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lammps/tools/moltemplate/moltemplate/extract_lammps_data.py
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extract_lammps_data.py
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#!/usr/bin/env python
"""
extract_lammps_data.py is a simple script which extracts sections of text from
a LAMMPS data file.
Typical usage:
extract_lammps_data.py SECTION_NAME < FILE.DATA > EXCERPT.TXT
This extracts a section from a LAMMPS data file and saves it in EXCERPT.TXT.
More general usage:
extract_lammps_data.py [-n] SECTION_LIST < FILE.DATA > EXCERPT.TXT
For more details, see "doc/utils/docs_extract_lammps_data.txt"
"""
import sys
lammps_data_sections = set(['Atoms',
'Masses',
'Bonds',
'Bond Coeffs',
'Angles',
'Angle Coeffs',
'Dihedrals',
'Dihedral Coeffs',
'Impropers',
'Improper Coeffs',
'BondBond Coeffs', # class2 angles
'BondAngle Coeffs', # class2 angles
'MiddleBondTorsion Coeffs', # class2 dihedrals
'EndBondTorsion Coeffs', # class2 dihedrals
'AngleTorsion Coeffs', # class2 dihedrals
'AngleAngleTorsion Coeffs', # class2 dihedrals
'BondBond13 Coeffs', # class2 dihedrals
'AngleAngle Coeffs', # class2 impropers
'Angles By Type', # new. not standard LAMMPS
'Dihedrals By Type', # new. not standard LAMMPS
'Angles By Type']) # new. not standard LAMMPS
def DeleteComments(string,
escape='\\',
comment_char='#'):
escaped_state = False
for i in range(0, len(string)):
if string[i] in escape:
if escaped_state:
escaped_state = False
else:
escaped_state = True
elif string[i] == comment_char:
if not escaped_state:
return string[0:i]
return string
def ExtractDataSection(f,
section_name,
comment_char='#',
include_section_name=False,
return_line_nums=False):
inside_section = False
if section_name in ('header', 'Header'): # "Header" section includes beginning
inside_section = True
nonblank_encountered = False
nonheader_encountered = False
i = 0
for line_orig in f:
return_this_line = False
line = DeleteComments(line_orig).strip()
if line in lammps_data_sections:
nonheader_encountered = True
if section_name in ('header', 'Header'):
# The "header" section includes all lines at the beginning of the
# before any other section is encountered.
if nonheader_encountered:
return_this_line = False
else:
return_this_line = True
elif line == section_name:
inside_section = True
nonblank_encountered = False
if include_section_name:
return_this_line = True
# A block of blank lines (which dont immediately follow
# the section_name) signal the end of a section:
elif len(line) == 0:
if inside_section and include_section_name:
return_this_line = True
if nonblank_encountered:
inside_section = False
elif line[0] != comment_char:
if inside_section:
nonblank_encountered = True
return_this_line = True
if return_this_line:
if return_line_nums:
yield i
else:
yield line_orig
i += 1
def main():
lines = sys.stdin.readlines()
exclude_sections = False
if sys.argv[1] == '-n':
exclude_sections = True
del sys.argv[1]
if not exclude_sections:
for section_name in sys.argv[1:]:
for line in ExtractDataSection(lines, section_name):
sys.stdout.write(line)
else:
line_nums_exclude = set([])
for section_name in sys.argv[1:]:
for line_num in ExtractDataSection(lines,
section_name,
include_section_name=True,
return_line_nums=True):
line_nums_exclude.add(line_num)
for i in range(0, len(lines)):
if i not in line_nums_exclude:
sys.stdout.write(lines[i])
return
if __name__ == "__main__":
main()
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