60 lines
2.0 KiB
Plaintext
60 lines
2.0 KiB
Plaintext
extract_lammps_data.py is a simple script which extracts sections of text from
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a LAMMPS data file. (Of coarse, you can accomplish the same thing with a text
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editor, but this script turns it into a one-line command.)
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Typical usage:
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extract_lammps_data.py SECTION_NAME < FILE.DATA > EXCERPT.TXT
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This extracts a section from a LAMMPS data file and saves it in EXCERPT.TXT.
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More general usage:
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extract_lammps_data.py [-n] SECTION_LIST < FILE.DATA > EXCERPT.TXT
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The SECTION_LIST is a list of sections you want in your output file
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(eg "EXCERPT.TXT"). Each section must be a quoted-string, and spaces
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(not commas) should separate each section name.
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The optional "-n" flag negates the selection. (Selecting instead, everything
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except the sections you listed.)
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Examples:
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extract_lammps_data.py "Atoms" < FILE.DATA > Atoms.txt
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extract_lammps_data.py "Header" < FILE.DATA > Header.txt
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extract_lammps_data.py -n "Header" < FILE.DATA > everything_except_Header.txt
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extract_lammps_data.py "Bonds" "Angles" "Dihedrals" "Impropers" \
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< FILE.DATA > topology.txt
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extract_lammps_data.py "Pair Coeffs" "Bond Coeffs" "Angle Coeffs" \
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"Dihedral Coeffs" "Improper Coeffs" \
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< FILE.DATA > force_field.txt
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The following section names are allowed:
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"Header" # The header section at the beginning of the file.
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"Atoms"
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"Masses"
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"Bonds"
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"Bond Coeffs"
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"Angles"
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"Angle Coeffs"
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"Dihedrals"
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"Dihedral Coeffs"
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"Impropers"
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"Improper Coeffs"
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"BondBond Coeffs" # class2 angles
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"BondAngle Coeffs" # class2 angles
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"MiddleBondTorsion Coeffs" # class2 dihedrals
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"EndBondTorsion Coeffs" # class2 dihedrals
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"AngleTorsion Coeffs" # class2 dihedrals
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"AngleAngleTorsion Coeffs" # class2 dihedrals
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"BondBond13 Coeffs" # class2 dihedrals
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"AngleAngle Coeffs" # class2 impropers
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"Angles By Type" # moltemplate-specific. (not standard LAMMPS)
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"Dihedrals By Type" # moltemplate-specific. (not standard LAMMPS)
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"Angles By Type' # moltemplate-specific. (not standard LAMMPS)
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