Fix errors in interface_builder execution and portability

[google-labs-jules]

This PR addresses several errors preventing the interface_builder package from running portably.

1. Hardcoded Paths: Replaced user-specific absolute paths (e.g., /Users/anthonca/...) with relative paths or function arguments in both Python code and LAMMPS input scripts.
2. Dependencies: Added missing lammps-logfile and pandas dependencies to setup.py.
3. Directory Creation: Replaced unsafe os.system('mkdir ...') calls with os.makedirs(..., exist_ok=True) to handle existing directories and parent directories correctly.
4. MPI Support: Added an oversubscribe parameter to execute_lammps (defaulting to True) to prevent mpirun failures on systems with limited slots.
5. Example Fixes: Corrected invalid method arguments in test_quartz.py (changed thickness to water_thickness) and updated generate_amorphous_system.py to handle output directories safely.
6. Cleanup: Added a .gitignore file to prevent committing build artifacts and simulation outputs.

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PR created automatically by Jules for task 16046138384743830340 started by @antble

[google-labs-jules]

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