Shoubhik Maiti

Handling of unit cell parameters when they are missing from the file

7

I am reading a DCD file (generated with NAMD) with chemfiles. In NAMD, the simulation was run without any periodic boundary conditions, however, it seems that NAMD sets the unit...

XTB crashes when run with large molecules (MSYS2/MinGW)

10

**Describe the bug** I am trying to run xtb on an 83 atom molecule. However, it crashes immediately after staring without any error message. For small molecules the error does...

Visualize localized molecular orbitals (LMO) from xTB

3

**Is your feature request related to a problem? Please describe.** When I run xtb with `xtb file.xyz --lmo` it generates two extra files, `xtblmoinfo` and `lmocent.coord`. The stdout from the...

Allow saving coordinate trajectory on disk

2

*** ## TODO * [ ] make history work with bracket methods * [ ] change the tests to be more consistent ## Checklist * [ ] The changes include...

First detected with https://github.com/duartegroup/autodE/actions/runs/7372991735/job/20062312828

Compiling a list of bugs found so far in the optimisers, so that they could be fixed one-by-one. 1. CRFOptimiser - coordinate building does not seem to always work. Number...

Image pair regen with spline or 1D cubic polynomial fit.

Currently autodE's NEB uses scipy's LBFGS. However, scipy uses a function value tolerance criteria that stops the optimiser when relative reduction in the value is below certain range "REL_REDUCTION_OF_F_

Add different levels of logging?

1

One minor issue I am having is that the `logging.INFO` and `logging.WARNING` levels are too verbose, they print a lot of information. For example, when you are running an optimisation,...

Implement multi-step generic reactions

1

Right now autodE only models single step elementary reactions automatically (for multi-step the intermediates must be known). If there are intermediates, they are ignored. Which is a problem for modelling...