From fe860000d4ff80e197c22b5f74936987d19a1e45 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 4 Sep 2018 17:29:39 -0500
Subject: [PATCH] Updated dnarbd script to better handle number-of-step
arguments such as '1e7'
---
bin/dnarbd | 8 ++++----
dnarbd/simulate.py | 4 ++--
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/bin/dnarbd b/bin/dnarbd
index 13b4026..95d921d 100755
--- a/bin/dnarbd
+++ b/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
)
diff --git a/dnarbd/simulate.py b/dnarbd/simulate.py
index 7805f08..011fb7a 100644
--- a/dnarbd/simulate.py
+++ b/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()
--
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