Homec4science
Diffusion lammps (runner) Browse

lammps/tools/moltemplate/src/docs_useful_scripts/docs_extract_lammps_data.txt
16eed7a05366runner

Last Change
Raw File

docs_extract_lammps_data.txt
View Options

extract_lammps_data.py is a simple script which extracts sections of text from
a LAMMPS data file. (Of coarse, you can accomplish the same thing with a text
editor, but this script performs the task automatically.)
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)
c4science · Help