Code

simple job running api#89

Code

Merged

YHordijk merged 149 commits intomainTheoChem-VU/TCutility:mainfrom 68-simple-job-running-apiTheoChem-VU/TCutility:68-simple-job-running-apiCopy head branch name to clipboardJan 30, 2024

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Commits

Commits on Jan 19, 2024

• Moved the atom_data module to tcutility.data.atom

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• Added the data.functionals module which gives information about functionals

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• Added the job module.

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• Added some more information to the ADF results. We added charge, relativistic_type and spin-polarization + multiplicity

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• Added the system charge to the AMS information

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• Fixing ruff issues

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• Added docstring for the AMSJob class

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• Moved molecule loading method to generic.Job

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• Added the CRESTJob class

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• Now checking if the setup was successfull

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• Now checking if the setup was successfull

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• Improved printing of error

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• Improved the postamble for default crest jobs

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• Added crest-job to init

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• Added an example workflow for conformer generation/optimization

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• Missing import

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• fixed wrong method call

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• Fixed early exit for missing molecuel path

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• Added some documentation

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• Directories were switched around

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• Added kill_on_invalid_dep when setting a dependency in case the previous job fails

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• Moved geometry opt convergence criteria to AMSJob

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• Moved default geometry_convergence settings to AMSJob

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Commits on Jan 20, 2024

• Added the orca job

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• Removed shell=True for subprocess call

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• Runfiles should now be correctly generated

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• Fixed incorrect reference

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• Stripping the orca_path, as it contained a \n

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• Testing the ORCA job now

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• Importing orcajob

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• Fixed typo

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• Added sbatch settings

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• Vibrations are calculated by default for optimization

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• Improved example

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• Changed append to add

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• Added preamble

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• Added preamble

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• Added preamble

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Commits on Jan 22, 2024

• Testing the conformer workflow example

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• Added the QCGJob class for running quantum cluster growth calculations

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• Setting default ORCA method and basis sets

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• Added a new example job

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• Added a new example job for QCG

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• Added the QCGJob to init

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• Added ensemble_mode option

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• Ensemble generation is now enabled for QCGJob

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• Enabled ADF calcs

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• Solvent molecules can now be given by name. tcutility will use data.molecules to find them

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• Prettified the example

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• Added a get_molecules function which returns molecules from the molecules directory. Optionally you can give tags that have to be defined in the xyz file

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• Fixing ruff warnings

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• Simplified options specification for crestjob

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• Changed tabs to spaces

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• Using property of CRESTJob instead of remaking the directory

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• Fixing atom data test

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• Fixed an issue with getting spin polarisation

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• Added a check for directory existence, if it does return the files in the folder

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• Added the hold argument for Job construction. This will make the script wait for the job to finish before continuing

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• Added the wait_for_job function which will wait for a job to finish before returning

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• Renamed hold to wait_for_finish

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• Now number defaults to None, if it is not set we return all files in the conformer or rotamer directories

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• Now waiting for CRESTJob to finish before submitting the DFTB and DFTJobs

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• Updated the example

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• Updated the example

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  d89b38c

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• Fixed logic

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• Fixed logic

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• Fixed logic

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• Fixed logic

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• Fixed logic

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• Debug printing

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• Sorting the files now

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Commits on Jan 23, 2024

• Added the ability to give fragments as a list of integer indices. This assumes you have a molecule supplied for the main job, otherwise it will raise an error

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• Fixed an issue where job would crash for ADFFragmentjobs because of missing molecule, even though it was supplied in the systems block in the settings object

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• Added a new example for running fragment calculations

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• Removed useless statement

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• Fixed formatting and commented line

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• Steven fixed the solvent molecules

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  b1d8af9

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• Fixing Ruff errors

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• Added postamble to QCG, as well as directory and file getting for ensemble

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• Fixed wrong reference to molecules.get_mol, which was renamed to molecules.get

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• Added alpb option

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• Added the nofix option

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• Added error message if solvent is not given

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• renamed best_conformer_path to best_ensemble_path

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• QCGJob will now attempt to get the alpb solvent name from the xyz file

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• Removed unused files

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• Fixed typo

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• Fixed missing import

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• Fixed ruff error

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• Fixed splitting of ensemble file into parts

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• Ensemble xyz files are now send to ensemble/ensemble

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• Now ignoring docs/_build

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• Now ignoring docs/_build

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• Started working on documentation for job

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• Started working on recipes. For now added the conformer_search recipe

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• Added the tabs extension for sphinx

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• Added new requirement for tabs in sphinx

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• Update build_docs_no_deploy.yaml

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• Moved sphinx-tabs requirement from pyproject to github workflow

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• Update build_docs.yml

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• Update build_docs_no_deploy.yaml

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• Update build_docs.yml

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Commits on Jan 24, 2024

• Added copybutton to documentation for easy copying of code blocks

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• Autodoc will now sort classes and functions by the order in the source

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• Added some more work for the documentation for the job module

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• Added a new function that is used to get fragments from a molecule object, if the fragments were defined in the xyz file

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• Improved documentation

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• Merge remote-tracking branch 'origin/68-simple-job-running-api' into 68-simple-job-running-api

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• Update build_docs_no_deploy.yaml

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• Update build_docs_no_deploy.yaml

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• Removed _build from repo

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Commits on Jan 25, 2024

• Now hiding some internal methods for Transform class

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• Fixed ruff complaints

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• Fixed ruff complaints

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Commits on Jan 26, 2024

• Added two tests for the KabschTransform class

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• Added job and results to modules rst

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• Added tuctility.job to the toctree and separated the API documentation

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• Changed headers to sections

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• Added more documentation

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• Added more documentation

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• Now hiding the setup_job method

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Commits on Jan 27, 2024

• Added an improved cache module implementing a normal caching decorator and a timed caching decorator

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• Using the timed cache for slurm calls

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• Now printing sbatch output

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• Now printing sbatch output

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• Added the sbatch command, which will submit a job to slurm and return the command used and the job ID

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• Reworked run to use the new slurm.sbatch function

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• The submit file should now be executable

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Commits on Jan 28, 2024

• Added an extra example

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• Added more documentation for the generic job class

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• Improved the index of the documentation

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• Started working on writing the job documentation

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• Added the NMRJob class

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• Added a start to the examples documentation page

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• Now writing nics coordinates to multipole coordinates in the pre_nmr job as required by AMS

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• Added documentation for the NMRJob

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• Removed unused get_sbatch_command and added more documentation

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• Added the preoptimization recipe

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• Enabling overwrite will now remove the original rundir

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• Tested the preoptimize workflow

  

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• Fixing ruff issues

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• Merge branch '68-simple-job-running-api' of github.com:TheoChem-VU/TCutility into 68-simple-job-running-api

  

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• Changed check for getting molecules

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• Added a script to write functional information to a json file

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• Removed charge, is handled by Siebe's PR

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• Improved the documentation

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Commits on Jan 29, 2024

• Added a function to convert path-safe functional name to the corresponding functional name

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Commits on Jan 30, 2024

• Geometry optimizations now calculate the hessian before-hand with a lower level of theory

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• removed _build

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