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