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extract_lammps_data.py

Description

extract_lammps_data.py is a simple script which extracts sections of text from a LAMMPS data file. (Of course, you can accomplish the same thing with a text editor, but this script turns it into a one-line command.) Although it was written in python, extract_lammps_data.py is a stand-alone executable intended to be run from the terminal (shell).

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

The SECTION_LIST is a list of sections you want in your output file (eg "EXCERPT.TXT"). Each section must be a quoted-string, and spaces (not commas) should separate each section name.

The optional "-n" flag negates the selection. (Selecting instead, everything except the sections you listed.)

Examples

extract_lammps_data.py "Atoms" < FILE.DATA > Atoms.txt
extract_lammps_data.py "Header" < FILE.DATA > Header.txt
extract_lammps_data.py -n "Header" < FILE.DATA > everything_except_Header.txt

extract_lammps_data.py "Bonds" "Angles" "Dihedrals" "Impropers" \
                       < FILE.DATA > topology.txt

extract_lammps_data.py "Pair Coeffs" "Bond Coeffs" "Angle Coeffs" \
                       "Dihedral Coeffs" "Improper Coeffs" \
                       < FILE.DATA > force_field.txt

The following section names are allowed:

"Header"                   # The header section at the beginning of the file.
"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"           # moltemplate-specific. (not standard LAMMPS)
"Dihedrals By Type"        # moltemplate-specific. (not standard LAMMPS)
"Angles By Type'           # moltemplate-specific. (not standard LAMMPS)