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- Remove hardcoded absolute paths in `interface_builder.py` and LAMMPS scripts. - Update `setup.py` to include missing dependencies `lammps-logfile` and `pandas`. - Use `os.makedirs` for safer directory creation. - Add `--oversubscribe` option to `mpirun` calls to support varied environments. - Fix API usage errors in example scripts (`generate_amorphous_system.py`, `test_quartz.py`). - Add `.gitignore` to exclude build artifacts and temporary files.
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This PR addresses several errors preventing the
interface_builderpackage from running portably./Users/anthonca/...) with relative paths or function arguments in both Python code and LAMMPS input scripts.lammps-logfileandpandasdependencies tosetup.py.os.system('mkdir ...')calls withos.makedirs(..., exist_ok=True)to handle existing directories and parent directories correctly.oversubscribeparameter toexecute_lammps(defaulting to True) to preventmpirunfailures on systems with limited slots.test_quartz.py(changedthicknesstowater_thickness) and updatedgenerate_amorphous_system.pyto handle output directories safely..gitignorefile to prevent committing build artifacts and simulation outputs.PR created automatically by Jules for task 16046138384743830340 started by @antble