Updated dnarbd script to better handle number-of-step arguments such as '1e7'

bin/dnarbd

@@ -15,9 +15,9 @@ parser.add_argument('-d','--directory', type=str,  default=None,
                     help='Directory for simulation; does not need to exist yet')
 parser.add_argument('-g','--gpu', type=int, default=0,
                     help='GPU for simulation; check nvidia-smi for availability')
-parser.add_argument('--coarse-steps', type=int, default=1e7,
+parser.add_argument('--coarse-steps', type=float, default=1e7,
                     help='Simulation steps for coarse model (200 fs/step)')
-parser.add_argument('--fine-steps', type=int, default=1e7,
+parser.add_argument('--fine-steps', type=float, default=1e7,
                     help='Simulation steps for fine model (50 fs/step)')
 parser.add_argument('--backbone-scale', type=float, default=1.0,
                     help='Factor to scale DNA backbone in atomic model; try 0.25 to avoid clashes for atomistic simulations')
@@ -59,8 +59,8 @@ if __name__ == '__main__':
         job_id = "job-" + prefix,
         directory = args.directory,
         gpu = args.gpu,
-        coarse_steps = args.coarse_steps,
-        fine_steps = args.fine_steps,
+        coarse_steps = int(args.coarse_steps),
+        fine_steps = int(args.fine_steps),
         backbone_scale = args.backbone_scale
     )
 

dnarbd/simulate.py

@@ -18,8 +18,8 @@ def multiresolution_simulation( model, output_name,
                             ):
 
     ## Round steps up to nearest multiple of output_period, plus 1
-    coarse_steps = ((coarse_steps//coarse_output_period)+1)*coarse_output_period+1
-    fine_steps = ((fine_steps//fine_output_period)+1)*fine_output_period+1
+    coarse_steps = ((coarse_steps+coarse_output_period-1)//coarse_output_period)*coarse_output_period+1
+    fine_steps = ((fine_steps+fine_output_period-1)//fine_output_period)*fine_output_period+1
 
     ret = None
     d_orig = os.getcwd()