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SCM-NV / pyZacros

Python Library for Automating Zacros Simulations
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Problems in the generation of state_input.dat #72

Closed mbracconi closed 2 years ago

mbracconi commented 2 years ago

Hi,

When the initial_state option is employed and a lattice state from an another simulation is used, pyZacros generates the state_input.dat file. However, there are problems when bidentate (and I guess multi-dentate) species are present in the lattice. The simulation crashes during the loading of the simulation with the following error: Error code 5004 from state_parser_module: seed_on_sites keyword must be followed by a species name (string) and nspecdent integers in state_input.dat.

This is due to fact that the state_input.dat generated by pyZacros list for multi-dentate species the following text: seed_on_sites O2** 306 However, Zacros expects: seed_on_sites O2** site1 site2 Or more generally as many sites as dentates on the surface.

Thanks

nfaguirrec commented 2 years ago

Hi Mauro! This is interesting. I wrote a test for this case, well only for a bidentate case, and it works well (see tests/test_LatticeInitialState.py), surely I forgot something. Could you please make a simple example script reproducing the error you found? Thanks!

mbracconi commented 2 years ago

Hi Nestor,

The difference between the tests/test_LatticeInitialState.py and my code is the fact that the information in my case comes from a previously run simulation. I attach a simple example able to reproduce the problem.

Thanks example_problem.tar.gz

nfaguirrec commented 2 years ago

Hi Mauro! Could you please try again? I think I fixed the bug. Thanks!