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raw2data.py
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Created
Sat, Aug 24, 15:45
Size
3 KB
Mime Type
text/x-python
Expires
Mon, Aug 26, 15:45 (2 d)
Engine
blob
Format
Raw Data
Handle
20147626
Attached To
rLAMMPS lammps
raw2data.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
from
dump2data
import
*
g_program_name
=
'raw2data.py'
g_date_str
=
'2014-12-19'
g_version_str
=
'v0.43'
####### Main Code Below: #######
sys
.
stderr
.
write
(
g_program_name
+
' '
+
g_version_str
+
' '
+
g_date_str
)
sys
.
stderr
.
write
(
'
\n
'
)
try
:
data_settings
=
DataSettings
()
misc_settings
=
MiscSettings
()
misc_settings
.
multi
=
False
warning_strings
=
[]
ParseArgs
(
sys
.
argv
,
misc_settings
,
data_settings
,
warning_strings
)
frame_coords
=
defaultdict
(
list
)
frame_coords_ixiyiz
=
defaultdict
(
list
)
frame_vects
=
defaultdict
(
list
)
frame_velocities
=
defaultdict
(
list
)
frame_xlo_str
=
frame_xhi_str
=
None
frame_ylo_str
=
frame_yhi_str
=
None
frame_zlo_str
=
frame_zhi_str
=
None
frame_xy_str
=
frame_xz_str
=
frame_yz_str
=
None
frame_natoms
=
-
1
frame_timestep_str
=
''
i_atomid
=
i_atomtype
=
i_molid
=
-
1
i_x
=
i_y
=
i_z
=
i_xu
=
i_yu
=
i_zu
=
-
1
i_xs
=
i_ys
=
i_zs
=
i_xsu
=
i_ysu
=
i_zsu
=
-
1
dump_column_names
=
[]
#num_frames_in = -1
num_frames_out
=
0
finished_reading_frame
=
False
read_last_frame
=
False
#in_coord_file = open('traj.raw','r')
#in_coord_file = open('tmp_atom_coords.dat','r')
in_coord_file
=
sys
.
stdin
read_last_frame
=
False
while
True
:
line
=
'
\n
'
while
(
line
!=
''
)
and
(
line
.
strip
()
==
''
):
line
=
in_coord_file
.
readline
()
if
line
==
''
:
# if EOF
break
frame_coords
=
defaultdict
(
list
)
while
line
.
strip
()
!=
''
:
n_crds
=
len
(
frame_coords
)
#sys.stdout.write("n_crds="+str(n_crds)+": \""+line.strip()+"\"\n")
frame_coords
[
str
(
n_crds
+
1
)]
=
line
.
split
()
line
=
in_coord_file
.
readline
()
# Check to see if there are any blank lines at this location in the file
# If there are, it means we are at a new "frame" (in the trajectory).
# Skip over any blank line(s) separating this frame from the next frame
# so that the next time we enter the loop, we are at the beginning
# of a new frame.
while
(
line
!=
''
)
and
(
line
.
strip
()
==
''
):
line
=
in_coord_file
.
readline
()
# Parse the DATA file specified by the user
# and replace appropriate lines or fields with
# the corresponding text from the input file.
if
misc_settings
.
multi
:
out_file_name
=
data_settings
.
file_name
+
'.'
\
+
str
(
num_frames_out
)
sys
.
stderr
.
write
(
' (creating file
\"
'
+
out_file_name
+
'
\"
)
\n
'
)
out_file
=
open
(
out_file_name
,
'w'
)
else
:
out_file
=
sys
.
stdout
WriteFrameToData
(
out_file
,
None
,
misc_settings
,
data_settings
,
frame_natoms
,
frame_coords
,
frame_coords_ixiyiz
,
frame_vects
,
frame_velocities
,
None
,
None
,
frame_xlo_str
,
frame_xhi_str
,
frame_ylo_str
,
frame_yhi_str
,
frame_zlo_str
,
frame_zhi_str
,
frame_xy_str
,
frame_xz_str
,
frame_yz_str
)
except
(
ValueError
,
InputError
)
as
err
:
sys
.
stderr
.
write
(
'
\n
'
+
str
(
err
)
+
'
\n
'
)
sys
.
exit
(
-
1
)
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