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nomad-lab
soap-plus-plus
Commits
bb674c8c
Commit
bb674c8c
authored
8 years ago
by
Carl Poelking
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Plain Diff
Utilities.
parent
926cd6dd
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Changes
2
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2 changed files
src/soap/soapy/util.py
+19
-4
19 additions, 4 deletions
src/soap/soapy/util.py
src/soap/tools/loadwrite.py
+2
-2
2 additions, 2 deletions
src/soap/tools/loadwrite.py
with
21 additions
and
6 deletions
src/soap/soapy/util.py
+
19
−
4
View file @
bb674c8c
...
@@ -66,6 +66,19 @@ def mp_compute_column_block(gi, gj_list, kfct):
...
@@ -66,6 +66,19 @@ def mp_compute_column_block(gi, gj_list, kfct):
krow
.
append
(
k
)
krow
.
append
(
k
)
return
krow
return
krow
def
mp_compute_column_block_idx
(
gi
,
gj_list
,
kfct
):
"""
Evaluates kfct for each pair (i, j), with j from j_list
"""
krow
=
[]
for
gj
in
gj_list
:
if
gj
<
gi
:
k
=
0.
else
:
k
=
kfct
(
gi
,
gj
)
krow
.
append
(
k
)
return
krow
def
compute_upper_triangle
(
def
compute_upper_triangle
(
kfct
,
kfct
,
g_list
,
g_list
,
...
@@ -79,7 +92,7 @@ def compute_upper_triangle(
...
@@ -79,7 +92,7 @@ def compute_upper_triangle(
gi
=
g_list
[
i
]
gi
=
g_list
[
i
]
for
j
in
range
(
i
,
dim
):
for
j
in
range
(
i
,
dim
):
gj
=
g_list
[
j
]
gj
=
g_list
[
j
]
kij
=
kfct
(
gi
,
gj
)
kij
=
kfct
_primed
(
gi
,
gj
)
kmat
[
i
,
j
]
=
kij
kmat
[
i
,
j
]
=
kij
kmat
[
j
,
i
]
=
kij
kmat
[
j
,
i
]
=
kij
return
kmat
return
kmat
...
@@ -93,6 +106,7 @@ def mp_compute_upper_triangle(
...
@@ -93,6 +106,7 @@ def mp_compute_upper_triangle(
tstart_twall
=
(
None
,
None
),
tstart_twall
=
(
None
,
None
),
backup
=
True
,
backup
=
True
,
verbose
=
True
,
verbose
=
True
,
embed_idx
=
True
,
**
kwargs
):
**
kwargs
):
"""
"""
Compute kernel matrix computed from pairs of objects in object list
Compute kernel matrix computed from pairs of objects in object list
...
@@ -110,8 +124,9 @@ def mp_compute_upper_triangle(
...
@@ -110,8 +124,9 @@ def mp_compute_upper_triangle(
t_wall
=
tstart_twall
[
1
]
t_wall
=
tstart_twall
[
1
]
dim
=
len
(
g_list
)
dim
=
len
(
g_list
)
kmat
=
np
.
zeros
((
dim
,
dim
))
kmat
=
np
.
zeros
((
dim
,
dim
))
# Embed mp index in g-list objects
if
embed_idx
:
for
mp_idx
,
g
in
enumerate
(
g_list
):
g
.
mp_idx
=
mp_idx
# Embed mp index in g-list objects
for
mp_idx
,
g
in
enumerate
(
g_list
):
g
.
mp_idx
=
mp_idx
# Divide onto column blocks
# Divide onto column blocks
col_idcs
=
np
.
arange
(
len
(
g_list
))
col_idcs
=
np
.
arange
(
len
(
g_list
))
col_div_list
=
np
.
array_split
(
col_idcs
,
n_blocks
)
col_div_list
=
np
.
array_split
(
col_idcs
,
n_blocks
)
...
@@ -130,7 +145,7 @@ def mp_compute_upper_triangle(
...
@@ -130,7 +145,7 @@ def mp_compute_upper_triangle(
pool
=
mp
.
Pool
(
processes
=
n_procs
)
pool
=
mp
.
Pool
(
processes
=
n_procs
)
# Prime mp function
# Prime mp function
mp_compute_column_block_primed
=
fct
.
partial
(
mp_compute_column_block_primed
=
fct
.
partial
(
mp_compute_column_block
,
mp_compute_column_block
if
embed_idx
else
mp_compute_column_block_idx
,
gj_list
=
gj_list
,
gj_list
=
gj_list
,
kfct
=
kfct_primed
)
kfct
=
kfct_primed
)
# Map & close
# Map & close
...
...
This diff is collapsed.
Click to expand it.
src/soap/tools/loadwrite.py
+
2
−
2
View file @
bb674c8c
...
@@ -46,8 +46,8 @@ def structure_from_ase(
...
@@ -46,8 +46,8 @@ def structure_from_ase(
log
=
None
):
log
=
None
):
# NOTE Center of mass is computed without considering PBC => Requires unwrapped coordinates
# NOTE Center of mass is computed without considering PBC => Requires unwrapped coordinates
structure
=
None
structure
=
None
frag_bond_matrix
=
None
frag_bond_matrix
=
np
.
array
([],
dtype
=
bool
)
atom_bond_matrix
=
None
atom_bond_matrix
=
np
.
array
([],
dtype
=
bool
)
frag_labels
=
[]
frag_labels
=
[]
atom_labels
=
[]
atom_labels
=
[]
# System properties
# System properties
...
...
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Click to expand it.
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