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69 lines
2.3 KiB
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69 lines
2.3 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>pair tool
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</H3>
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<P><B>Purpose:</B>
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</P>
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<P>Compute LAMMPS pairwise energies.
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</P>
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<P><B>Description:</B>
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</P>
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<P>The pair tool computes a pairwise energy between 2 particles using a
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LAMMPS molecular dynamics force field. Thus it can be used in an
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analysis script to compute energies between groups of atoms from a
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LAMMPS snapshot file.
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</P>
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<P>The pair constructor specifies the force field style. Only some of
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the LAMMPS pair styles are currently included in this tool, but new
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styles can easily be added. Code from the LAMMPS pair*.cpp file needs
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to be re-coded in Python to make this work.
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</P>
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<P>The coeff() method reads the pairwise coefficients for the force field
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from a data file object (see the <A HREF = "data.html">data</A> tool). The init()
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method does pre-computations for the force field parameters needed by
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the single() method which does a pairwise computation between two
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atoms of type = itype,jtype separated by a squared distance rsq. The
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arguments for init() and single() can be different for a particular
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force field style. When you write the init() and single() methods for
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a new style, you can define what arguments are needed.
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</P>
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<P><B>Usage:</B>
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</P>
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<PRE>p = pair("lj/charmm/coul/charmm") create pair object for specific pair style
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</PRE>
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<PRE> available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm
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</PRE>
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<PRE>p.coeff(d) extract pairwise coeffs from data object
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p.init(cut1,cut2,...) setup based on coeffs and cutoffs
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</PRE>
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<PRE> init args are specific to pair style:
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lj/cut = cutlj
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lj/cut/coul/cut = cutlj,cut_coul (cut_coul optional)
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lj/charmm/coul/charmm = cutlj_inner,cutlj,cutcoul_inner,cut_coul
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(last 2 optional)
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</PRE>
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<PRE>e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...) compute LJ/Coul energy
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</PRE>
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<PRE> pairwise energy between 2 atoms at distance rsq with their attributes
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args are specific to pair style:
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lj/cut = rsq,itype,jtype
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lj/cut/coul/cut = rsq,itype,jtype,q1,q2
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lj/charmm/coul/charmm = rsq,itype,jtype,q1,q2
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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>
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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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