modified output path to scratch

Author: AngelikaH123

chromo/mc/__init__.py

@@ -47,7 +47,7 @@ def _polymer_in_field(
     mu_schedule: Optional[Callable[[float], float]] = None,
     lt_schedule: Optional[Callable[[str],float]] = None,
     temperature_schedule: Optional[Callable[[str],float]] = None,
-    output_dir: Optional[DIR] = '.',
+    output_dir: Optional[DIR] = '.', # defaults to  current location, same level as chromo folder: name = output
     path_to_run_script: Optional[str] = None,
     path_to_chem_mods: Optional[List[str]] = None,
     run_command: Optional[str] = None,
@@ -161,14 +161,10 @@ def _polymer_in_field(
                 print("Not a valid lt schedule option")
         else:
             print("Missing lt schedule option")
-        #print("lt change " + str(lt_change))
-
-        temperature_adjust_factor = 1
-        lt_value_adjust= lt_change
 
         decorator_timed_path(output_dir)(mc_sim)(
             polymers, binders, num_save_mc, mc_move_controllers, field,
-            mu_adjust_factor, random_seed, temperature_adjust_factor, lt_value_adjust
+            mu_adjust_factor, random_seed, temperature_adjust_factor, lt_change
         )
 
         for poly in polymers:

chromo/run_simulation.py

@@ -127,7 +127,8 @@
     num_saves = num_snapshots,
     bead_amp_bounds = amp_bead_bounds,
     move_amp_bounds = amp_move_bounds,
-    output_dir = 'output',
+    output_dir = '/scratch/users/ahirsch1/output', # for running on sherlock
+    #output_dir = 'output',
     mc_move_controllers = moves_to_use,
     temperature_schedule = "no schedule",
     lt_schedule = "linear increase"