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interpolate_coords.py
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Created
Sat, Sep 7, 05:12
Size
1 KB
Mime Type
text/x-python
Expires
Mon, Sep 9, 05:12 (2 d)
Engine
blob
Format
Raw Data
Handle
20601670
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rLAMMPS lammps
interpolate_coords.py
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#!/usr/bin/env python
err_msg
=
"""
Usage:
interpolate_coords.py Ndesired [scale] < coords_orig.raw > coords.raw
Example:
interpolate_coords.py 30118 3.0 < coords_orig.raw > coords.raw
# (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner.
# See the supplemental section of Naumova et al Science 2013, p 18.)
"""
import
sys
from
math
import
*
# Parse the argument list:
if
len
(
sys
.
argv
)
<=
1
:
sys
.
stderr
.
write
(
"Error:
\n\n
Typical Usage:
\n\n
"
+
err_msg
+
"
\n
"
)
exit
(
1
)
n_new
=
int
(
sys
.
argv
[
1
])
if
len
(
sys
.
argv
)
>
2
:
scale
=
float
(
sys
.
argv
[
2
])
else
:
scale
=
1.0
coords_orig
=
[]
lines
=
sys
.
stdin
.
readlines
()
for
line
in
lines
:
tokens
=
line
.
split
()
if
(
len
(
tokens
)
>
0
):
coords_orig
.
append
(
map
(
float
,
tokens
))
g_dim
=
len
(
tokens
)
n_orig
=
len
(
coords_orig
)
if
n_orig
<
2
:
sys
.
stderr
.
write
(
"Error:
\n\n
Input file contains less than two lines of coordinates
\n
"
)
exit
(
1
)
if
n_new
<
2
:
sys
.
stderr
.
write
(
"Error:
\n\n
Output file will contain less than two lines of coordinates
\n
"
)
exit
(
1
)
coords_new
=
[[
0.0
for
d
in
range
(
0
,
g_dim
)]
for
i
in
range
(
0
,
n_new
)]
for
i_new
in
range
(
0
,
n_new
):
I_orig
=
(
i_new
)
*
(
float
(
n_orig
-
1
)
/
float
(
n_new
-
1
))
i_orig
=
int
(
floor
(
I_orig
))
i_remainder
=
I_orig
-
i_orig
if
(
i_new
<
n_new
-
1
):
for
d
in
range
(
0
,
g_dim
):
coords_new
[
i_new
][
d
]
=
scale
*
(
coords_orig
[
i_orig
][
d
]
+
i_remainder
*
(
coords_orig
[
i_orig
+
1
][
d
]
-
coords_orig
[
i_orig
][
d
]))
else
:
for
d
in
range
(
0
,
g_dim
):
coords_new
[
i_new
][
d
]
=
scale
*
coords_orig
[
n_orig
-
1
][
d
]
# print the coordates
for
d
in
range
(
0
,
g_dim
-
1
):
sys
.
stdout
.
write
(
str
(
coords_new
[
i_new
][
d
])
+
' '
)
sys
.
stdout
.
write
(
str
(
coords_new
[
i_new
][
g_dim
-
1
])
+
"
\n
"
)
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