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tbgl
tools
mrdna
Commits
97bf7281
Commit
97bf7281
authored
Oct 21, 2021
by
cmaffeo2
Browse files
Add 'arbd' argument to model.simulate()
parent
e93e6468
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/simulate.py
View file @
97bf7281
...
...
@@ -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
)
...
...
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