forked from lijiext/lammps
137 lines
3.4 KiB
Plaintext
137 lines
3.4 KiB
Plaintext
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This program converts a contiguous set of LAMMPS dump (position) files
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to a MSI .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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by Michael Peachey & John Carpenter (SGI/Cray)
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currently maintained by Kelly L. Anderson (AFRL/ML)
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Version 0.1: 8/14/97 MJP
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Version 1.0: 7/27/98 JEC
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Version 1.1: 10/22/98 JEC
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Version 1.2: 11/04/98 JEC
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Version 1.3: 4/10/05 KLA
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1. To build the program
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% cd src
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% make
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% cp lmp2arc.exe ../bin
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The program is only a few files so should compile
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quickly.
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2. Testing the program
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There are three test jobs in the test directory
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that one can run
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% ../bin/lmp2arc.exe -car water8.car <<EOF > water8.arc
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> water8.pos
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> EOF
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% diff water8.arc correct/water8.arc
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% ../bin/lmp2arc.exe -move_mol -car water8.car <<EOF > water8.arc
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> water8.pos
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> EOF
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% diff water8.arc correct/water8.arc.unwrap
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% ../bin/lmp2arc.exe -trueflags -move_mol -car water8.car \
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<<EOF > water8.arc
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> water8.pos
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> EOF
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% diff water8.arc correct/water8.arc.trueflags
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The only differences you should see are date differences.
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3. Usage
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Usage: lmp2arc.exe [options] -car carfile < infile > outfile
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options
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-trueflags (optional)
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trueflags are present in the LAMMPS position file.
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-move_mol (optional)
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Unwraps molecules. All atoms in the position file are in
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the 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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-2001 (default is 2005)
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Version of LAMMPS to convert from.
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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 -2001 -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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4. Questions or comments?
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Send them to Kelly L. Anderson (kelly.anderson@cantab.net)
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