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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4470 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2010-08-09 14:09:03 +00:00
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7 changed files with 144 additions and 12 deletions
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7
doc/Section_commands.html
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@ -386,9 +386,10 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri_pmb.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if

6
doc/Section_howto.html
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@ -505,9 +505,9 @@ LJ epsilon, sigma of OH, HH = 0.0 <BR>
<P>r0 of OH bond = 1.0<BR>
theta of HOH angle = 109.47 <BR>
</P>
<P>To use SPC with a long-range Coulombic solver (Ewald or PPPM in
LAMMPS), the only parameters that change are the partial charge
assignments:
<P>To use an SPC model with a long-range Coulombic solver (Ewald or
PPPM in LAMMPS), the only parameters that change are the partial
charge assignments:
</P>
<P>O charge = -0.8476<BR>
H charge = 0.4238 <BR>

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doc/Section_howto.txt
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@ -501,9 +501,9 @@ LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
r0 of OH bond = 1.0
theta of HOH angle = 109.47 :all(b),p
To use SPC with a long-range Coulombic solver (Ewald or PPPM in
LAMMPS), the only parameters that change are the partial charge
assignments:
To use an SPC model with a long-range Coulombic solver (Ewald or
PPPM in LAMMPS), the only parameters that change are the partial
charge assignments:
O charge = -0.8476
H charge = 0.4238 :all(b),p

2
doc/Section_intro.html
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@ -237,7 +237,7 @@ molecular dynamics options:
<LI><A HREF = "temper.html">parallel tempering</A>
<LI><A HREF = "prd.html">parallel replica dynamics</A>
<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
<LI><A HREF = "pair_peri_pmb.html">Peridynamics mesoscale modeling</A>
<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
<LI><A HREF = "fix_ttm.html">two-temperature electron model</A>
</UL>

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doc/pair_coeff.html
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@ -134,7 +134,8 @@ the pair_style command, and coefficients specified by the associated
<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
<LI><A HREF = "pair_morse.html">pair_style morse/opt</A> - optimized version of Morse potential
<LI><A HREF = "pair_peri_pmb.html">pair_style peri/pmb</A> - peridynamic PMB potential
<LI><A HREF = "pair_peri.html">pair_style peri/lps</A> - peridynamic LPS potential
<LI><A HREF = "pair_peri.html">pair_style peri/pmb</A> - peridynamic PMB potential
<LI><A HREF = "pair_reax.html">pair_style reax</A> - ReaxFF potential
<LI><A HREF = "pair_resquared.html">pair_style resquared</A> - Everaers RE-Squared ellipsoidal potential
<LI><A HREF = "pair_soft.html">pair_style soft</A> - Soft (cosine) potential

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doc/pair_peri.html Normal file
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@ -0,0 +1,129 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>pair_style peri/pmb command
</H3>
<H3>pair_style peri/lps command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style
</PRE>
<UL><LI>style = <I>peri/pmb</I> or <I>peri/lps</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
</PRE>
<PRE>pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
</PRE>
<P><B>Description:</B>
</P>
<P>The peridynamic pair styles implement material models that can be used
at the mescscopic and macroscopic scales.
</P>
<P>Style <I>peri/pmb</I> implements the Peridynamic bond-based prototype
microelastic brittle (PMB) model.
</P>
<P>Style <I>peri/lps</I> implements the Peridynamic state-based linear
peridynamic solid (LPS) model.
</P>
<P>The canonical papers on Peridynamics are <A HREF = "#Silling2000">(Silling 2000)</A>
and <A HREF = "#Silling2007">(Silling 2007)</A>. The implementation of Peridynamics
in LAMMPS is described in <A HREF = "#Parks">(Parks)</A>. Also see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS
user guide</A> for
more details about the implementation of peridynamics in LAMMPS.
</P>
<P>The following coefficients must be defined for each pair of atom types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below.
</P>
<P>For the <I>peri/pmb</I> style:
</P>
<UL><LI>c (energy/distance/volume^2 units)
<LI>horizon (distance units)
<LI>s00 (unitless)
<LI>alpha (unitless)
</UL>
<P>C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
alpha are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume^2, where stiffness is
energy/distance^2 and volume is distance^3. See the users guide for
more details.
</P>
<P>For the <I>peri/lps</I> style:
</P>
<UL><LI>K (force/area units)
<LI>G (force/area units)
<LI>horizon (distance units)
<LI>s00 (unitless)
<LI>alpha (unitless)
</UL>
<P>K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. See the users guide for more
details.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
relevant for these pair styles.
</P>
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The <I>peri/pmb</I> and <I>peri/lps</I> styles are part of the "peri"
package. They are only enabled if LAMMPS was built with that package.
See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Parks"></A>
<P><B>(Parks)</B> Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
</P>
<A NAME = "Silling2000"></A>
<P><B>(Silling 2000)</B> Silling, J Mech Phys Solids, 48, 175-209 (2000).
</P>
<A NAME = "Silling2007"></A>
<P><B>(Silling 2007)</B> Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
</P>
</HTML>

3
doc/pair_style.html
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@ -136,7 +136,8 @@ the pair_style command, and coefficients specified by the associated
<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
<LI><A HREF = "pair_morse.html">pair_style morse/opt</A> - optimized version of Morse potential
<LI><A HREF = "pair_peri_pmb.html">pair_style peri/pmb</A> - peridynamic PMB potential
<LI><A HREF = "pair_peri.html">pair_style peri/lps</A> - peridynamic LPS potential
<LI><A HREF = "pair_peri.html">pair_style peri/pmb</A> - peridynamic PMB potential
<LI><A HREF = "pair_reax.html">pair_style reax</A> - ReaxFF potential
<LI><A HREF = "pair_resquared.html">pair_style resquared</A> - Everaers RE-Squared ellipsoidal potential
<LI><A HREF = "pair_soft.html">pair_style soft</A> - Soft (cosine) potential