95 lines
2.7 KiB
Plaintext
95 lines
2.7 KiB
Plaintext
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lmp2arc.exe
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by Michael Peachey & John Carpenter (SGI/Cray)
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Version 0.1: 8/14/97 MJP initial version NVT only
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Version 1.0: 7/27/98 JEC rewrote to reduce storage and generalize programs
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Version 1.1: 10/22/98 JEC geometric molecule "unwrapping" algorithm included
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Version 1.2: 11/04/98 JEC multiple position files in input; data structures
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standardized with lmp2gxf
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This program converts a LAMMPS dump (position) file to a MSI
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.arc file using a .car file as the template. This enables one to
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visualize a LAMMPS trajectory using Insight II.
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Usage: lmp2arc.exe [options] -car carfile < infile > outfile
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options
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-trueflags (default is not present)
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trueflags are present in the LAMMPS position file.
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-move_mol (default is not present)
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Unwraps molecules. All atoms in the position file are in
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simulation cell. This means that molecules which
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are sticking out of the cell will have some of its
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atoms "wrapped" to the other side of the periodic cell.
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This leads to very messy visualizations. Specification
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of -move_mol will attempt to "unwrap" or straighten
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molecules and yield a reasonable visualization. However,
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molecules which oscillate around half in or out of the
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box may appear to jump from one side of the box to
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the other.
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Two algorithms are used depending upon the presence of
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trueflags. The algorithm that uses trueflags is the
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most robust, but the other geometric based algorithm
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should be adequate.
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-car filename
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the name of the .car file that corresponds to the
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position information. This is required.
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-skip n (default is 0)
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Skip every n timesteps in the position file.
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-npico n (default is 2000)
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Number of timesteps in 1 picosecond of simulation
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stdin
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file containing one or more names of LAMMPS position files
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stdout
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the name of the new .arc file
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Examples:
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% lmp2arc.exe -trueflags -move_mol -skip 4 -car water.car <<EOF > water.arc
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water1.pos
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water2.pos
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EOF
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>>>> Program output <<<<<
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lmp2arc v1.2 - LAMMPS MD trajectory to MSI .arc file conversion
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Car file name is water.car
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Number of Atoms = 24
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Number of Molecules = 8
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Position file names:
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water1.pos
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water2.pos
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Processing Timesteps
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20 40 60 80 100
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102 frames were written to the ArcFile
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Program Exiting Normally
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