Add 'arbd' argument to model.simulate()

mrdna/simulate.py

@@ -88,7 +88,8 @@ def multiresolution_simulation( model, output_name,
                                 backbone_scale=1.0,
                                 oxdna_steps = None,
                                 oxdna_output_period = None,
-                                run_enrg_md = False
+                                run_enrg_md = False,
+                                arbd = None
                             ):
 
     ## Round steps up to nearest multiple of output_period, plus 1
@@ -154,13 +155,13 @@ def multiresolution_simulation( model, output_name,
 
         """ Minimization """
         if minimization_steps > 0:
-            simargs = dict(timestep=200e-6, output_period=minimization_output_period, gpu=gpu)
+            simargs = dict(timestep=200e-6, output_period=minimization_output_period, gpu=gpu, arbd=arbd)
             run_step(num_steps=minimization_steps, simargs=simargs)
             model.clear_beads()
             model.generate_bead_model( **coarse_model_args )
 
         """ Coarse simulation """
-        simargs = dict(timestep=100e-6 if coarse_local_twist else 200e-6, output_period=coarse_output_period, gpu=gpu)
+        simargs = dict(timestep=100e-6 if coarse_local_twist else 200e-6, output_period=coarse_output_period, gpu=gpu, arbd=arbd)
         if bond_cutoff > 0 and minimization_steps <= 0:
             run_step(num_steps=0.25*coarse_steps, simargs=simargs)
             model.clear_beads()
@@ -170,7 +171,7 @@ def multiresolution_simulation( model, output_name,
             run_step(num_steps=coarse_steps, simargs=simargs)
 
         """ Fine simulation """ 
-        simargs = dict(timestep=40e-6, output_period=fine_output_period, gpu=gpu)
+        simargs = dict(timestep=40e-6, output_period=fine_output_period, gpu=gpu, arbd=arbd)
         if not fix_linking_number:
             model.clear_beads()
             model.generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )