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Miscellaneous changes #109

Merged
merged 42 commits into from
Apr 3, 2019
Merged

Miscellaneous changes #109

merged 42 commits into from
Apr 3, 2019

Commits on Apr 3, 2019

  1. Added examples to gitignore 

    Also removed settings.py which has no effect, since git cannot ignore
files it started tracking
    @alongd
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  2. Allow users to specify the number of cpu's to use per server

    @alongd
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  3. Minor: changed except Error as e if e isn't being used

    @alongd
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  4. Download additional info re failed jobs 

    Download out.txt and err.txt from OGE
and slurm_<job id>.out from Slurm
    @alongd
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  5. Minor: Convert if to elif in job ess error identification

    @alongd
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  6. Minor: Modification to job error messages

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  7. Make sure initial and final job times are defined 

    before determining run time
    @alongd
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  8. Added fail-safe try-except blocks in ssh 

    to download and get modified time
    @alongd
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  9. Renamed visualize_orbitals as run_orbitals 

    since this directive doesn't actually visuallizes anything
Also changed the default to False, since this might take too long
(longer than all other jobs for the species)
    @alongd
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  10. Minor robustness changes to Species

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  11. Correcting scan_level assignments, particularly for composite methods

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  12. Avoid paranthesis in unique species name 

    This could be read by RMG as the species index
use `_` instead
    @alongd
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  13. Don't crush if a stat_mech job fails

    @alongd
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  14. Append species to thermo library only after calculating thermo for it

    @alongd
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  15. Make sure we get initial_xyz from conformers_path 

    before running optimization (or composite)
    @alongd
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  16. Troubleshooting improvements

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  17. Added levels_ess to settings 

    To allow users to associate levels of theory (phrases of methods or
basis sets) with the desired ESS
    @alongd
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  18. Changed ess_settings to contain a list of servers 

    Also renamed it to ess_settings throughout
Also using levels_ess from settings
    @alongd
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  19. Tests: Adapt ess_settings syntax

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  20. Tests: Update to the run_orbitals syntax 

    and new default value
    @alongd
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  21. Added ess_settings to settings.py instead of the API 

    and removed precedence from servers dictionary

Also modified determine_ess_settings() accordingly
    @alongd
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  22. Added testing to job

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  23. Tests: Functions in main

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  24. Changed default levels of theory for conformers and orbitals 

    Also minor line relocation in rotor settings
    @alongd
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  25. Added number_of_atoms as a property of Species

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  26. Tests: Species number of atoms

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  27. Minor: Chnaged syntax of input_dict['verbose'] in ARC.py

    @alongd
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  28. Minor: Enhanced error and debug messages in Job

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  29. Corrected default values for max_job_time and job_memory 

    in main.py when loading from a dictionary.
(Also added job_memory to the input file)
    @alongd
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  30. Run statemech in Processor using a single method 

    Also output a species YAML file w/o BAC iff BAC is used for thermo
    @alongd
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  31. Dont run opt if geo is present in the output dictionary

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  32. Don't crush ARC if cannot order atoms

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  33. Correctly assing S/D BAC to aromatic species 

    using their Kekulized form
    @alongd
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  34. TS species are allowed to be loaded w/o structure or xyz

    @alongd
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  35. Combine TSError for unrecognized TSGuess methods

    @alongd
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  36. Minor: Reordered Exceptions

    @alongd
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  37. Don't throw a SpecieError of no structure if conformers are available

    @alongd
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  38. Minor: Text addition to project info file

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  39. Capture AutoTST TSErrors in Scheduler

    @alongd
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  40. BugFix: Only consider converged TSGuesses for min(energies)

    @alongd
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  41. BugFix: Determine stable conformers and run them 

    Corrected conditions
    @alongd
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  42. Minor: Changed if not x in to if x not in

    @alongd
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