Pynta v2.0.0

v2.0.0 represents a complete rewrite of Pynta. The rewritten Pynta uses ACAT for site detection, FireWorks for job management and implements it's own algorithms for generating initial guess structures for adsorbates, gas phase species and transition states. This Pynta can handle arbitrary reactions, gas phase species and monodentate and bidentate chemisorbed species on metal surfaces.

What's Changed

• Merge Rewritten Pynta by @mjohnson541 in #12
• General Fixes Particularly for Slab Generation by @mjohnson541 in #14
• Non-queue operational fixes and Enable use of XTB by @mjohnson541 in #15
• Testing by @mjohnson541 in #13
• Update Documentation by @mjohnson541 in #17
• properly update docs by @mjohnson541 in #18
• Postprocessing by @mjohnson541 in #20
• Enable Arbitrary Layer Freezing by @mjohnson541 in #23
• Enable computation of reaction thermochemistry by @mjohnson541 in #26
• Conda Build FIles by @mjohnson541 in #25
• Fix bug in reactant and product energy calculations by @mjohnson541 in #27

New Contributors

• @mjohnson541 made their first contribution in #12

Full Changelog: v1.1.1...v2.0.0

Release v1.1.1

• minor bug fixes
• added utils methods to convert traj files into xyz files
• fixed formating output of Show().not_finieshed()
• fixed requirements
• fixed typos causing minima_vib step to fail

Release v1.1.0

• added an automated logic to specify which adsorbate atom connects to the surface, rather that specifying it by hand
• fixed atoms numbering during 02 step input generation that led to specifying wrong atomic indicies for a penalty function calculation for some molecules
• added a new method Restart().remove_empty_pickle_files() that removes all empty *.pckl files from unfinished calculations
• added a new method Restart().remove_error_files() that removes all temp files from unfinished calculations
• added a new method
• rewritten part where various balsam calculators are imported
• added Dockerfile
• new graphics
• updated docs
• setup.cfg added and setup.py refactored - getting ready for PyPI released
• fixed requirements.txt
• other bug fixes and improvements

Release v1.0.1

• added a method to remove large temp files from previous run while restarting the workflow
• fixed bug preventing running 02 step
• created a CI workflow for testing
• updates in README.md and docs
• fixed minor bugs and inconsistencies in the codebase

Initial pynta release

Initial pynta release