Add sim and path config yaml files #16
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jedyeo
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geoffwoollard and
ninamiolane
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temp_workspace/input/sim_config.yaml
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| molecular_model: | |||
| voxel_size: 0.1 # [nm] | |||
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are these string paths ever read by the TEM simulator? Or do we have freedom to change their names?
e.g. voxel_size to pixel_size_ang. If these are the "expected fields" to the TEM simulator, then I'm thinking we can have another layer above where standard params that are shared between different simulation routines are converted into "tem simulator" specific ones (units, etc).
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| pdb_dir: '../temp_workspace/input/' | |||
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I thought we were going to get rid of a working directory... if it's something that only exists for the length of the simulation, perhaps it could be created and deleted with the os module
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This particular working directory exists only for demonstration purposes - this path would be changed out by the user. temp_workspace/ should not be in the PR - I'll look into addressing this after work today.
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Maybe:
- having the pdb data in a
data/orpdb_structures/directory insidesimSPI/simSPI - having the config files at the root of the
simSPI/simSPIrepo
would be more intuitive?
We do not need to tell the users how to organize their workspace.
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And the user can call the simulator by providing a path output_dir to tell it where to store the output of the simulation?
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Good ideas, thank you!
I've edited the folder structure - temp_workspace is gone (as I mentioned earlier it's best not left in the main branch anyhow) and the config files now sit in the "root" simSPI/ directory. The PDBs are stored in simSPI/data as you suggested.
For now, I think simSPI/output/ makes sense as a default output directory and the user can change it in the config file if desired.
Add sim and path config yaml files for the simulator to use.
Code to receive and parse these yamls will be added in a future PR (soon).
@calhep @thisTyler @arjunsingh3600