diff --git a/bin/dnarbd b/bin/dnarbd index 13b402675a02fdb77fce790c2da0092080ae9af5..95d921d9487e95f47c8954c297042bd668e7c772 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 7805f08a03d97941e823868d65b597a64bd7fc2c..011fb7a3a625c51dd3439e655d23d78ac82b4ea5 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()