46 lines
1.8 KiB
Plaintext
46 lines
1.8 KiB
Plaintext
NOTE: This example requires the "Al99.eam.alloy" file.
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(It was not included in this directory because if its large size.)
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As of 2012-11, I was able to obtain it here:
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http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy
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Copy it to the directory containing this README file.
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------------------------------------------------------------------------
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3D fractal test
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Moltemplate is useful for building larger molecular structures from
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smaller pieces. Although this simulation is of no scientific value, thiss
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example illustrates how to build large (many-level) heirarchical objects
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(Serpinski cubes) using moltemplate. (This is also called a "Menger Sponge".)
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The files in this directory demonstrate a way to build a periodic lattice of
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3-dimensional Serpinski-cubes (with 3 levels of recursive self-similarity).
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In this example, the basic indivisible units are 4-atoms of Aluminum
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(arranged in a cubic FCC unit-cell for bulk Aluminum).
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This was an arbitrary choice. The resulting construct is not stable.
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(But it makes pretty movies while collapsing.)
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To understand what is going on with this example, look at this file:
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./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt
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(This approach uses too much memory to be practical for large simulaions.
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The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt)
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--- To build the system ---
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Carry out the instructions in README_setup.sh,
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to generate the LAMMPS DATA file and input scripts you need:
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system.data, system.in.init, system.in.settings.
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(The run.in script contains references to these files.)
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--- To run LAMMPS, try a command like: ---
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lmp_mpi -i run.in
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or (if you have mpi installed)
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mpirun -np 4 lmp_mpi -i run.in
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This will create an ordinary LAMMPS dump file you can visualize with VMD
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traj.lammpstrj (See README_visualize.txt)
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