mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4466 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
26f888dd14
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8b8b994b52
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@ -576,7 +576,8 @@ potentials. Click on the style itself for a full description:
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"meam"_pair_meam.html,
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"morse"_pair_morse.html,
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"morse/opt"_pair_morse.html,
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"peri/pmb"_pair_peri_pmb.html,
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"peri/lps"_pair_peri.html,
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"peri/pmb"_pair_peri.html,
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"reax"_pair_reax.html,
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"resquared"_pair_resquared.html,
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"soft"_pair_soft.html,
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@ -233,7 +233,7 @@ coupled rigid body integration via the "POEMS"_fix_poems.html library
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"parallel tempering"_temper.html
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"parallel replica dynamics"_prd.html
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"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
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"Peridynamics mesoscale modeling"_pair_peri_pmb.html
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"Peridynamics mesoscale modeling"_pair_peri.html
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"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
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"two-temperature electron model"_fix_ttm.html :ul
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@ -131,7 +131,8 @@ the pair_style command, and coefficients specified by the associated
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"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
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"pair_style morse"_pair_morse.html - Morse potential
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"pair_style morse/opt"_pair_morse.html - optimized version of Morse potential
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"pair_style peri/pmb"_pair_peri_pmb.html - peridynamic PMB potential
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"pair_style peri/lps"_pair_peri.html - peridynamic LPS potential
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"pair_style peri/pmb"_pair_peri.html - peridynamic PMB potential
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"pair_style reax"_pair_reax.html - ReaxFF potential
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"pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
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"pair_style soft"_pair_soft.html - Soft (cosine) potential
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@ -0,0 +1,120 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style peri/pmb command :h3
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pair_style peri/lps command :h3
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[Syntax:]
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pair_style style :pre
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style = {peri/pmb} or {peri/lps} :ul
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[Examples:]
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pair_style peri/pmb
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pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre
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pair_style peri/lps
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pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 :pre
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[Description:]
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The peridynamic pair styles implement material models that can be used
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at the mescscopic and macroscopic scales.
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Style {peri/pmb} implements the Peridynamic bond-based prototype
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microelastic brittle (PMB) model.
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Style {peri/lps} implements the Peridynamic state-based linear
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peridynamic solid (LPS) model.
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The canonical papers on Peridynamics are "(Silling 2000)"_#Silling2000
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and "(Silling 2007)"_#Silling2007. The implementation of Peridynamics
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in LAMMPS is described in "(Parks)"_#Parks. Also see the "PDLAMMPS
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user guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for
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more details about the implementation of peridynamics in LAMMPS.
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The following coefficients must be defined for each pair of atom types
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via the "pair_coeff"_pair_coeff.html command as in the examples above,
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or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below.
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For the {peri/pmb} style:
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c (energy/distance/volume^2 units)
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horizon (distance units)
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s00 (unitless)
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alpha (unitless) :ul
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C is the effectively a spring constant for Peridynamic bonds, the
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horizon is a cutoff distance for truncating interactions, and s00 and
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alpha are used as a bond breaking criteria. The units of c are such
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that c/distance = stiffness/volume^2, where stiffness is
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energy/distance^2 and volume is distance^3. See the users guide for
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more details.
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For the {peri/lps} style:
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K (force/area units)
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G (force/area units)
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horizon (distance units)
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s00 (unitless)
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alpha (unitless) :ul
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K is the bulk modulus and G is the shear modulus. The horizon is a
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cutoff distance for truncating interactions, and s00 and alpha are
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used as a bond breaking criteria. See the users guide for more
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details.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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These pair styles do not support mixing. Thus, coefficients for all
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I,J pairs must be specified explicitly.
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These pair styles do not support the "pair_modify"_pair_modify.html
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shift option.
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The "pair_modify"_pair_modify.html table and tail options are not
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relevant for these pair styles.
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These pair styles write their information to "binary restart
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files"_restart.html, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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These pair styles can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. They do not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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The {peri/pmb} and {peri/lps} styles are part of the "peri"
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package. They are only enabled if LAMMPS was built with that package.
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See the "Making LAMMPS"_Section_start.html#2_3 section for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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:line
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:link(Parks)
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[(Parks)] Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
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:link(Silling2000)
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[(Silling 2000)] Silling, J Mech Phys Solids, 48, 175-209 (2000).
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:link(Silling2007)
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[(Silling 2007)] Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
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@ -1,98 +0,0 @@
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>pair_style peri/pmb 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 peri/pmb
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style peri/pmb
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pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>peri/pmb</I> style implements the Peridynamic bond-based prototype
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microelastic brittle (PMB) model, which can be used to model materials
|
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at the mesoscopic or macroscopic scale. The canonical paper on
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Peridynamics is <A HREF = "#Silling">(Silling)</A>. The implementation of
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Peridynamics in LAMMPS is described in <A HREF = "#Parks">(Parks)</A>. Also see the
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<A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
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guide</A> for more
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details about this particular potential and using it in LAMMPS.
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</P>
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<P>The following coefficients must be defined for each pair of atom
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types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands, or by mixing as described below:
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</P>
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<UL><LI>c (energy/distance/volume^2 units)
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<LI>horizon (distance units)
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<LI>s00 (unitless)
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<LI>alpha (unitless)
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</UL>
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<P>C is the effectively a spring constant for Peridynamic bonds, the
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horizon is a cutoff distance for truncating interactions, and s00 and
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alpha are used as a bond breaking criteria. The units of c are such
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that c/distance = stiffness/volume^2, where stiffness is
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energy/distance^2 and volume is distance^3. See the users guide for
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more details.
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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>This pair style does not support mixing. Thus, coefficients for all
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I,J pairs must be specified explicitly.
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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shift option.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
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relevant for this pair style.
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</P>
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<P>This pair style writes its information to <A HREF = "restart.html">binary restart
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files</A>, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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</P>
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<P>This pair style can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>The <I>peri/pmb</I> style is part of the "peri" package. It is only
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enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Parks"></A>
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<P><B>(Parks)</B> Parks, Lehoucq, Plimpton, Silling, to appear in Comp Phys
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Comm, (2008).
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</P>
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<A NAME = "Silling"></A>
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<P><B>(Silling)</B> Silling, J Mech Phys Solids, 48, 175-209 (2000).
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</P>
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</HTML>
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@ -1,91 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
|
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style peri/pmb command :h3
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[Syntax:]
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pair_style peri/pmb :pre
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|
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[Examples:]
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pair_style peri/pmb
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pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre
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|
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[Description:]
|
||||
|
||||
Style {peri/pmb} style implements the Peridynamic bond-based prototype
|
||||
microelastic brittle (PMB) model, which can be used to model materials
|
||||
at the mesoscopic or macroscopic scale. The canonical paper on
|
||||
Peridynamics is "(Silling)"_#Silling. The implementation of
|
||||
Peridynamics in LAMMPS is described in "(Parks)"_#Parks. Also see the
|
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"PDLAMMPS user
|
||||
guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for more
|
||||
details about this particular potential and using it in LAMMPS.
|
||||
|
||||
The following coefficients must be defined for each pair of atom
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands, or by mixing as described below:
|
||||
|
||||
c (energy/distance/volume^2 units)
|
||||
horizon (distance units)
|
||||
s00 (unitless)
|
||||
alpha (unitless) :ul
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support mixing. Thus, coefficients for all
|
||||
I,J pairs must be specified explicitly.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift option.
|
||||
|
||||
The "pair_modify"_pair_modify.html table and tail options are not
|
||||
relevant for this pair style.
|
||||
|
||||
This pair style writes its information to "binary restart
|
||||
files"_restart.html, so pair_style and pair_coeff commands do not need
|
||||
to be specified in an input script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {peri/pmb} style is part of the "peri" package. It is only
|
||||
enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Parks)
|
||||
[(Parks)] Parks, Lehoucq, Plimpton, Silling, to appear in Comp Phys
|
||||
Comm, (2008).
|
||||
|
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:link(Silling)
|
||||
[(Silling)] Silling, J Mech Phys Solids, 48, 175-209 (2000).
|
||||
|
|
@ -133,7 +133,8 @@ the pair_style command, and coefficients specified by the associated
|
|||
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
|
||||
"pair_style morse"_pair_morse.html - Morse potential
|
||||
"pair_style morse/opt"_pair_morse.html - optimized version of Morse potential
|
||||
"pair_style peri/pmb"_pair_peri_pmb.html - peridynamic PMB potential
|
||||
"pair_style peri/lps"_pair_peri.html - peridynamic LPS potential
|
||||
"pair_style peri/pmb"_pair_peri.html - peridynamic PMB potential
|
||||
"pair_style reax"_pair_reax.html - ReaxFF potential
|
||||
"pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
|
||||
"pair_style soft"_pair_soft.html - Soft (cosine) potential
|
||||
|
|
|
|||
|
|
@ -0,0 +1,106 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
read_dump command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
read_dump filename N col1 col2 ... keyword value ... :pre
|
||||
|
||||
filename = name of dump file to read snapshot from :ulb,l
|
||||
N = timestamp to read in :l
|
||||
col1, col2, ... = {x} or {y} or {z} or {xs} or {ys} or {zs} or {xu} or {yu} or {zu} or {ix} or {iy} or {iz} or {vx} or {vy} or {vz} :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {procs} or {box} :l
|
||||
{procs} value = P
|
||||
P = number of processors that wrote out dump file
|
||||
{box} value = {reset} or {ignore} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
read_dump dump.run 1000 x y z
|
||||
read_dump dump.poly.% 50000 xs ys zs vx vy vz procs 100 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Read a snapshot at timestamp N from the specified dump file and use
|
||||
the specified per-atom column information from the snapshot to
|
||||
overwrite current per-atom values. The dump file must be in the
|
||||
native LAMMPS format, as produced by an {atom} or {custom} style
|
||||
"dump"_dump.html command.
|
||||
|
||||
The specified filename can contain the "%" wild-card character. This
|
||||
means that individual dump files were written by each of the P
|
||||
processors the original simulation was running on, where "%" is
|
||||
replaced by the processor ID from 0 to P-1. If the current simulation
|
||||
is not running on the same number of processors, then the {procs}
|
||||
keyword must be used to specify what P was in the original simulation,
|
||||
so that the current simulation knows which files to read. If the "%"
|
||||
wild-card character is not used, or the current simulation is running
|
||||
on the same number of processors, then the {procs} keyword should not
|
||||
be used.
|
||||
|
||||
{N} is the timestamp of the snapshot that will be read from the dump
|
||||
file. The file will be scanned until the snapshot with that timestamp
|
||||
is found. The timestep of the current simulation will not be reset to
|
||||
{N}. Use the "reset_timestep"_reset_timestep.html command if this is
|
||||
desired.
|
||||
|
||||
The dump file snapshot defines a simulation box size via its ITEM: BOX
|
||||
BOUNDS field. If the setting for the optional {box} keyword is
|
||||
{ignore} then the box size settings are ignored. If the setting for
|
||||
the {box} keyword is {reset} then the current simulation box size is
|
||||
reset to the values in the dump snapshot. Note that due to the finite
|
||||
precision at which numeric values are written into a dump file, box
|
||||
sizes values which are identical to the current box size may be read
|
||||
in as slightly different values. Hence you should not reset the box
|
||||
size if you expect it to be the same.
|
||||
|
||||
The dump file snapshot defines the number of atom in the snapshot via
|
||||
its ITEM: NUMBER OF ATOMS field. If this number does not match the
|
||||
number of atoms in the current simulation, then a WARNING is printed.
|
||||
|
||||
The dump file snapshot defines a list of per-atom quantities via its
|
||||
ITEM: ATOMS field. Any of the quantities listed above may be
|
||||
specified, in which case that per-atom quantity is read from the dump
|
||||
file and overwrites the corresponding current quantity. See the
|
||||
"dump"_dump.html command for an explanation of these quantities.
|
||||
|
||||
Atom IDs must also appear in the dump file. They are used to map
|
||||
read-in atoms to current atoms one by one. Note that if some current
|
||||
atoms do not appear in the dump file, their values are not
|
||||
overwritten. Likewise if atom IDs appear in the dump file which do
|
||||
not exist in the current simulation, their read-in values are ignored.
|
||||
|
||||
The various flavors of atom coordinates that can appear in the dump
|
||||
file ({x} or {xs} or {xu}) are all converted into internal LAMMPS
|
||||
coordinates (equivalent to {x}). Each atom is also remapped to the
|
||||
current simulation box, if it is outside periodic boundaries. Note
|
||||
that the current simulation box size may have been reset to the dump
|
||||
snapshot box size before this takes place.
|
||||
|
||||
IMPORTANT NOTE: Image flags from the dump file ({ix}, {iy}, {iz})
|
||||
should only be read-in if the corresponding coordinates are of the {x}
|
||||
or {xs} form. In this case, the remap of each atom to the (new)
|
||||
periodic box should update its read-in image flags correctly. If the
|
||||
read-in coordinates are of the {xu} form, then no corresponding image
|
||||
flags should be read-in. This is because the image flags are
|
||||
initialized to 0 when {xu} style coordinates are read. The remap of
|
||||
atoms to the (new) periodic box should update the re-initialized image
|
||||
flags correctly.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"read_data"_read_data.html, "read_restart"_read_restart.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are box = ignore.
|
||||
Loading…
Reference in New Issue