dft to xc_functionals list.  If method == "dft" (MolSSI#204)
      entos: Updated QCER hash and program_overview.rst
      black reformatting
      entos: AO reordering added to unrestricted wavefunction properties
      ...
    muammar committed Jan 9, 2020
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  3. General improvements:

    - Removed Molpro references.
    - Removed restricted/unrestricted case guessing.
    muammar committed Jan 9, 2020
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  4. Pyflakes clean.

    muammar committed Jan 9, 2020
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  5. Bohr by default.

    muammar committed Jan 9, 2020
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Commits on Jan 10, 2020

  1. General improvements following reviews.

    - `conversion_factor()` function used to convert from eV to Hartree.
    - cclib is just imported when invoking `.parse_output()`.
    - `.get_gradient()` renamed to `._get_gradient()` so that it becomes
      a private function.
    muammar committed Jan 10, 2020
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Commits on Jan 16, 2020

  1. More changes based on review.

    muammar committed Jan 16, 2020
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  2. Merge remote-tracking branch 'origin/master' into orca

    * origin/master:
      simplify
      better error message from get_program, closes MolSSI#213
      pass for psi w/o --module
      prep env for psithon or psiapi, get the other for free
      psithon _or_ psiapi for p4
    muammar committed Jan 16, 2020
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Commits on Jan 17, 2020

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  2. Remove print.

    muammar committed Jan 17, 2020
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Commits on Feb 7, 2020

  1. Merge branch 'master' into orca

    * master: (40 commits)
      Docs: Minor changelog tweaks based on comments
      remove the  unnecessary if else blocks
      Docs: Cleans up code blocks
      OpenMM: Switches method/basis as discussed
      Docs: Adds notes on molecular mechancs programs
      Docs: Patches up doc errors
      Docs: Adds OpenMM to the overview
      Docs: Adds 0.14.0 changelog
      fix logic only check Nalpha ==Nbeta if already in psivar
      OpenMM: Now requires openforcefield as well
      make psi4 harness safe for psiapi file cleaning
      CI: Re-enables TorchANI CI testing
      CI: Removes duplicate RDKit build
      OpenMM: Adds tests for other openff, ffs
      Psi4: Bumps dev branch to 500
      Testing: Patches up tests after QCElemental sparse molecule changes
      OpenMM: Fixes forces and adds an optimization example
      OpenMM: Adds openmm tests to canonical tests
      OpenMM: Simplifies method/basis in accordance with MolSSI#192
      OpenMM: Testing now depends on rdkit
      ...
    muammar committed Feb 7, 2020
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Commits on Mar 13, 2020

  1. Merge branch 'master' into orca

    * master:
      fixed format
      add procedure for pyberny geometry optimizer
      Add MDI version check
      Linted mdi_server.py
      Update to support MDI v1.1.3
      added optional param for execute: exit_code
      add conda-envs readme
      fixing my h20v2 mistake
      add homo lumo test
      added homo lumo test
      caputure +- 0 and exponent all at once, remove if-else
      format
      comment for clarity
      if else for for +/- exponent
    muammar committed Mar 13, 2020
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