- Adjust pysis .yaml files with --solvent argument as well
- Improve file and directory handling in Python
- Switch from os.system to subprocess.run
- Better file names
- Implement restart option
- Write checkpoint (.json) file during run
- "Passive" restart for cancelled jobs
- Restart from a certain step with different conditions - is it possible without input files?
- Hardcode step numbers
- ORCA stage statistics: if reached; paths to start ORCA jobs; check ORCA termination
- Clean in ORCA directory (keep .err, .inp, .out, .xyz, .hess, .engrad, .log, .gbw)\
- Scrape data immediately after finishing of ORCA compound job: put relevant data into one output file (e.g., energies)
- Transfer part of the data_collector code to core to get ΔE and barriers when the user follows the standard pipe
- Check ORCA in the config, but do not stop if it is not found
- Scrape generated .xyz files and output into .json results (actual geometries)
- Add automatic TS checks for imaginary frequencies
- Rework detect neighbors for longer moieties
- Add charge and multiplicity selection
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Switch over to using ORCA for all steps
- Investigate possibility of using NEB
-
Switch over to using input files for all steps
- Rethink scratch usage when input files are implemented
- Implement three-point TS search to allow search for higher-energy mechanisms
- Investigate possibility to first find TS and then apply substitutions
- Add option to perform conformational analysis before TS search (or triple-crest)
- Improve data collector tool
- Write messages and useful information to log file (now under --verbose argument)
- Report both barriers and assign Stable/Metastable based on relative heights
- Clean up pysisyphus/qm_calcs folder after completion
- Fix fragment combiner (RDKit)
- Include data collector tool