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Orca Harness. #178
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Orca Harness. #178
Commits on Nov 22, 2019
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Commits on Dec 3, 2019
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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 ...
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Commits on Dec 4, 2019
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Commits on Dec 5, 2019
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- 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.
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Commits on Dec 9, 2019
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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
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Commits on Dec 10, 2019
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- Cleaned up unneeded comments. - Added support for HF method. - Parallel computation support using %pal. - Black beautification.
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Commits on Dec 11, 2019
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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 ...
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Commits on Dec 18, 2019
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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
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Commits on Jan 9, 2020
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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 ...
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- Removed Molpro references. - Removed restricted/unrestricted case guessing.
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Commits on Jan 10, 2020
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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.
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Commits on Jan 16, 2020
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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
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Commits on Jan 17, 2020
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Commits on Feb 7, 2020
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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 ...
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Commits on Mar 13, 2020
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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
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