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73 lines
2.7 KiB
HTML
73 lines
2.7 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> - <A HREF = "Manual.html">Pizza.py Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A>
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<HR>
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<H3>chain tool
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</H3>
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<P><B>Purpose:</B>
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</P>
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<P>Create bead-spring chains for LAMMPS input.
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</P>
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<P><B>Description:</B>
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</P>
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<P>The chain tool creates random, overlapping bead-spring (FENE) chains
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and writes them out as a LAMMPS data file. They need to be simulated
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with a soft potential in LAMMPS to un-overlap them before they form
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a proper melt.
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</P>
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<P>The chain constructor uses the total number of monomers and the
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Lennard-Jones reduced density to create a simulation box of the
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appropriate size. Optionally, the box shape can also be specified.
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</P>
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<P>The build() method creates N chains, each with M monomers. It can be
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invoked multiple times to create sets of chains with different
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properties. The starting point of each chain is chosen randomly, as
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is the position of subsequent monomers. The seed value sets the
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random number generator used for coordinate generation.
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</P>
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<P>The mtype, btype, blen, and dmin settings affect how the chain and its
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monomers are created. Dmin is the minimum distance allowed between a
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new monomer and the monomer two before it, so it determines the
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stiffness of the chain. Each monomer is assigned a molecule ID as it
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is created, in accord with the id setting.
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</P>
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<P>Once N total monomers have been created, the ensemble of chains is
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written to a LAMMPS data file via the write() method.
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</P>
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<P><B>Usage:</B>
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</P>
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<PRE>c = chain(N,rho) setup box with N monomers at reduced density rho
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c = chain(N,rho,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1)
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</PRE>
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<PRE>c.seed = 48379 set random # seed (def = 12345)
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c.mtype = 2 set type of monomers (def = 1)
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c.btype = 1 set type of bonds (def = 1)
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c.blen = 0.97 set length of bonds (def = 0.97)
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c.dmin = 1.02 set min dist from i-1 to i+1 site (def = 1.02)
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</PRE>
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<PRE>c.id = "chain" set molecule ID to chain # (default)
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c.id = "end1" set molecule ID to count from one end of chain
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c.id = "end2" set molecule ID to count from either end of chain
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</PRE>
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<PRE>c.build(100,10) create 100 chains, each of length 10
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</PRE>
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<PRE> can be invoked multiple times interleaved with different settings
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must fill box with total of N monomers
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</PRE>
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<PRE>c.write("data.file") write out all built chains to LAMMPS data file
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</PRE>
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<P><B>Related tools:</B>
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</P>
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<P><A HREF = "data.html">data</A>, <A HREF = "patch.html">patch</A>
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</P>
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<P><B>Prerequisites:</B> none
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</P>
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</HTML>
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