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conformer search with solvation effect #737

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conformer search with solvation effect #737

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Commits on Mar 4, 2024

  1. main.py sets up conf_generation_level

    @JintaoWu98
    JintaoWu98 committed Mar 4, 2024
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  2. scheduler.py sets up conf_generation_level

    @JintaoWu98
    JintaoWu98 committed Mar 4, 2024
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  3. generate_conformer in species.py considers solvent

    @JintaoWu98
    JintaoWu98 committed Mar 4, 2024
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  4. get_force_field_energies_solvation in conformers.py 

    The new added function get_force_field_energies_solvation is created to find conformers considering solvation effect.
It opens a subprocess to run multi_species opt job with solvent over the conformers from the RDkit conformers (without solvent)
    @JintaoWu98
    JintaoWu98 committed Mar 4, 2024
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  5. settings.py include default conf_generation level of theory

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    JintaoWu98 committed Mar 4, 2024
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  6. ARC.set_levels_of_theory in main.py considers conf_generation_level

    @JintaoWu98
    JintaoWu98 committed Mar 4, 2024
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  7. Prevent update of running_job list to empty one if it exists

    @JintaoWu98
    JintaoWu98 committed Mar 4, 2024
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  8. New conditions to decide which jobs to run for given xyzs

    @JintaoWu98
    JintaoWu98 committed Mar 4, 2024
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Commits on Mar 7, 2024

  1. Write conformer yaml file including xyz and energy 

    Add log information for conformer with solvation spawned from the subprocess
    @JintaoWu98
    JintaoWu98 committed Mar 7, 2024
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Commits on Mar 28, 2024

  1. Rewrite the log info for multi_species consideration process

    @JintaoWu98
    JintaoWu98 committed Mar 28, 2024
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  2. Divide the multi_species cluster into smaller amount 

    This allows us to launch more opt jobs with smaller amount of conformers individually and parallelly, to speed up the process.
    @JintaoWu98
    JintaoWu98 committed Mar 28, 2024
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