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nomad-lab
analytics-tools-forcefield
Commits
cd4f4f8f
Commit
cd4f4f8f
authored
Jan 26, 2017
by
Adam Fekete
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update notebook part 1
parent
5a1be7b2
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4
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712 additions
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598 deletions
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-598
.gitignore
.gitignore
+3
-0
notebook/FF-fit.bkr
notebook/FF-fit.bkr
+458
-333
notebook/FF-fit_adam.bkr
notebook/FF-fit_adam.bkr
+215
-260
read_lammps_data.py
read_lammps_data.py
+36
-5
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.gitignore
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cd4f4f8f
...
...
@@ -36,3 +36,6 @@ syntax: glob
#emacs TAGS
TAGS
.idea
notebook/FF-fit_adam.bkr
notebook/FF-fit_aldo.bkr
notebook/FF-fit.bkr
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cd4f4f8f
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notebook/FF-fit_adam.bkr
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read_lammps_data.py
View file @
cd4f4f8f
...
...
@@ -17,18 +17,46 @@ class TimeStep(object):
import
ase
atoms
=
ase
.
atoms
.
Atoms
(
'Si'
,
positions
=
self
.
confs
,
'Si'
*
len
(
self
.
confs
)
,
positions
=
np
.
asarray
(
self
.
confs
,
dtype
=
np
.
float
)
,
cell
=
[
self
.
xhi
-
self
.
xlo
,
self
.
yhi
-
self
.
xlo
,
self
.
zhi
-
self
.
zlo
],
pbc
=
[
1
,
1
,
1
],
)
N
=
207
num_lines
=
sum
(
1
for
line
in
open
(
'disloiron.xyz'
))
steps
=
100
# num_lines/(N+2)
# N = 207
# num_lines = sum(1 for line in open('disloiron.xyz'))
# steps = 100 # num_lines/(N+2)
N
=
len
(
self
.
confs
)
r_cut
=
5
# 3.5 4.4
cutoffs
=
np
.
ones
(
len
(
atoms
))
*
r_cut
/
2.
nl
=
NeighborList
(
cutoffs
,
skin
=
0.
,
sorted
=
False
,
self_interaction
=
False
,
bothways
=
True
)
nl
.
build
(
atoms
)
confs
=
[]
cell
=
atoms
.
get_cell
()
indices
,
offsets
=
nl
.
get_neighbors
(
0
)
offsets
=
np
.
dot
(
offsets
,
cell
)
conf
=
np
.
zeros
((
len
(
indices
),
3
))
for
i
,
(
a2
,
offset
)
in
enumerate
(
zip
(
indices
,
offsets
)):
d
=
atoms
.
positions
[
a2
]
+
offset
-
atoms
.
positions
[
0
]
conf
[
i
]
=
d
confs
.
append
(
conf
)
print
(
confs
)
cutoffs
=
np
.
ones
(
N
)
*
r_cut
/
2.
print
(
cutoffs
)
...
...
@@ -160,6 +188,9 @@ if __name__ == '__main__':
filename
=
'data-lammps/Silic_300/Si_300_dump.atom'
with
ReadLammpsDumpFile
(
filename
)
as
file
:
for
timestep
in
file
:
...
...
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