Improve argument handling and clean up unecessary files

run_simulation.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+
+from auto_namd.functions import *
+from auto_namd.job import get_next_job
+
+
+def main(**kwargs):
+
+    while True:
+        job = get_next_job(kwargs['jobs_path'])
+        job.simulate(kwargs['ffs_path'], kwargs['steps'], kwargs['namdbin'], kwargs['params'])
+
+
+if __name__ == '__main__':
+
+    # Defaults
+    args = {
+        'jobs_path': ['/home/bryan/MD/CFTR/4-jobs', 'Number of timesteps to run'],
+        'ffs_path': ['/home/bryan/MD/CFTR/0-forcefields', 'Location of the forcefield files'],
+        'steps': [1000000, 'Number of timesteps to run the simulation'],
+        'namdbin': ['namd2', 'Location of the namd2 executable'],
+        'params': [f'+p{os.cpu_count() - 1}', 'Optional namd parameters']
+    }
+
+    # Override defaults with user input
+    args = sim_parser(args)
+    main(**args)