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64 lines
2.1 KiB
Plaintext
64 lines
2.1 KiB
Plaintext
"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c
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:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html)
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:link(pd,Manual.html)
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:link(pc,Section_tools.html)
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:line
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pair tool :h3
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[Purpose:]
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Compute LAMMPS pairwise energies.
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[Description:]
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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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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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The coeff() method reads the pairwise coefficients for the force field
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from a data file object (see the "data"_data.html 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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[Usage:]
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p = pair("lj/charmm/coul/charmm") create pair object for specific pair style :pre
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available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm :pre
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p.coeff(d) extract pairwise coeffs from data object
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p.init(cut1,cut2,...) setup based on coeffs and cutoffs :pre
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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) :pre
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e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...) compute LJ/Coul energy :pre
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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 :pre
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[Related tools:]
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"data"_data.html
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[Prerequisites:] none
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