AutoTST

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AutoTST is not being maintained frequently and thus runs into environment issues due to package updates etc. This PR intends to rebuild the environment file and locking all versions of...

calvinp0

[Bug Report] AttributeError: module 'scipy.stats' has no attribute 'gibrat'

2

## Describe the bug The package 'descriptastorus' has had a recent fix in the naming convention for the attribute 'gibrat' - https://github.com/bp-kelley/descriptastorus/blob/86eedc60546abe6f59cdbcb12025a61157ba178d/descriptastorus/descriptors/dists.py#L207C1-L207C1 as in scipy they used to refer it...

calvinp0

How to run AutoTST

3

Hello, developers. I have created AutoTST environment on my Mac, but there is no guide to tell us how to run or activate AutoTST simulation. Because the AutoTST is based...

AH9316

Gaussian doesn't like writing scratch temp files to '/tmp' in discovery

6

Gaussian crashes when $GAUSS_SCRDIR is set to /tmp in Discovery sample error message ``` PGFIO/stdio: No such file or directory PGFIO-F-/OPEN/unit=11/error code returned by host stdio - 2. File name...

davidfarinajr

input file for Job

1

There are a lot of options for Kinetics and ThermoJob (optimize, conformer rmsd/energy cutoff, single_point, arkane,etc.). We could make this better by creating input files, similar to how Arkane works.

davidfarinajr

Loading RMG-database and TS database

1

When estimating TS distances for a reaction, we currently load RMG-database and AutoTST database. For example, when we create an autotst H Abstraction reaction and want to generate a TS,...

davidfarinajr

To update the TS database, we need to work backwards: generate a TS from a log file. We currently rely on the atom sorting labels to identify the atoms in...

davidfarinajr

I just saw that ASE now has native TS optimizers and IRC calculations for Gaussian. This may be worth looking into 🤔 See the link below: https://wiki.fysik.dtu.dk/ase/dev/ase/calculators/gaussian.html

ndharms

Building of TSs with reactant and product species geometries

1

Conformational changes like inversion of chiral centers and rotation about double bonds rarely occur when reactants go to TSs (e.g. a reactant containing a cis double bond will probably have...

ndharms

- We can use pyslurm instead of subprocess to submit jobs to SLURM using the following example, [test_job](https://github.com/PySlurm/pyslurm/blob/17.11.0/tests/test-job.py#L8l)

skrsna