2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A>
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<HR>
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<H3>5. Example problems
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</H3>
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<P>The LAMMPS distribution includes an examples sub-directory with
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several sample problems. Each problem is in a sub-directory of its
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own. Most are 2d models so that they run quickly, requiring at most a
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couple of minutes to run on a desktop machine. Each problem has an
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input script (in.*) and produces a log file (log.*) and dump file
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(dump.*) when it runs. Some use a data file (data.*) of initial
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coordinates as additional input. A few sample log file outputs on
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different machines and different numbers of processors are included in
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the directories to compare your answers to. E.g. a log file like
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log.crack.foo.P means it ran on P processors of machine "foo".
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</P>
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<P>The dump files produced by the example runs can be animated using the
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2007-06-23 07:41:35 +08:00
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xmovie tool described in the <A HREF = "Section_tools.html">Additional Tools</A>
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section of the LAMMPS documentation. Animations of many of these
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examples can be viewed on the Movies section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
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Site</A>.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>These are the sample problems in the examples sub-directories:
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</P>
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2007-09-28 07:25:52 +08:00
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
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<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
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<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
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<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
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<TR><TD >flow</TD><TD > Couette and Poisseuille flow in a 2d channel</TD></TR>
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<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
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<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
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<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
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<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
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<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
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<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
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<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
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<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
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<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
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<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
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<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
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<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void
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</TD></TR></TABLE></DIV>
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<P>Here is how you might run and visualize one of the sample problems:
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</P>
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<PRE>cd indent
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cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
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lmp_linux < in.indent # run the problem
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</PRE>
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<P>Running the simulation produces the files <I>dump.indent</I> and
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<I>log.lammps</I>. You can visualize the dump file as follows:
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</P>
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<PRE>../../tools/xmovie/xmovie -scale dump.indent
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</PRE>
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<P>There is also a directory "couple" in the examples sub-directory,
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which contains a stand-alone code umbrella.cpp that links LAMMPS as a
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library. The README describes how to build the code. The code itself
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runs LAMMPS on a subset of processors, sets up a LAMMPS problem
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by invoking LAMMPS input script commands one at a time, does
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a run, grabs atom coordinates, changes one atom position, puts
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them back into LAMMPS, and does another run.
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</P>
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<P>This illustrates how an umbrella code could include new models and
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physics while using LAMMPS to perform MD, or how the umbrella code
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could call both LAMMPS and some other code to perform a coupled
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calculation.
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</P>
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