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tbgl
tools
arbdmodel
Commits
02b65fe7
Commit
02b65fe7
authored
5 years ago
by
cmaffeo2
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Brought in changes from mrdna package to arbdmodel.py from commits 8dafa9f..205bb86
parent
5ed0da54
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arbdmodel/__init__.py
+21
-6
21 additions, 6 deletions
arbdmodel/__init__.py
with
21 additions
and
6 deletions
arbdmodel/__init__.py
+
21
−
6
View file @
02b65fe7
...
@@ -99,17 +99,21 @@ class Parent():
...
@@ -99,17 +99,21 @@ class Parent():
x
.
parent
=
None
x
.
parent
=
None
def
add_bond
(
self
,
i
,
j
,
bond
,
exclude
=
False
):
def
add_bond
(
self
,
i
,
j
,
bond
,
exclude
=
False
):
assert
(
i
is
not
j
)
## TODO: how to handle duplicating and cloning bonds
## TODO: how to handle duplicating and cloning bonds
# beads = [b for b in self]
# beads = [b for b in self]
# for b in (i,j): assert(b in beads)
# for b in (i,j): assert(b in beads)
self
.
bonds
.
append
(
(
i
,
j
,
bond
,
exclude
)
)
self
.
bonds
.
append
(
(
i
,
j
,
bond
,
exclude
)
)
def
add_angle
(
self
,
i
,
j
,
k
,
angle
):
def
add_angle
(
self
,
i
,
j
,
k
,
angle
):
assert
(
len
(
set
((
i
,
j
,
k
)))
==
3
)
# beads = [b for b in self]
# beads = [b for b in self]
# for b in (i,j,k): assert(b in beads)
# for b in (i,j,k): assert(b in beads)
self
.
angles
.
append
(
(
i
,
j
,
k
,
angle
)
)
self
.
angles
.
append
(
(
i
,
j
,
k
,
angle
)
)
def
add_dihedral
(
self
,
i
,
j
,
k
,
l
,
dihedral
):
def
add_dihedral
(
self
,
i
,
j
,
k
,
l
,
dihedral
):
assert
(
len
(
set
((
i
,
j
,
k
,
l
)))
==
4
)
# beads = [b for b in self]
# beads = [b for b in self]
# for b in (i,j,k,l): assert(b in beads)
# for b in (i,j,k,l): assert(b in beads)
self
.
dihedrals
.
append
(
(
i
,
j
,
k
,
l
,
dihedral
)
)
self
.
dihedrals
.
append
(
(
i
,
j
,
k
,
l
,
dihedral
)
)
...
@@ -326,6 +330,7 @@ class ParticleType():
...
@@ -326,6 +330,7 @@ class ParticleType():
def
__hash_key
(
self
):
def
__hash_key
(
self
):
l
=
[
self
.
name
,
self
.
charge
]
l
=
[
self
.
name
,
self
.
charge
]
for
keyval
in
sorted
(
self
.
__dict__
.
items
()):
for
keyval
in
sorted
(
self
.
__dict__
.
items
()):
if
isinstance
(
keyval
[
1
],
list
):
keyval
=
(
keyval
[
0
],
tuple
(
keyval
[
1
]))
l
.
extend
(
keyval
)
l
.
extend
(
keyval
)
return
tuple
(
l
)
return
tuple
(
l
)
...
@@ -622,7 +627,7 @@ class PdbModel(Transformable, Parent):
...
@@ -622,7 +627,7 @@ class PdbModel(Transformable, Parent):
class
ArbdModel
(
PdbModel
):
class
ArbdModel
(
PdbModel
):
def
__init__
(
self
,
children
,
dimensions
=
(
1000
,
1000
,
1000
),
temperature
=
291
,
timestep
=
50e-6
,
cutoff
=
50
,
decompPeriod
=
10000
,
pairlistDistance
=
None
,
nonbondedResolution
=
0.1
,
remove_duplicate_bonded_terms
=
True
):
def
__init__
(
self
,
children
,
dimensions
=
(
1000
,
1000
,
1000
),
temperature
=
291
,
timestep
=
50e-6
,
cutoff
=
50
,
decompPeriod
=
10000
,
pairlistDistance
=
None
,
nonbondedResolution
=
0.1
,
remove_duplicate_bonded_terms
=
True
,
extra_bd_file_lines
=
""
):
PdbModel
.
__init__
(
self
,
children
,
dimensions
,
remove_duplicate_bonded_terms
)
PdbModel
.
__init__
(
self
,
children
,
dimensions
,
remove_duplicate_bonded_terms
)
self
.
temperature
=
temperature
self
.
temperature
=
temperature
...
@@ -635,6 +640,8 @@ class ArbdModel(PdbModel):
...
@@ -635,6 +640,8 @@ class ArbdModel(PdbModel):
self
.
decompPeriod
=
decompPeriod
self
.
decompPeriod
=
decompPeriod
self
.
pairlistDistance
=
pairlistDistance
self
.
pairlistDistance
=
pairlistDistance
self
.
extra_bd_file_lines
=
extra_bd_file_lines
self
.
numParticles
=
0
self
.
numParticles
=
0
self
.
particles
=
[]
self
.
particles
=
[]
self
.
type_counts
=
None
self
.
type_counts
=
None
...
@@ -697,7 +704,7 @@ class ArbdModel(PdbModel):
...
@@ -697,7 +704,7 @@ class ArbdModel(PdbModel):
if
typeA
!=
typeB
:
if
typeA
!=
typeB
:
self
.
nbSchemes
.
append
(
(
nbScheme
,
typeB
,
typeA
)
)
self
.
nbSchemes
.
append
(
(
nbScheme
,
typeB
,
typeA
)
)
def
simulate
(
self
,
output_name
,
output_directory
=
'
output
'
,
num_steps
=
100000000
,
timestep
=
None
,
gpu
=
0
,
output_period
=
1e4
,
arbd
=
None
,
directory
=
'
.
'
,
replicas
=
1
):
def
simulate
(
self
,
output_name
,
output_directory
=
'
output
'
,
num_steps
=
100000000
,
timestep
=
None
,
gpu
=
0
,
output_period
=
1e4
,
arbd
=
None
,
directory
=
'
.
'
,
replicas
=
1
,
log_file
=
None
):
assert
(
type
(
gpu
)
is
int
)
assert
(
type
(
gpu
)
is
int
)
num_steps
=
int
(
num_steps
)
num_steps
=
int
(
num_steps
)
...
@@ -753,10 +760,16 @@ class ArbdModel(PdbModel):
...
@@ -753,10 +760,16 @@ class ArbdModel(PdbModel):
cmd
=
tuple
(
str
(
x
)
for
x
in
cmd
)
cmd
=
tuple
(
str
(
x
)
for
x
in
cmd
)
print
(
"
Running ARBD with: %s
"
%
"
"
.
join
(
cmd
))
print
(
"
Running ARBD with: %s
"
%
"
"
.
join
(
cmd
))
process
=
subprocess
.
Popen
(
cmd
,
stdout
=
subprocess
.
PIPE
,
universal_newlines
=
True
)
if
log_file
is
None
or
(
hasattr
(
log_file
,
'
write
'
)
and
callable
(
log_file
.
write
)):
for
line
in
process
.
stdout
:
fd
=
sys
.
stdout
if
log_file
is
None
else
log_file
sys
.
stdout
.
write
(
line
)
process
=
subprocess
.
Popen
(
cmd
,
stdout
=
subprocess
.
PIPE
,
universal_newlines
=
True
)
sys
.
stdout
.
flush
()
for
line
in
process
.
stdout
:
fd
.
write
(
line
)
fd
.
flush
()
else
:
with
open
(
log_file
,
'
w
'
)
as
fd
:
process
=
subprocess
.
Popen
(
cmd
,
stdout
=
log_file
,
universal_newlines
=
True
)
process
.
communicate
()
except
:
except
:
raise
raise
...
@@ -851,6 +864,8 @@ pairlistDistance {pairlistDistance}
...
@@ -851,6 +864,8 @@ pairlistDistance {pairlistDistance}
origin {originX} {originY} {originZ}
origin {originX} {originY} {originZ}
systemSize {dimX} {dimY} {dimZ}
systemSize {dimX} {dimY} {dimZ}
{extra_bd_file_lines}
\n
"""
.
format
(
**
params
))
\n
"""
.
format
(
**
params
))
## Write entries for each type of particle
## Write entries for each type of particle
...
...
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