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SParTA
PuReMD
Commits
4b21e4ec
Commit
4b21e4ec
authored
3 years ago
by
Kurt A. O'Hearn
Browse files
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Plain Diff
Tools: update Python example driver code.
parent
9d87c5b6
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Changes
2
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2 changed files
tools/driver.py
+9
-3
9 additions, 3 deletions
tools/driver.py
tools/driver_qmmm.py
+122
-78
122 additions, 78 deletions
tools/driver_qmmm.py
with
131 additions
and
81 deletions
tools/driver.py
+
9
−
3
View file @
4b21e4ec
...
@@ -200,9 +200,10 @@ class SimulationData(Structure):
...
@@ -200,9 +200,10 @@ class SimulationData(Structure):
(
"
iso_bar
"
,
IsotropicBarostat
),
(
"
iso_bar
"
,
IsotropicBarostat
),
(
"
flex_bar
"
,
FlexibleBarostat
),
(
"
flex_bar
"
,
FlexibleBarostat
),
(
"
inv_W
"
,
c_double
),
(
"
inv_W
"
,
c_double
),
(
"
int_press
"
,
c_double
*
3
),
# requires OpenMP enabled
(
"
ext_press
"
,
c_double
*
3
),
(
"
press_local
"
,
c_double
*
9
),
(
"
kin_press
"
,
c_double
),
(
"
press
"
,
c_double
*
9
),
(
"
kin_press
"
,
c_double
*
9
),
(
"
tot_press
"
,
c_double
*
3
),
(
"
tot_press
"
,
c_double
*
3
),
(
"
timing
"
,
ReaxTiming
),
(
"
timing
"
,
ReaxTiming
),
]
]
...
@@ -211,12 +212,17 @@ class SimulationData(Structure):
...
@@ -211,12 +212,17 @@ class SimulationData(Structure):
class
ReaxAtom
(
Structure
):
class
ReaxAtom
(
Structure
):
_fields_
=
[
_fields_
=
[
(
"
type
"
,
c_int
),
(
"
type
"
,
c_int
),
(
"
is_dummy
"
,
c_int
),
(
"
rel_map
"
,
c_int
*
3
),
(
"
rel_map
"
,
c_int
*
3
),
(
"
name
"
,
c_char
*
9
),
(
"
name
"
,
c_char
*
9
),
(
"
x
"
,
c_double
*
3
),
(
"
x
"
,
c_double
*
3
),
(
"
v
"
,
c_double
*
3
),
(
"
v
"
,
c_double
*
3
),
(
"
f
"
,
c_double
*
3
),
(
"
f
"
,
c_double
*
3
),
(
"
q
"
,
c_double
),
(
"
q
"
,
c_double
),
# requires QM/MM support enabled
#("qmmm_mask", c_int),
# requires QM/MM support enabled
#("q_init", c_double),
]
]
...
...
This diff is collapsed.
Click to expand it.
tools/driver_qmmm.py
+
122
−
78
View file @
4b21e4ec
...
@@ -200,9 +200,10 @@ class SimulationData(Structure):
...
@@ -200,9 +200,10 @@ class SimulationData(Structure):
(
"
iso_bar
"
,
IsotropicBarostat
),
(
"
iso_bar
"
,
IsotropicBarostat
),
(
"
flex_bar
"
,
FlexibleBarostat
),
(
"
flex_bar
"
,
FlexibleBarostat
),
(
"
inv_W
"
,
c_double
),
(
"
inv_W
"
,
c_double
),
(
"
int_press
"
,
c_double
*
3
),
# requires OpenMP enabled
(
"
ext_press
"
,
c_double
*
3
),
(
"
press_local
"
,
c_double
*
9
),
(
"
kin_press
"
,
c_double
),
(
"
press
"
,
c_double
*
9
),
(
"
kin_press
"
,
c_double
*
9
),
(
"
tot_press
"
,
c_double
*
3
),
(
"
tot_press
"
,
c_double
*
3
),
(
"
timing
"
,
ReaxTiming
),
(
"
timing
"
,
ReaxTiming
),
]
]
...
@@ -211,12 +212,17 @@ class SimulationData(Structure):
...
@@ -211,12 +212,17 @@ class SimulationData(Structure):
class
ReaxAtom
(
Structure
):
class
ReaxAtom
(
Structure
):
_fields_
=
[
_fields_
=
[
(
"
type
"
,
c_int
),
(
"
type
"
,
c_int
),
(
"
is_dummy
"
,
c_int
),
(
"
rel_map
"
,
c_int
*
3
),
(
"
rel_map
"
,
c_int
*
3
),
(
"
name
"
,
c_char
*
9
),
(
"
name
"
,
c_char
*
9
),
(
"
x
"
,
c_double
*
3
),
(
"
x
"
,
c_double
*
3
),
(
"
v
"
,
c_double
*
3
),
(
"
v
"
,
c_double
*
3
),
(
"
f
"
,
c_double
*
3
),
(
"
f
"
,
c_double
*
3
),
(
"
q
"
,
c_double
),
(
"
q
"
,
c_double
),
# requires QM/MM support enabled
(
"
qmmm_mask
"
,
c_int
),
# requires QM/MM support enabled
(
"
q_init
"
,
c_double
),
]
]
...
@@ -358,12 +364,10 @@ def create_db(name='spuremd.db'):
...
@@ -358,12 +364,10 @@ def create_db(name='spuremd.db'):
if
__name__
==
'
__main__
'
:
if
__name__
==
'
__main__
'
:
lib
=
cdll
.
LoadLibrary
(
"
libspuremd.so.1
"
)
lib
=
cdll
.
LoadLibrary
(
"
libspuremd.so.1
"
)
setup_qmmm
=
lib
.
setup_qmmm_
setup_qmmm
=
lib
.
setup_qmmm
setup_qmmm
.
argtypes
=
[
c_int
,
POINTER
(
c_int
),
setup_qmmm
.
argtypes
=
[
c_int
,
c_char_p
,
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
c_int
,
c_char_p
,
POINTER
(
c_double
),
c_int
,
POINTER
(
c_int
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
c_char_p
,
c_char_p
]
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
c_char_p
,
c_char_p
]
setup_qmmm
.
restype
=
c_void_p
setup_qmmm
.
restype
=
c_void_p
simulate
=
lib
.
simulate
simulate
=
lib
.
simulate
...
@@ -374,12 +378,10 @@ if __name__ == '__main__':
...
@@ -374,12 +378,10 @@ if __name__ == '__main__':
cleanup
.
argtypes
=
[
c_void_p
]
cleanup
.
argtypes
=
[
c_void_p
]
cleanup
.
restype
=
c_int
cleanup
.
restype
=
c_int
reset_qmmm
=
lib
.
reset_qmmm_
reset_qmmm
=
lib
.
reset_qmmm
reset_qmmm
.
argtypes
=
[
c_void_p
,
c_int
,
POINTER
(
c_int
),
reset_qmmm
.
argtypes
=
[
c_void_p
,
c_int
,
c_char_p
,
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
c_int
,
c_char_p
,
POINTER
(
c_double
),
c_int
,
POINTER
(
c_int
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
c_char_p
,
c_char_p
]
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
c_char_p
,
c_char_p
]
reset_qmmm
.
restype
=
c_int
reset_qmmm
.
restype
=
c_int
CALLBACKFUNC
=
CFUNCTYPE
(
None
,
c_int
,
POINTER
(
ReaxAtom
),
CALLBACKFUNC
=
CFUNCTYPE
(
None
,
c_int
,
POINTER
(
ReaxAtom
),
...
@@ -393,19 +395,15 @@ if __name__ == '__main__':
...
@@ -393,19 +395,15 @@ if __name__ == '__main__':
set_control_parameter
.
argtypes
=
[
c_void_p
,
c_char_p
,
POINTER
(
c_char_p
)]
set_control_parameter
.
argtypes
=
[
c_void_p
,
c_char_p
,
POINTER
(
c_char_p
)]
set_control_parameter
.
restype
=
c_int
set_control_parameter
.
restype
=
c_int
get_atom_positions_qmmm
=
lib
.
get_atom_positions_qmmm_
get_atom_positions_qmmm
=
lib
.
get_atom_positions_qmmm
get_atom_positions_qmmm
.
argtypes
=
[
c_void_p
,
get_atom_positions_qmmm
.
argtypes
=
[
c_void_p
,
POINTER
(
c_double
),
POINTER
(
c_double
)]
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
)]
get_atom_positions_qmmm
.
restype
=
c_int
get_atom_positions_qmmm
.
restype
=
c_int
get_atom_forces_qmmm
=
lib
.
get_atom_forces_qmmm_
get_atom_forces_qmmm
=
lib
.
get_atom_forces_qmmm
get_atom_forces_qmmm
.
argtypes
=
[
c_void_p
,
get_atom_forces_qmmm
.
argtypes
=
[
c_void_p
,
POINTER
(
c_double
),
POINTER
(
c_double
)]
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
),
POINTER
(
c_double
)]
get_atom_forces_qmmm
.
restype
=
c_int
get_atom_forces_qmmm
.
restype
=
c_int
get_atom_charges_qmmm
=
lib
.
get_atom_charges_qmmm
_
get_atom_charges_qmmm
=
lib
.
get_atom_charges_qmmm
get_atom_charges_qmmm
.
argtypes
=
[
c_void_p
,
POINTER
(
c_double
),
POINTER
(
c_double
)]
get_atom_charges_qmmm
.
argtypes
=
[
c_void_p
,
POINTER
(
c_double
),
POINTER
(
c_double
)]
get_atom_charges_qmmm
.
restype
=
c_int
get_atom_charges_qmmm
.
restype
=
c_int
...
@@ -418,18 +416,33 @@ if __name__ == '__main__':
...
@@ -418,18 +416,33 @@ if __name__ == '__main__':
num_qm_atoms
=
10
num_qm_atoms
=
10
num_mm_atoms
=
10
num_mm_atoms
=
10
num_atoms
=
num_qm_atoms
+
num_mm_atoms
num_atoms
=
num_qm_atoms
+
num_mm_atoms
qm_types
=
(
c_int
*
num_qm_atoms
)(
2
,
1
,
1
,
2
,
1
,
1
,
2
,
1
,
1
,
2
)
qm_types
=
''
.
join
(
'
{0:<2}
'
.
format
(
s
)
for
s
in
[
'
H
'
,
'
O
'
,
'
O
'
,
'
H
'
,
'
O
'
,
'
O
'
,
'
H
'
,
'
O
'
,
'
O
'
,
'
H
'
]).
encode
(
'
utf-8
'
)
qm_p_x
=
(
c_double
*
num_qm_atoms
)(
5.690
,
4.760
,
5.800
,
15.551
,
14.981
,
14.961
,
17.431
,
17.761
,
17.941
,
11.351
)
# (x-position, y-position, z-position) atom tuples (units of Angstroms)
qm_p_y
=
(
c_double
*
num_qm_atoms
)(
12.751
,
12.681
,
13.641
,
15.111
,
14.951
,
15.211
,
6.180
,
7.120
,
5.640
,
7.030
)
qm_p
=
(
c_double
*
(
3
*
num_qm_atoms
))(
5.690
,
12.751
,
11.651
,
qm_p_z
=
(
c_double
*
num_qm_atoms
)(
11.651
,
11.281
,
12.091
,
7.030
,
7.840
,
6.230
,
8.560
,
8.560
,
9.220
,
7.170
)
4.760
,
12.681
,
11.281
,
mm_types
=
(
c_int
*
num_qm_atoms
)(
1
,
1
,
2
,
1
,
1
,
2
,
1
,
1
,
2
,
1
)
5.800
,
13.641
,
12.091
,
mm_p_x
=
(
c_double
*
num_mm_atoms
)(
11.921
,
10.751
,
17.551
,
17.431
,
17.251
,
7.680
,
6.900
,
8.020
,
8.500
,
8.460
)
15.551
,
15.111
,
7.030
,
mm_p_y
=
(
c_double
*
num_mm_atoms
)(
7.810
,
7.290
,
6.070
,
5.940
,
5.260
,
11.441
,
11.611
,
12.311
,
7.980
,
8.740
)
14.981
,
14.951
,
7.840
,
mm_p_z
=
(
c_double
*
num_mm_atoms
)(
6.920
,
7.930
,
2.310
,
1.320
,
2.800
,
10.231
,
10.831
,
9.871
,
18.231
,
18.881
)
14.961
,
15.211
,
6.230
,
mm_q
=
(
c_double
*
num_mm_atoms
)(
-
2.0
,
1.0
,
1.0
,
-
2.0
,
1.0
,
1.0
,
-
2.0
,
1.0
,
1.0
,
-
2.0
)
17.431
,
6.180
,
8.560
,
17.761
,
7.120
,
8.560
,
handle
=
setup_qmmm
(
c_int
(
num_qm_atoms
),
qm_types
,
qm_p_x
,
qm_p_y
,
qm_p_z
,
17.941
,
5.640
,
9.220
,
c_int
(
num_mm_atoms
),
mm_types
,
mm_p_x
,
mm_p_y
,
mm_p_z
,
mm_q
,
sim_box
,
11.351
,
7.030
,
7.170
)
mm_types
=
''
.
join
(
'
{0:<2}
'
.
format
(
s
)
for
s
in
[
'
O
'
,
'
O
'
,
'
H
'
,
'
O
'
,
'
O
'
,
'
H
'
,
'
O
'
,
'
O
'
,
'
H
'
,
'
O
'
]).
encode
(
'
utf-8
'
)
# (x-position, y-position, z-position, charge) atom tuples (units of Angstroms / Coulombs)
mm_p_q
=
(
c_double
*
(
4
*
num_mm_atoms
))(
11.921
,
7.810
,
6.920
,
-
2.0
,
10.751
,
7.290
,
7.930
,
1.0
,
17.551
,
6.070
,
2.310
,
1.0
,
17.431
,
5.940
,
1.320
,
-
2.0
,
17.251
,
5.260
,
2.800
,
1.0
,
7.680
,
11.441
,
10.231
,
1.0
,
6.900
,
11.611
,
10.831
,
-
2.0
,
8.020
,
12.311
,
9.871
,
1.0
,
8.500
,
7.980
,
18.231
,
1.0
,
8.460
,
8.740
,
18.881
,
-
2.0
)
handle
=
setup_qmmm
(
c_int
(
num_qm_atoms
),
qm_types
,
qm_p
,
c_int
(
num_mm_atoms
),
mm_types
,
mm_p_q
,
sim_box
,
b
"
data/benchmarks/water/ffield.water
"
,
b
"
data/benchmarks/water/ffield.water
"
,
b
"
environ/control_water
"
)
b
"
environ/control_water
"
)
...
@@ -442,6 +455,13 @@ if __name__ == '__main__':
...
@@ -442,6 +455,13 @@ if __name__ == '__main__':
values
=
(
c_char_p
)(
b
"
10
"
)
values
=
(
c_char_p
)(
b
"
10
"
)
ret
=
set_control_parameter
(
handle
,
keyword
,
values
)
ret
=
set_control_parameter
(
handle
,
keyword
,
values
)
if
ret
!=
0
:
print
(
"
[ERROR] set_control_parameter returned {0}
"
.
format
(
ret
))
keyword
=
b
"
charge_method
"
values
=
(
c_char_p
)(
b
"
1
"
)
ret
=
set_control_parameter
(
handle
,
keyword
,
values
)
if
ret
!=
0
:
if
ret
!=
0
:
print
(
"
[ERROR] set_control_parameter returned {0}
"
.
format
(
ret
))
print
(
"
[ERROR] set_control_parameter returned {0}
"
.
format
(
ret
))
...
@@ -452,25 +472,16 @@ if __name__ == '__main__':
...
@@ -452,25 +472,16 @@ if __name__ == '__main__':
if
ret
!=
0
:
if
ret
!=
0
:
print
(
"
[ERROR] simulate returned {0}
"
.
format
(
ret
))
print
(
"
[ERROR] simulate returned {0}
"
.
format
(
ret
))
qm_p_x
=
(
c_double
*
num_qm_atoms
)()
qm_p
=
(
c_double
*
(
3
*
num_qm_atoms
))()
qm_p_y
=
(
c_double
*
num_qm_atoms
)()
mm_p
=
(
c_double
*
(
3
*
num_mm_atoms
))()
qm_p_z
=
(
c_double
*
num_qm_atoms
)()
ret
=
get_atom_positions_qmmm
(
handle
,
qm_p
,
mm_p
)
mm_p_x
=
(
c_double
*
num_mm_atoms
)()
mm_p_y
=
(
c_double
*
num_mm_atoms
)()
mm_p_z
=
(
c_double
*
num_mm_atoms
)()
ret
=
get_atom_positions_qmmm
(
handle
,
qm_p_x
,
qm_p_y
,
qm_p_z
,
mm_p_x
,
mm_p_y
,
mm_p_z
)
if
ret
!=
0
:
if
ret
!=
0
:
print
(
"
[ERROR] get_atom_positions_qmmm returned {0}
"
.
format
(
ret
))
print
(
"
[ERROR] get_atom_positions_qmmm returned {0}
"
.
format
(
ret
))
qm_f_x
=
(
c_double
*
num_qm_atoms
)()
qm_f
=
(
c_double
*
(
3
*
num_qm_atoms
))()
qm_f_y
=
(
c_double
*
num_qm_atoms
)()
mm_f
=
(
c_double
*
(
3
*
num_mm_atoms
))()
qm_f_z
=
(
c_double
*
num_qm_atoms
)()
ret
=
get_atom_forces_qmmm
(
handle
,
qm_f
,
mm_f
)
mm_f_x
=
(
c_double
*
num_mm_atoms
)()
mm_f_y
=
(
c_double
*
num_mm_atoms
)()
mm_f_z
=
(
c_double
*
num_mm_atoms
)()
ret
=
get_atom_forces_qmmm
(
handle
,
qm_f_x
,
qm_f_y
,
qm_f_z
,
mm_f_x
,
mm_f_y
,
mm_f_z
)
if
ret
!=
0
:
if
ret
!=
0
:
print
(
"
[ERROR] get_atom_forces_qmmm returned {0}
"
.
format
(
ret
))
print
(
"
[ERROR] get_atom_forces_qmmm returned {0}
"
.
format
(
ret
))
...
@@ -487,21 +498,63 @@ if __name__ == '__main__':
...
@@ -487,21 +498,63 @@ if __name__ == '__main__':
num_qm_atoms
=
15
num_qm_atoms
=
15
num_mm_atoms
=
15
num_mm_atoms
=
15
num_atoms
=
num_qm_atoms
+
num_mm_atoms
num_atoms
=
num_qm_atoms
+
num_mm_atoms
qm_types
=
(
c_int
*
num_qm_atoms
)(
2
,
2
,
2
,
2
,
10
,
2
,
10
,
2
,
2
,
10
,
2
,
10
,
2
,
2
)
qm_types
=
''
.
join
(
'
{0:<2}
'
.
format
(
s
)
for
s
in
[
'
O
'
,
'
O
'
,
'
O
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
O
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
O
'
]).
encode
(
'
utf-8
'
)
qm_p_x
=
(
c_double
*
num_qm_atoms
)(
56.987
,
32.795
,
26.543
,
27.616
,
26.560
,
54.035
,
54.425
,
29.979
,
38.008
,
48.769
,
57.113
,
26.458
,
52.299
,
55.789
,
45.752
)
# (x-position, y-position, z-position) atom tuples (units of Angstroms)
qm_p_y
=
(
c_double
*
num_qm_atoms
)(
39.868
,
24.104
,
26.261
,
27.534
,
39.146
,
39.112
,
37.117
,
43.558
,
47.170
,
42.454
,
35.565
,
35.477
,
39.113
,
41.444
,
44.237
)
qm_p
=
(
c_double
*
(
3
*
num_qm_atoms
))(
56.987
,
39.868
,
41.795
,
qm_p_z
=
(
c_double
*
num_qm_atoms
)(
41.795
,
25.968
,
36.254
,
24.459
,
32.281
,
23.745
,
32.278
,
21.696
,
27.275
,
20.461
,
31.366
,
23.522
,
26.519
,
30.466
,
10.521
)
32.795
,
24.104
,
25.968
,
mm_types
=
(
c_int
*
num_qm_atoms
)(
10
,
2
,
10
,
2
,
2
,
2
,
10
,
2
,
10
,
2
,
2
,
10
,
2
,
2
,
10
)
26.543
,
26.261
,
36.254
,
mm_p_x
=
(
c_double
*
num_mm_atoms
)(
49.617
,
26.736
,
58.166
,
36.655
,
55.773
,
53.905
,
52.254
,
32.196
,
53.817
,
56.164
,
28.678
,
58.824
,
24.807
,
51.299
,
28.950
)
27.616
,
27.534
,
24.459
,
mm_p_y
=
(
c_double
*
num_mm_atoms
)(
42.379
,
37.815
,
5.488
,
48.615
,
36.249
,
1.450
,
35.399
,
6.595
,
8.586
,
1.585
,
7.208
,
36.067
,
6.365
,
25.234
,
11.190
)
26.560
,
39.146
,
32.281
,
mm_p_z
=
(
c_double
*
num_mm_atoms
)(
21.790
,
33.119
,
0.945
,
25.664
,
31.954
,
22.720
,
33.665
,
23.147
,
31.684
,
23.550
,
30.801
,
40.036
,
24.849
,
29.146
,
24.542
)
54.035
,
39.112
,
23.745
,
mm_q
=
(
c_double
*
num_mm_atoms
)(
-
1.0
,
-
2.0
,
-
1.0
,
-
2.0
,
-
2.0
,
-
2.0
,
-
1.0
,
-
2.0
,
-
1.0
,
-
2.0
,
-
2.0
,
-
1.0
,
-
2.0
,
-
2.0
,
-
1.0
)
54.425
,
37.117
,
32.278
,
29.979
,
43.558
,
21.696
,
ret
=
reset_qmmm
(
handle
,
c_int
(
num_qm_atoms
),
qm_types
,
qm_p_x
,
qm_p_y
,
qm_p_z
,
38.008
,
47.170
,
27.275
,
c_int
(
num_mm_atoms
),
mm_types
,
mm_p_x
,
mm_p_y
,
mm_p_z
,
mm_q
,
sim_box
,
48.769
,
42.454
,
20.461
,
57.113
,
35.565
,
31.366
,
26.458
,
35.477
,
23.522
,
52.299
,
39.113
,
26.519
,
55.789
,
41.444
,
30.466
,
45.752
,
44.237
,
10.521
)
mm_types
=
''
.
join
(
'
{0:<2}
'
.
format
(
s
)
for
s
in
[
'
Si
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
O
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
O
'
,
'
Si
'
,
'
O
'
,
'
O
'
,
'
Si
'
]).
encode
(
'
utf-8
'
)
# (x-position, y-position, z-position, charge) atom tuples (units of Angstroms / Coulombs)
mm_p_q
=
(
c_double
*
(
4
*
num_mm_atoms
))(
49.617
,
42.379
,
21.790
,
-
1.0
,
26.736
,
37.815
,
33.119
,
-
2.0
,
58.166
,
5.488
,
0.945
,
-
1.0
,
36.655
,
48.615
,
25.664
,
-
2.0
,
55.773
,
36.249
,
31.954
,
-
2.0
,
53.905
,
1.450
,
22.720
,
-
2.0
,
52.254
,
35.399
,
33.665
,
-
1.0
,
32.196
,
6.595
,
23.147
,
-
2.0
,
53.817
,
8.586
,
31.684
,
-
1.0
,
56.164
,
1.585
,
23.550
,
-
2.0
,
28.678
,
7.208
,
30.801
,
-
2.0
,
58.824
,
36.067
,
40.036
,
-
1.0
,
24.807
,
6.365
,
24.849
,
-
2.0
,
51.299
,
25.234
,
29.146
,
-
2.0
,
28.950
,
11.190
,
24.542
,
-
1.0
)
ret
=
reset_qmmm
(
handle
,
c_int
(
num_qm_atoms
),
qm_types
,
qm_p
,
c_int
(
num_mm_atoms
),
mm_types
,
mm_p_q
,
sim_box
,
b
"
data/benchmarks/silica/ffield-bio
"
,
b
"
data/benchmarks/silica/ffield-bio
"
,
b
"
environ/control_silica
"
)
b
"
environ/control_silica
"
)
if
ret
!=
0
:
print
(
"
[ERROR] reset_qmmm returned {0}
"
.
format
(
ret
))
keyword
=
b
"
nsteps
"
values
=
(
c_char_p
)(
b
"
10
"
)
ret
=
set_control_parameter
(
handle
,
keyword
,
values
)
if
ret
!=
0
:
print
(
"
[ERROR] set_control_parameter returned {0}
"
.
format
(
ret
))
keyword
=
b
"
charge_method
"
values
=
(
c_char_p
)(
b
"
1
"
)
ret
=
set_control_parameter
(
handle
,
keyword
,
values
)
if
ret
!=
0
:
print
(
"
[ERROR] set_control_parameter returned {0}
"
.
format
(
ret
))
print
(
"
\n
{0:24}|{1:24}|{2:24}
"
.
format
(
"
Total Energy
"
,
"
Kinetic Energy
"
,
"
Potential Energy
"
))
print
(
"
\n
{0:24}|{1:24}|{2:24}
"
.
format
(
"
Total Energy
"
,
"
Kinetic Energy
"
,
"
Potential Energy
"
))
ret
=
simulate
(
handle
)
ret
=
simulate
(
handle
)
...
@@ -509,25 +562,16 @@ if __name__ == '__main__':
...
@@ -509,25 +562,16 @@ if __name__ == '__main__':
if
ret
!=
0
:
if
ret
!=
0
:
print
(
"
[ERROR] simulate returned {0}
"
.
format
(
ret
))
print
(
"
[ERROR] simulate returned {0}
"
.
format
(
ret
))
qm_p_x
=
(
c_double
*
num_qm_atoms
)()
qm_p
=
(
c_double
*
(
3
*
num_qm_atoms
))()
qm_p_y
=
(
c_double
*
num_qm_atoms
)()
mm_p
=
(
c_double
*
(
3
*
num_mm_atoms
))()
qm_p_z
=
(
c_double
*
num_qm_atoms
)()
ret
=
get_atom_positions_qmmm
(
handle
,
qm_p
,
mm_p
)
mm_p_x
=
(
c_double
*
num_mm_atoms
)()
mm_p_y
=
(
c_double
*
num_mm_atoms
)()
mm_p_z
=
(
c_double
*
num_mm_atoms
)()
ret
=
get_atom_positions_qmmm
(
handle
,
qm_p_x
,
qm_p_y
,
qm_p_z
,
mm_p_x
,
mm_p_y
,
mm_p_z
)
if
ret
!=
0
:
if
ret
!=
0
:
print
(
"
[ERROR] get_atom_positions_qmmm returned {0}
"
.
format
(
ret
))
print
(
"
[ERROR] get_atom_positions_qmmm returned {0}
"
.
format
(
ret
))
qm_f_x
=
(
c_double
*
num_qm_atoms
)()
qm_f
=
(
c_double
*
(
3
*
num_qm_atoms
))()
qm_f_y
=
(
c_double
*
num_qm_atoms
)()
mm_f
=
(
c_double
*
(
3
*
num_mm_atoms
))()
qm_f_z
=
(
c_double
*
num_qm_atoms
)()
ret
=
get_atom_forces_qmmm
(
handle
,
qm_f
,
mm_f
)
mm_f_x
=
(
c_double
*
num_mm_atoms
)()
mm_f_y
=
(
c_double
*
num_mm_atoms
)()
mm_f_z
=
(
c_double
*
num_mm_atoms
)()
ret
=
get_atom_forces_qmmm
(
handle
,
qm_f_x
,
qm_f_y
,
qm_f_z
,
mm_f_x
,
mm_f_y
,
mm_f_z
)
if
ret
!=
0
:
if
ret
!=
0
:
print
(
"
[ERROR] get_atom_forces_qmmm returned {0}
"
.
format
(
ret
))
print
(
"
[ERROR] get_atom_forces_qmmm returned {0}
"
.
format
(
ret
))
...
...
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