forked from lijiext/lammps
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This commit is contained in:
parent
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@ -15,13 +15,15 @@
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</H3>
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<H3>pair_style lj/charmm/coul/long command
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</H3>
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<H3>pair_style lj/charmm/coul/long/gpu command
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</H3>
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<H3>pair_style lj/charmm/coul/long/opt command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style style args
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</PRE>
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<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I> or <I>lj/charmm/coul/long/opt</I>
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<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I> or <I>lj/charmm/coul/long/gpu</I> or <I>lj/charmm/coul/long/opt</I>
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<LI>args = list of arguments for a particular style
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</UL>
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<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
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@ -31,6 +33,9 @@
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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<I>lj/charmm/coul/long</I> args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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<I>lj/charmm/coul/long/gpu</I> args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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</PRE>
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|
@ -86,6 +91,9 @@ applied to the Coulombic term, as in the discussion for pair style
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command, then the outer LJ cutoff is used as the single Coulombic
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cutoff.
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</P>
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<P>Style <I>lj/charmm/coul/long/gpu</I> is a GPU-enabled version of style <I>lj/charmm/coul/long</I>.
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See more details below.
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</P>
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<P>Style <I>lj/charmm/coul/long/opt</I> is an optimized version of style
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<I>lj/charmm/coul/long</I> that should give identical answers. Depending
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on system size and the processor you are running on, it may be 5-25%
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@ -115,6 +123,26 @@ the pair_style command.
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</P>
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<HR>
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<P>The <I>lj/charmm/coul/long/gpu</I> style is identical to the <I>lj/charmm/coul/long</I>
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style, except that each processor off-loads its pairwise calculations to
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a GPU chip. Depending on the hardware available on your system this can
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provide a significant speed-up. See the <A HREF = "Section_start.html#2_8">Running on
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GPUs</A> section of the manual for more details
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about hardware and software requirements for using GPUs.
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</P>
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<P>More details about these settings and various possible hardware
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configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
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manual.
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</P>
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<P>Additional requirements in your input script to run with style
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<I>lj/charmm/coul/long/gpu</I> are as follows:
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</P>
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<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
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<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
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essential GPU selection and initialization steps.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
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|
@ -154,7 +182,9 @@ support the <I>pair</I> keyword of run_style respa. See the
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</P>
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<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
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styles are part of the "molecule" package. The <I>lj/charmm/coul/long</I>
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style is part of the "kspace" package. The <I>lj/charmm/coul/long/opt</I>
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style is part of the "kspace" package. The <I>lj/charmm/coul/long/gpu</I>
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style is part of the "gpu" package and also requires the "kspace"
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package. The <I>lj/charmm/coul/long/opt</I>
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style is part of the "opt" package and also requires the "kspace"
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package. They are only enabled if LAMMPS was built with those
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package(s) (molecule and kspace are by default). See the <A HREF = "Section_start.html#2_3">Making
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|
|
|
@ -9,13 +9,14 @@
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pair_style lj/charmm/coul/charmm command :h3
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pair_style lj/charmm/coul/charmm/implicit command :h3
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pair_style lj/charmm/coul/long command :h3
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pair_style lj/charmm/coul/long/gpu command :h3
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pair_style lj/charmm/coul/long/opt command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/long/opt}
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style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/long/gpu} or {lj/charmm/coul/long/opt}
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args = list of arguments for a particular style :ul
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{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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|
@ -24,6 +25,9 @@ args = list of arguments for a particular style :ul
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
|
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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{lj/charmm/coul/long} args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
|
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{lj/charmm/coul/long/gpu} args = inner outer (cutoff)
|
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
|
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
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|
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|
@ -79,6 +83,9 @@ applied to the Coulombic term, as in the discussion for pair style
|
|||
command, then the outer LJ cutoff is used as the single Coulombic
|
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cutoff.
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|
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Style {lj/charmm/coul/long/gpu} is a GPU-enabled version of style {lj/charmm/coul/long}.
|
||||
See more details below.
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|
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Style {lj/charmm/coul/long/opt} is an optimized version of style
|
||||
{lj/charmm/coul/long} that should give identical answers. Depending
|
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on system size and the processor you are running on, it may be 5-25%
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|
@ -108,6 +115,26 @@ the pair_style command.
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:line
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The {lj/charmm/coul/long/gpu} style is identical to the {lj/charmm/coul/long}
|
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style, except that each processor off-loads its pairwise calculations to
|
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a GPU chip. Depending on the hardware available on your system this can
|
||||
provide a significant speed-up. See the "Running on
|
||||
GPUs"_Section_start.html#2_8 section of the manual for more details
|
||||
about hardware and software requirements for using GPUs.
|
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|
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More details about these settings and various possible hardware
|
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configuration are in "this section"_Section_start.html#2_8 of the
|
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manual.
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|
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Additional requirements in your input script to run with style
|
||||
{lj/charmm/coul/long/gpu} are as follows:
|
||||
|
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The "newton pair"_newton.html setting must be {off} and
|
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"fix gpu"_fix_gpu.html must be used. The fix controls the
|
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essential GPU selection and initialization steps.
|
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|
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:line
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|
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
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|
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For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
|
||||
|
@ -147,7 +174,9 @@ support the {pair} keyword of run_style respa. See the
|
|||
|
||||
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
|
||||
styles are part of the "molecule" package. The {lj/charmm/coul/long}
|
||||
style is part of the "kspace" package. The {lj/charmm/coul/long/opt}
|
||||
style is part of the "kspace" package. The {lj/charmm/coul/long/gpu}
|
||||
style is part of the "gpu" package and also requires the "kspace"
|
||||
package. The {lj/charmm/coul/long/opt}
|
||||
style is part of the "opt" package and also requires the "kspace"
|
||||
package. They are only enabled if LAMMPS was built with those
|
||||
package(s) (molecule and kspace are by default). See the "Making
|
||||
|
|
|
@ -119,6 +119,7 @@ the pair_style command, and coefficients specified by the associated
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
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||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
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||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long/gpu</A> - GPU-enabled version of CHARMM with long-range Coulomb
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long/opt</A> - optimized version of CHARMM with long-range Coulomb
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||||
<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
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||||
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
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||||
|
@ -127,14 +128,17 @@ the pair_style command, and coefficients specified by the associated
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<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A> - GPU-enabled version of cutoff LJ
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A> - optimized version of cutoff LJ
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut/gpu</A> - GPU-enabled version of LJ with cutoff Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye screening added to Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
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||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/gpu</A> - GPU-enabled version of LJ with long-range Coulomb
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||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
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<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
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<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
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<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
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<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
|
||||
<LI><A HREF = "pair_lj96_cut.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
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<LI><A HREF = "pair_lj96_cut.html">pair_style lj96/cut/gpu</A> - GPU-enabled version of Lennard-Jones 9/6
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<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
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<LI><A HREF = "pair_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
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<LI><A HREF = "pair_morse.html">pair_style morse</A> - Morse potential
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|
|
|
@ -116,6 +116,7 @@ the pair_style command, and coefficients specified by the associated
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"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
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"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
|
||||
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
|
||||
"pair_style lj/charmm/coul/long/gpu"_pair_charmm.html - GPU-enabled version of CHARMM with long-range Coulomb
|
||||
"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized version of CHARMM with long-range Coulomb
|
||||
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
|
||||
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
|
||||
|
@ -124,14 +125,17 @@ the pair_style command, and coefficients specified by the associated
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"pair_style lj/cut/gpu"_pair_lj.html - GPU-enabled version of cutoff LJ
|
||||
"pair_style lj/cut/opt"_pair_lj.html - optimized version of cutoff LJ
|
||||
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
|
||||
"pair_style lj/cut/coul/cut/gpu"_pair_lj.html - GPU-enabled version of LJ with cutoff Coulomb
|
||||
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
|
||||
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
|
||||
"pair_style lj/cut/coul/long/gpu"_pair_lj.html - GPU-enabled version of LJ with long-range Coulomb
|
||||
"pair_style lj/cut/coul/long/tip4p"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
|
||||
"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
|
||||
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
|
||||
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
|
||||
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
|
||||
"pair_style lj96/cut"_pair_lj96_cut.html - Lennard-Jones 9/6 potential
|
||||
"pair_style lj96/cut/gpu"_pair_lj96_cut.html - GPU-enabled version of Lennard-Jones 9/6
|
||||
"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
|
||||
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
|
||||
"pair_style morse"_pair_morse.html - Morse potential
|
||||
|
|
|
@ -199,22 +199,6 @@ speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> sectio
|
|||
the manual for more details about hardware and software requirements
|
||||
for using GPUs.
|
||||
</P>
|
||||
<P>The <I>gpumode</I> and <I>gpuID</I> settings in the pair_style command refer to
|
||||
how the GPUs on your system are configured.
|
||||
</P>
|
||||
<P>Set <I>gpumode</I> to <I>one/node</I> if you have a single compute "node" on
|
||||
your system, which may have multiple cores and/or GPUs. <I>GpuID</I>
|
||||
should be set to the ID of the (first) GPU you wish to use with LAMMPS
|
||||
(another GPU might be driving your display).
|
||||
</P>
|
||||
<P>Set <I>gpumode</I> to <I>one/gpu</I> if you have multiple compute "nodes" on
|
||||
your system, with one GPU per node. <I>GpuID</I> should be set to the ID
|
||||
of the GPU.
|
||||
</P>
|
||||
<P>Set <I>gpumode</I> to <I>multi/gpu</I> if you have multiple compute "nodes" on
|
||||
your system, each with multiple GPUs. <I>GpuID</I> should be set to the
|
||||
number of GPUs per node.
|
||||
</P>
|
||||
<P>More details about these settings and various possible hardware
|
||||
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
|
||||
manual.
|
||||
|
|
|
@ -188,22 +188,6 @@ speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
|
|||
the manual for more details about hardware and software requirements
|
||||
for using GPUs.
|
||||
|
||||
The {gpumode} and {gpuID} settings in the pair_style command refer to
|
||||
how the GPUs on your system are configured.
|
||||
|
||||
Set {gpumode} to {one/node} if you have a single compute "node" on
|
||||
your system, which may have multiple cores and/or GPUs. {GpuID}
|
||||
should be set to the ID of the (first) GPU you wish to use with LAMMPS
|
||||
(another GPU might be driving your display).
|
||||
|
||||
Set {gpumode} to {one/gpu} if you have multiple compute "nodes" on
|
||||
your system, with one GPU per node. {GpuID} should be set to the ID
|
||||
of the GPU.
|
||||
|
||||
Set {gpumode} to {multi/gpu} if you have multiple compute "nodes" on
|
||||
your system, each with multiple GPUs. {GpuID} should be set to the
|
||||
number of GPUs per node.
|
||||
|
||||
More details about these settings and various possible hardware
|
||||
configuration are in "this section"_Section_start.html#2_8 of the
|
||||
manual.
|
||||
|
|
|
@ -121,6 +121,7 @@ the pair_style command, and coefficients specified by the associated
|
|||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long/gpu</A> - GPU-enabled version of CHARMM with long-range Coulomb
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long/opt</A> - optimized version of CHARMM with long-range Coulomb
|
||||
<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
|
||||
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
|
||||
|
@ -129,14 +130,17 @@ the pair_style command, and coefficients specified by the associated
|
|||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A> - GPU-enabled version of cutoff LJ
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A> - optimized version of cutoff LJ
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut/gpu</A> - GPU-enabled version of LJ with cutoff Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye screening added to Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/gpu</A> - GPU-enabled version of LJ with long-range Coulomb
|
||||
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
|
||||
<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
|
||||
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
|
||||
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
|
||||
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
|
||||
<LI><A HREF = "pair_lj96_cut.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
|
||||
<LI><A HREF = "pair_lj96_cut.html">pair_style lj96/cut/gpu</A> - GPU-enabled version of Lennard-Jones 9/6
|
||||
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
|
||||
<LI><A HREF = "pair_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
|
||||
<LI><A HREF = "pair_morse.html">pair_style morse</A> - Morse potential
|
||||
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@ -118,6 +118,7 @@ the pair_style command, and coefficients specified by the associated
|
|||
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
|
||||
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
|
||||
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
|
||||
"pair_style lj/charmm/coul/long/gpu"_pair_charmm.html - GPU-enabled version of CHARMM with long-range Coulomb
|
||||
"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized version of CHARMM with long-range Coulomb
|
||||
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
|
||||
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
|
||||
|
@ -126,14 +127,17 @@ the pair_style command, and coefficients specified by the associated
|
|||
"pair_style lj/cut/gpu"_pair_lj.html - GPU-enabled version of cutoff LJ
|
||||
"pair_style lj/cut/opt"_pair_lj.html - optimized version of cutoff LJ
|
||||
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
|
||||
"pair_style lj/cut/coul/cut/gpu"_pair_lj.html - GPU-enabled version of LJ with cutoff Coulomb
|
||||
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
|
||||
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
|
||||
"pair_style lj/cut/coul/long/gpu"_pair_lj.html - GPU-enabled version of LJ with long-range Coulomb
|
||||
"pair_style lj/cut/coul/long/tip4p"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
|
||||
"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
|
||||
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
|
||||
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
|
||||
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
|
||||
"pair_style lj96/cut"_pair_lj96_cut.html - Lennard-Jones 9/6 potential
|
||||
"pair_style lj96/cut/gpu"_pair_lj96_cut.html - GPU-enabled version of Lennard-Jones 9/6
|
||||
"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
|
||||
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
|
||||
"pair_style morse"_pair_morse.html - Morse potential
|
||||
|
|
Loading…
Reference in New Issue