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simple job running api #89

Merged
merged 149 commits into from
Jan 30, 2024
Merged

simple job running api #89

merged 149 commits into from
Jan 30, 2024

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YHordijk
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This PR will bring the job API. It is still a draft for now, as I am still working on it.

YHordijk added 30 commits January 19, 2024 16:25
@YHordijk
Moved the atom_data module to tcutility.data.atom
328eb7a
@YHordijk
Added the data.functionals module which gives information about funct…
e1ce16c 
…ionals
@YHordijk
Added the job module.
d4258a4
@YHordijk
Added some more information to the ADF results. We added charge, rela…
4a30759 
…tivistic_type and spin-polarization + multiplicity
@YHordijk
Added the system charge to the AMS information
487a3c9
@YHordijk
Fixing ruff issues
6993a54
@YHordijk
Added docstring for the AMSJob class
c9ba898
@YHordijk
Moved molecule loading method to generic.Job
d13673c
@YHordijk
Added the CRESTJob class
551fd50
@YHordijk
Now checking if the setup was successfull
9d70169
@YHordijk
Now checking if the setup was successfull
d576c4e
@YHordijk
Improved printing of error
3975b8b
@YHordijk
Improved the postamble for default crest jobs
90ce5fa
@YHordijk
Added crest-job to init
57723c8
@YHordijk
Added an example workflow for conformer generation/optimization
0609244
@YHordijk
Missing import
25173ee
@YHordijk
fixed wrong method call
242a53f
@YHordijk
Fixed early exit for missing molecuel path
b79cd9d
@YHordijk
Added some documentation
34dc684
@YHordijk
Directories were switched around
bffaf9a
@YHordijk
Added kill_on_invalid_dep when setting a dependency in case the previ…
f6d1d5d 
…ous job fails
@YHordijk
Moved geometry opt convergence criteria to AMSJob
ec2bd4a
@YHordijk
Moved default geometry_convergence settings to AMSJob
985c28e
@YHordijk
Added the orca job
abfb43b
@YHordijk
Removed shell=True for subprocess call
4628ed2
@YHordijk
Runfiles should now be correctly generated
c2bc128
@YHordijk
Fixed incorrect reference
58bf583
@YHordijk
Stripping the orca_path, as it contained a \n
ac07ebf
@YHordijk
Testing the ORCA job now
12f8449
@YHordijk
Importing orcajob
3ac36c6
SiebeLeDe
SiebeLeDe requested changes Jan 27, 2024
View reviewed changes
src/tcutility/data/available_functionals.txt Show resolved Hide resolved
docs/_build/doctrees/__modules.doctree Show resolved Hide resolved
src/tcutility/data/molecules.py Show resolved Hide resolved
src/tcutility/job/adf.py Show resolved Hide resolved
src/tcutility/results/ams.py Outdated Show resolved Hide resolved
YHordijk and others added 18 commits January 27, 2024 21:19
@YHordijk
The submit file should now be executable
270802b
@YHordijk
Added an extra example
cb236c4
@YHordijk
Added more documentation for the generic job class
9bac267
@YHordijk
Improved the index of the documentation
2d1bd51
@YHordijk
Started working on writing the job documentation
0e47063
@YHordijk
Added the NMRJob class
4aa91f5
@YHordijk
Added a start to the examples documentation page
d307d68
@YHordijk
Now writing nics coordinates to multipole coordinates in the pre_nmr …
6510f27 
…job as required by AMS
@YHordijk
Added documentation for the NMRJob
5d45a00
@YHordijk
Removed unused get_sbatch_command and added more documentation
8792764
@YHordijk
Added the preoptimization recipe
7768279
@YHordijk
Enabling overwrite will now remove the original rundir
ca9e017
Tested the preoptimize workflow
12e4fc0
@YHordijk
Fixing ruff issues
1297936
Merge branch '68-simple-job-running-api' of github.com:TheoChem-VU/TC…
9fedad3 
…utility into 68-simple-job-running-api
@YHordijk
Changed check for getting molecules
cd34669
@YHordijk
Added a script to write functional information to a json file
a962a7b
@YHordijk
Removed charge, is handled by Siebe's PR
dfdbc08
@YHordijk YHordijk requested a review from SiebeLeDe January 28, 2024 20:02
@YHordijk YHordijk merged commit 8094845 into main Jan 30, 2024
6 checks passed
@YHordijk YHordijk deleted the 68-simple-job-running-api branch January 30, 2024 10:39
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@SiebeLeDe SiebeLeDe Awaiting requested review from SiebeLeDe

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Guess fragments based on xyz files Simple job running API
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@YHordijk @SiebeLeDe