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