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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13836 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp 2015-08-05 00:28:53 +00:00
parent e5beeb163b
commit fbfd916c69
38 changed files with 1898 additions and 28 deletions
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15
doc/doc2/Section_commands.html
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@ -438,8 +438,9 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qbmsst.html">qbmsst</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
<TR ALIGN="center"><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_smd_adjust_dt.html">smd/adjust/dt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_smd_integrate_tlsph.html">smd/integrate/tlsph</A></TD><TD ><A HREF = "fix_smd_integrate_ulsph.html">smd/integrate/ulsph</A></TD><TD ><A HREF = "fix_smd_move_triangulated_surface.html">smd/move/triangulated/surface</A></TD><TD ><A HREF = "fix_smd_setvel.html">smd/setvel</A></TD><TD ><A HREF = "fix_smd_tlsph_reference_configuration.html">smd/tlsph/reference/configuration</A></TD><TD ><A HREF = "fix_smd_wall_surface.html">smd/wall/surface</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
</TD></TR></TABLE></DIV>
<HR>
@ -474,8 +475,11 @@ package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_fep.html">fep</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_smd_contact_radius.html">smd/contact/radius</A></TD><TD ><A HREF = "compute_smd_damage.html">smd/damage</A></TD><TD ><A HREF = "compute_smd_hourglass_error.html">smd/hourglass/error</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_internal_energy.html">smd/internal/energy</A></TD><TD ><A HREF = "compute_smd_plastic_strain.html">smd/plastic/strain</A></TD><TD ><A HREF = "compute_smd_plastic_strain_rate.html">smd/plastic/strain/rate</A></TD><TD ><A HREF = "compute_smd_rho.html">smd/rho</A></TD><TD ><A HREF = "compute_smd_tlsph_defgrad.html">smd/tlsph/defgrad</A></TD><TD ><A HREF = "compute_smd_tlsph_dt.html">smd/tlsph/dt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_tlsph_num_neighs.html">smd/tlsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_tlsph_shape.html">smd/tlsph/shape</A></TD><TD ><A HREF = "compute_smd_tlsph_strain.html">smd/tlsph/strain</A></TD><TD ><A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_tlsph_stress.html">smd/tlsph/stress</A></TD><TD ><A HREF = "compute_smd_triangle_mesh_vertices.html">smd/triangle/mesh/vertices</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_num_neighs.html">smd/ulsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph/strain</A></TD><TD ><A HREF = "compute_smd_ulsph_strain/rate.html">smd/ulsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_ulpsh_stress.html">smd/ulpsh/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
</TD></TR></TABLE></DIV>
<HR>
@ -530,7 +534,8 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (gko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_smd_hertz.html">smd/hertz</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_smd_tlsph.html">smd/tlsph</A></TD><TD ><A HREF = "pair_smd_triangulated_surface.html">smd/triangulated/surface</A></TD><TD ><A HREF = "pair_smd_ulsph.html">smd/ulsph</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_thole.html">thole</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>

17
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@ -140,6 +140,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
<TR ALIGN="center"><TD >USER-QTB</TD><TD > quantum nuclear effects</TD><TD > Yuan Shen (Stanford)</TD><TD > <A HREF = "fix_qtb.html">fix qtb</A> <A HREF = "fix_qbmsst.html">fix_qbmsst</A></TD><TD > qtb</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-QUIP</TD><TD > QUIP/libatoms interface</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "pair_quip.html">pair_style quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</TD></TR>
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SMD</TD><TD > smoothed Mach dynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/smd/SMD_user_guide.pdf">userguide.pdf</A></TD><TD > USER/smd</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
@ -639,6 +640,22 @@ questions.
</P>
<HR>
<H4>USER-SMD package
</H4>
<P>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
</P>
<P>???
</P>
<P>See the file doc/USER/smd/SPH_user_guide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/smd.
</P>
<P>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
</P>
<H4>USER-SPH package
</H4>
<P>This package implements smoothed particle hydrodynamics (SPH) in

10
doc/doc2/atom_style.html
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@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>template</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>smd</I> or <I>sphere</I> or <I>tri</I> or <I>template</I> or <I>hybrid</I>
<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
<I>body</I> args = bstyle bstyle-args
@ -80,6 +80,7 @@ quantities.
<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
<TR><TD ><I>smd</I> </TD><TD > volume, kernel diameter, contact radius, mass </TD><TD > solid and fluid SPH particles </TD></TR>
<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
<TR><TD ><I>template</I> </TD><TD > template index, template atom </TD><TD > small molecules with fixed topology </TD></TR>
<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
@ -128,6 +129,13 @@ per-particle mass and volume.
particles which store a density (rho), energy (e), and heat capacity
(cv).
</P>
<P>The <I>smd</I> style is for a general formulation of Smooth Particle
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetretating each other.
</P>
<P>The <I>wavepacket</I> style is similar to <I>electron</I>, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate

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@ -0,0 +1,58 @@
<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>compute smd/contact_radius command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/contact_radius
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/contact_radius = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/contact_radius
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other.
The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles,
e.g., smd/hertz and smd/tri_surface.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in
LAMMPS.
</P>
<P>The value of the contact radius will be 0.0 for particles not in the
specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-particle vector values will be in distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A> smd/hertz smd/tri_surface
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,53 @@
<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>compute smd/damage command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/damage
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/damage = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/damage
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the damage status of SPH particles
according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output Info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle values are dimensionless an in the range of zero to one.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_plastic_strain.html">smd/plastic_strain</A>, <A HREF = "compute_smd_tlsph_stress.html">smd/tlsph_stress</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,61 @@
<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>compute smd/hourglass_error command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/hourglass_error
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/hourglass_error = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/hourglass_error
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation which outputs the error of the approximated
relative separation with respect to the actual relative separation of
the particles i and j. Ideally, if the deformation gradient is exact,
and there exists a unique mapping between all particles' positions
within the neighborhood of the central node and the deformation gradient,
the approximated relative separation will coincide with the actual relative
separation of the particles i and j in the deformed configuration.
This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output Info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle vector values will are dimensionless. See <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>This quantity will be computed only for particles which interact with tlsph pair style.
</P>
<P><B>Related Commands:</B>
</P>
<P><A HREF = "compute_smd_tlsph_defgrad.html">smd/tlsph_defgrad</A>
</P>
<P><B>Default:</B>
</P>
</HTML>

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@ -0,0 +1,51 @@
<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>compute smd/internal_energy command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/internal_energy
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/smd/internal_energy = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/internal_energy
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output Info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle vector values will be given in <A HREF = "units.html">units</A> of energy.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.
</P>
<P><B>Related Commands:</B>
</P>
<P><B>Default:</B>
</P>
</HTML>

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<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>compute smd/plastic_strain command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/plastic_strain
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/plastic_strain = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/plastic_strain
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the equivalent plastic strain per particle.
This command is only meaningful if a material model with plasticity is defined.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output Info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle values will be given dimensionless. See <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_tlsph_strain.html">smd/plastic_strain_rate</A>, <A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph_strain_rate</A>,
<A HREF = "compute_smd_tlsph_strain.html">smd/tlsph_strain</A>
</P>
<P><B>Default:</B> none</P>
</HTML>

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<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>compute smd/plastic_strain_rate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/plastic_strain_rate
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/plastic_strain_rate = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/plastic_strain_rate
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the time rate of the equivalent plastic strain.
This command is only meaningful if a material model with plasticity is defined.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output Info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle values will be given in <A HREF = "units.html">units</A> of one over time.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_plastic_strain.html">smd/plastic_strain</A>, <A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph_strain_rate</A>,
<A HREF = "compute_smd_tlsph_strain.html">smd/tlsph_strain</A>
</P>
<P><B>Default:</B> none</P>
</HTML>

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<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>compute smd/rho command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/rho
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/rho = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/rho
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-particle mass density.
The mass density is the mass of a particle which is constant during
the course of a simulation, divided by its volume, which can change due to mechanical deformation.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle values will be in <A HREF = "units.html">units</A> of mass over volume.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_vol.html">smd/vol</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/tlsph_defgrad command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/tlsph_defgrad
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/tlsph_defgrad = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/tlsph_defgrad
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the deformation gradient.
It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in
LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute outputss a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle vector values will be given dimensionless. See <A HREF = "units.html">units</A>.
The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components
of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info. TThis compute can only be used for particles which interact via the
total Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_hourglass_error.html">smd/hourglass_error</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/tlsph_dt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/tlsph_dt
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/tlsph_dt = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/tlsph_dt
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the CFL-stable time increment per particle.
This time increment is essentially given by the speed of sound, divided by the SPH smoothing length.
Because both the speed of sound and the smoothing length typically change during the course of a simulation,
the stable time increment needs to be recomputed every time step.
This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle values will be given in <A HREF = "units.html">units</A> of time.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_smd_adjust_dt.html">smd/adjust_dt</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/tlsph_num_neighs command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/tlsph_num_neighs
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/tlsph_num_neighs = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/tlsph_num_neighs
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the number of particles
inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle values are dimensionless. See <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>This quantity will be computed only for particles which interact with the Total-Lagrangian pair style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd/ulsph_num_neighs.html">smd/ulsph_num_neighs</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/tlsph_shape command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/tlsph_shape
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/tlsph_shape = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/tlsph_shape
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid.
It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of length.
These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle.
The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_contact_radius.html">smd/contact_radius</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/tlsph_strain command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/tlsph_strain
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/tlsph_strain = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/tlsph_strain
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle tensor values will be given dimensionless. See <A HREF = "units.html">units</A>.
</P>
<P>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain tensor.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph_strain_rate</A>, <A HREF = "compute_smd_tlsph_stress.html">smd/tlsph_stress</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/tlsph_strain_rate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/tlsph_strain_rate
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/tlsph_strain_rate = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/tlsph_strain_rate
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The values will be given in <A HREF = "units.html">units</A> of one over time.
</P>
<P>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_tlsph_strain.html">smd/tlsph_strain</A>, <A HREF = "compute_smd_tlsph_stress.html">smd/tlsph_stress</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/tlsph_stress command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/tlsph_stress
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/tlsph_stress = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/tlsph_stress
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The values will be given in <A HREF = "units.html">units</A> of pressure.
</P>
<P>The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components
of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e.,
the von Mises equivalent stress.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_tlsph_strain.html">smd/tlsph_strain</A>, <A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph_strain_rate</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/triangle_mesh_vertices
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/triangle_mesh_vertices
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/triangle_mesh_vertices = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/triangle_mesh_vertices
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that returns the coordinates of the vertices
corresponding to the triangle-elements of a mesh created by the <A HREF = "fix_smd_wall_surface.html">fix smd/wall_surface</A>.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute returns a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute as
input. See <A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding
to the first, second, and third vertex of each triangle.
</P>
<P>It is only meaningful to use this compute for a group of particles which is created via the
<A HREF = "fix_smd_wall_surface.html">fix smd/wall_surface</A> command.
</P>
<P>The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the
smd/wall_surace mesh for visualization purposes.
</P>
<P>The values will be given in <A HREF = "units.html">units</A> of distance.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_smd_move_triangulated_surface.html">smd/move_tri_surf</A>, <A HREF = "fix_smd_wall_surface.html">smd/wall_surface</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/ulsph_num_neighs command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/ulsph_num_neighs
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/ulsph_num_neighs = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/ulsph_num_neighs
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that returns the number of neighbor particles
inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute returns a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-particle values will be given dimentionless, see <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P>smd/tlsph_num_neighs
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/ulsph_strain command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/ulsph_strain
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/ulsph_strain = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/ulsph_strain
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the logarithmic strain tensor.
for particles interacting via the updated Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle tensor, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.
</P>
<P>The per-particle tensor values will be given dimensionless, see <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P>smd/tlsph_strain
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/ulsph_strain_rate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/ulsph_strain_rate
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/ulsph_strain_rate = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/ulsph_strain_rate
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the rate of the logarithmic strain tensor
for particles interacting via the updated Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector of vectors (tensors), which
can be accessed by any command that uses per-particle values from a compute
as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The values will be given in <A HREF = "units.html">units</A> of one over time.
</P>
<P>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<P>smd/utsph_strain_rate
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/ulsph_stress command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/ulsph_stress
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/ulsph_stress = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/ulsph_stress
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that outputs the Cauchy stress tensor.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
for an overview of LAMMPS output options.
</P>
<P>The values will be given in <A HREF = "units.html">units</A> of pressure.
</P>
<P>The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components
of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e.,
the von Mises equivalent stress.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
</P>
<P><B>Related commands:</B>
</P>
<PRE><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph_strain</A>, <A HREF = "compute_smd_ulsph_strain_rate.html">smd/ulsph_strain_rate</A>
<A HREF = "compute_smd_tlsph_stress.html">smd/tlsph_stress</A>
</PRE>
<P><B>Default:</B> none
</P>
</HTML>

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<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>compute smd/vol command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID smd/vol
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>smd/vol = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all smd/vol
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the
group for which the fix is defined.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in
LAMMPS.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">How-to discussions, section 6.15</A>
for an overview of LAMMPS output options.
</P>
<P>The per-particle vector values will be given in <A HREF = "units.html">units</A> of volume.
</P>
<P>Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the
group for which the fix is defined.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_rho.html">smd/rho</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

18
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@ -148,13 +148,9 @@ coordinates are chosen at a random position within the current
simulation cell or region, and new atom velocities are randomly chosen from
the specified temperature distribution given by T. Relative
coordinates for atoms in a molecule are taken from the template
molecule provided by the user, with the origin of the relative
coordinates coinciding with the chosen insertion point. This means
that if the origin of the template molecule coordinate system
lies far from the center of the template molecule,
the inserted molecule will lie far from the insertion point.
A random initial rotation is used in
the case of molecule insertions.
molecule provided by the user. The center of mass of the molecule
is placed at the insertion point. The orientation of the molecule
is chosen at random by rotating about this point.
</P>
<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
specifies a <I>template-ID</I> previously defined using the
@ -182,11 +178,9 @@ the angle in degrees. Rotations are performed by generating a random
point on the unit sphere and a random rotation angle on the
range [0,maxangle). The molecule is then rotated by that angle about an
axis passing through the molecule center of mass. The axis is parallel
to the unit vector defined by the point on the unit sphere. The
same procedure is used for randomly rotating molecules when they
are inserted, except that the rotation axis passes through whatever
origin is used for the molecule template, and the maximum angle is
360 degrees.
to the unit vector defined by the point on the unit sphere.
The same procedure is used for randomly rotating molecules when they
are inserted, except that the maximum angle is 360 degrees.
</P>
<P>Note that fix GCMC does not use configurational bias
MC or any other kind of sampling of intramolecular degrees of freedom.

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<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>fix smd/adjust_dt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID smd/adjust_dt arg
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>smd/adjust_dt = style name of this fix command
<LI>arg = <I>s_fact</I>
<PRE> <I>s_fact</I> = safety factor
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all smd/adjust_dt 0.1
</PRE>
<P><B>Description:</B>
</P>
<P>The fix calculates a new stable time increment for use with the SMD time integrators.
</P>
<P>The stable time increment is based on multiple conditions. For the SPH pair styles, a
CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of
sound cannot propagate further than a typical spacing between particles within a single time step to ensure
no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
stable maximum time step.
</P>
<P>This fix inquires the minimum stable time increment across all particles contained in the group for which this
fix is defined. An additional safety factor <I>s_fact</I> is applied to the time increment.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>Currently, no part of USER-SMD supports restarting nor minimization.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_tlsph_dt.html">smd/tlsph_dt</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,59 @@
<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>fix smd/integrate_tlsph command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID smd/integrate_tlsph keyword values
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>smd/integrate_tlsph = style name of this fix command
<LI>zero or more keyword/value pairs may be appended
</UL>
<LI>keyword = <I>limit_velocity</I>
<PRE> <I>limit_velocity</I> value = max_vel
max_vel = maximum allowed velocity
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all smd/integrate_tlsph
fix 1 all smd/integrate_tlsph limit_velocity 1000
</PRE>
<P><B>Description:</B>
</P>
<P>The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P>The <I>limit_velocity</I> keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_smd_integrate_ulsph.html">smd/integrate_ulsph</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>fix smd/integrate_ulsph command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID smd/integrate_ulsph keyword
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>smd/integrate_ulsph = style name of this fix command
<LI>zero or more keyword/value pairs may be appended
</UL>
<P>keyword = adjust_radius or limit_velocity
</P>
<P>adjust_radius values = adjust_radius_factor min_nn max_nn
adjust_radius_factor = factor which scale the smooth/kernel radius
min_nn = minimum number of neighbors
max_nn = maximum number of neighbors
limit_velocity values = max_velocity
max_velocity = maximum allowed velocity.
</P>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
</PRE>
<PRE>fix 1 all smd/integrate_ulsph limit_velocity 1000
</PRE>
<P><B>Description:</B>
</P>
<P>The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style.
See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P>The <I>adjust_radius</I> keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
within the interval <I>min_nn</I> to <I>max_nn</I>. The parameter <I>adjust_radius_factor</I> determines the amount of adjustment per timestep. Typical values are
<I>adjust_radius_factor</I>=1.02, <I>min_nn</I>=15, and <I>max_nn</I>=20.
</P>
<P>The <I>limit_velocity</I> keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,81 @@
<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>fix smd/move_tri_surf command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID smd/move_tri_surf keyword
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>smd/move_tri_surf keyword = style name of this fix command
<LI>keyword = <I>*LINEAR</I> or <I>*WIGGLE</I> or <I>*ROTATE</I>
<PRE> <I>*LINEAR</I> args = Vx Vy Vz
Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
<I>*WIGGLE</I> args = Vx Vy Vz max_travel
vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
max_travel = wiggle amplitude
<I>*ROTATE</I> args = Px Py Pz Rx Ry Rz period
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
period = period of rotation (time units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
</PRE>
<P><B>Description:</B>
</P>
<P>This fix applies only to rigid surfaces read from .STL files via fix <A HREF = "fix_smd_wall_surface.html">smd/wall_surface</A> .
It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
The rigid surfaces can thus be moved along simple trajectories during the simulation.
</P>
<P>The <I>*LINEAR</I> style moves particles with the specified constant velocity
vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
to V = (Vx,Vy,Vz).
</P>
<P>The <I>*WIGGLE</I> style moves particles in an oscillatory fashion.
Particles are moved along (vx, vy, vz) with constant velocity until a
displacement of max_travel is reached. Then, the velocity vector is
reversed. This process is repeated.
</P>
<P>The <I>*ROTATE</I> style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
goes through a point P = (Px,Py,Pz). The period of the rotation is also
specified. This style also sets the velocity of each particle to (omega cross
Rperp) where omega is its angular velocity around the rotation axis and
Rperp is a perpendicular vector from the rotation axis to the particle.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to using Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_triangle_mesh_vertices.html">smd/triangle_mesh_vertices</A>, <A HREF = "fix_smd_wall_surface.html">smd/wall_surface</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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<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>fix smd/setvel command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID smd/setvel vx vy vz keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>smd/setvel = style name of this fix command
<LI>vx,vy,vz = velocity component values
<LI>any of vx,vy,vz can be a variable (see below)
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>region</I>
<PRE> <I>region</I> value = region-ID
region-ID = ID of region particles must be in to have their velocities set
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix top_velocity top_group setvel 1.0 0.0 0.0
</PRE>
<P><B>Description:</B>
</P>
<P>Set each component of velocity on each particle in the group to the specified
values vx,vy,vz, regardless of the forces acting on the particle. This command can
be used to impose velocity boundary conditions.
</P>
<P>Any of the vx,vy,vz values can be specified as NULL which means do not
alter the velocity component in that dimension.
</P>
<P>This fix is indented to be used together with a time integration fix.
</P>
<P>Any of the 3 quantities defining the velocity components can be specified
as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>vx</I>,
<I>vy</I>, <I>vz</I>. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent velocity field.
</P>
<P>Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent velocity
field with optional time-dependence as well.
</P>
<P>If the <I>region</I> keyword is used, the particle must also be in the
specified geometric <A HREF = "region.html">region</A> in order to have its velocity set by this command.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>Currently, no part of USER-SMD supports restarting nor minimization
None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a global 3-vector of forces, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
total force on the group of atoms. The vector values calculated by this
fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,2 @@
<HTML>
</HTML>

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<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>fix smd/wall_surface command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID smd/wall_surface arg type mol-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>smd/wall_surface = style name of this fix command
<LI>arg = <I>file</I>
<PRE> <I>file</I> = file name of a triangular mesh in stl format
</PRE>
<LI>type = particle type to be given to the new particles created by this fix
<LI>mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix stl_surf all smd/wall_surface tool.stl 2 65535
</PRE>
<P><B>Description:</B>
</P>
<P>This fix creates reads a traingulated surface from a file in .STL format.
For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions.
The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.
</P>
<P>The triangulated surface can be used as a complex rigid wall via the <A HREF = "pair_smd_triangulated_surface.html">smd/tri_surface</A> pair style.
It is possible to move the triangulated surface via the <A HREF = "fix_smd_move_triangulated_surface.html">smd/move_tri_surf</A> fix style.
</P>
<P>Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
in the system. See the "funnel_flow" example in the USER-SMD examples directory.
</P>
<P>See <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</A> to use Smooth Mach Dynamics in LAMMPS.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535.
</P>
<P>Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_smd_triangle_mesh_vertices.html">smd/triangle_mesh_vertices</A>, <A HREF = "fix_smd_move_triangulated_surface.html">smd/move_tri_surf</A>, <A HREF = "pair_smd_triangulated_surface.html">smd/tri_surface</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,60 @@
<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 smd/hertz command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style smd/hertz scale_factor
</PRE>
<P><B>Examples:</B>
</P>
<P>pair_style smd/hertz 1.0
pair_coeff 1 1 <contact_stiffness>
</P>
<P><B>Description:</B>
</P>
<P>The <I>smd/hertz</I> style calculates contact forces between SPH particles belonging to different physical bodies.
</P>
<P>The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles
(whose spatial extents are defined via its contact radius).
The effect is that a particles cannot penetrate into each other.
The parameter <contact_stiffness> has units of pressure and should equal roughly one half
of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
</P>
<P>The parameter <I>scale_factor</I> can be used to scale the particles' contact radii. This can be useful to control how close
particles can approach each other. Usually, <I>scale_factor</I>=1.0.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_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>
</HTML>

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@ -0,0 +1,70 @@
<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 smd/tlsph command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style smd/tlsph args
</PRE>
<P><B>Examples:</B>
</P>
<P>pair_style smd/tlsph
</P>
<P><B>Description:</B>
</P>
<P>The <I>smd/tlsph</I> style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.
</P>
<P>This pair style is invoked with the following command:
</P>
<PRE>pair_style smd/tlsph
pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
*END
</PRE>
<P>Here, <I>i</I> and <I>j</I> denote the <I>LAMMPS</I> particle types for which this pair style is
defined. Note that <I>i</I> and <I>j</I> must be equal, i.e., no <I>tlsph</I> cross interactions
between different particle types are allowed.
In contrast to the usual <I>LAMMPS</I> <I>pair coeff</I> definitions, which are given solely a
number of floats and integers, the <I>tlsph</I> <I>pair coeff</I> definition is organised using
keywords. These keywords mark the beginning of different sets of parameters for particle properties,
material constitutive models, and damage models. The <I>pair coeff</I> line must be terminated with
the <I>*END</I> keyword. The use the line continuation operator <I>&</I> is recommended. A typical
invocation of the <I>tlsph</I> for a solid body would consist of an equation of state for computing
the pressure (the diagonal components of the stress tensor), and a material model to compute shear
stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.
</P>
<P>Please see the <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">SMD user guide</A> for a complete listing of the possible keywords and material models.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_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>
</HTML>

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@ -0,0 +1,61 @@
<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 smd/tri_surface command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style smd/tri_surface scale_factor
</PRE>
<P><B>Examples:</B>
</P>
<P>pair_style smd/tri_surface 1.0
pair_coeff 1 1 <contact_stiffness>
</P>
<P><B>Description:</B>
</P>
<P>The <I>smd/tri_surface</I> style calculates contact forces between SPH particles and a rigid wall boundary defined via the
<A HREF = "fix_smd_wall_surface.html">smd/wall_surface</A> fix.
</P>
<P>The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle
(whose spatial extents are defined via its contact radius) and the triangle.
The effect is that a particle cannot penetrate into the triangular surface.
The parameter <contact_stiffness> has units of pressure and should equal roughly one half
of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
</P>
<P>The parameter <I>scale_factor</I> can be used to scale the particles' contact radii. This can be useful to control how close
particles can approach the triangulated surface. Usually, <I>scale_factor</I>=1.0.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_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>
</HTML>

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@ -0,0 +1,76 @@
<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 smd/ulsph command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style smd/ulsph args
</PRE>
<LI>these keywords must be given
<P>keyword = <I>*DENSITY_SUMMATION</I> or <I>*DENSITY_CONTINUITY</I> and <I>*VELOCITY_GRADIENT</I> or <I>*NO_VELOCITY_GRADIENT</I> and <I>*GRADIENT_CORRECTION</I> or <I>*NO_GRADIENT_CORRECTION</I>
</P>
<P><B>Examples:</B>
</P>
<P>pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
</P>
<P><B>Description:</B>
</P>
<P>The <I>smd/ulsph</I> style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.
</P>
<P>This pair style is invoked similar to the following command:
</P>
<PRE>pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
*END
</PRE>
<P>Here, <I>i</I> and <I>j</I> denote the <I>LAMMPS</I> particle types for which this pair style is
defined. Note that <I>i</I> and <I>j</I> can be different, i.e., <I>ulsph</I> cross interactions
between different particle types are allowed. However, <I>i</I>--<I>i</I> respectively <I>j</I>--<I>j</I> pair_coeff lines have to preceed a cross interaction.
In contrast to the usual <I>LAMMPS</I> <I>pair coeff</I> definitions, which are given solely a
number of floats and integers, the <I>ulsph</I> <I>pair coeff</I> definition is organised using
keywords. These keywords mark the beginning of different sets of parameters for particle properties,
material constitutive models, and damage models. The <I>pair coeff</I> line must be terminated with
the <I>*END</I> keyword. The use the line continuation operator <I>&</I> is recommended. A typical
invocation of the <I>ulsph</I> for a solid body would consist of an equation of state for computing
the pressure (the diagonal components of the stress tensor), and a material model to compute shear
stresses (the off-diagonal components of the stress tensor).
</P>
<P>Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.
</P>
<P>Please see the <A HREF = "USER/smd/SMD_LAMMPS_userguide.pdf">SMD user guide</A> for a complete listing of the possible keywords and material models.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_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>
</HTML>

8
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View File

@ -43,8 +43,8 @@
<I>vel</I> values = loop dist
loop = <I>all</I> or <I>local</I> or <I>geom</I>, used in dephasing
dist = <I>uniform</I> or <I>gaussian</I>, used in dephasing
<I>time</I> value = <I>step</I> or <I>clock</I>
<I>step</I> = simulation runs for N timesteps on each replica (default)
<I>time</I> value = <I>steps</I> or <I>clock</I>
<I>steps</I> = simulation runs for N timesteps on each replica (default)
<I>clock</I> = simulation runs for N timesteps across all replicas
</PRE>
@ -171,7 +171,7 @@ dynamics have been performed. Note that <I>N</I> only includes the
dynamics of stages 2 and 3, not the steps taken during dephasing or
the minimization iterations of quenching. The specified <I>N</I> is
interpreted in one of two ways, depending on the <I>time</I> keyword. If
the <I>time</I> value is <I>step</I>, which is the default, then each replica
the <I>time</I> value is <I>steps</I>, which is the default, then each replica
runs for <I>N</I> timesteps. If the <I>time</I> value is <I>clock</I>, then the
simulation runs until <I>N</I> aggregate timesteps across all replicas have
elapsed. This aggregate time is the "clock" time defined below, which
@ -323,7 +323,7 @@ dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
<P><B>Default:</B>
</P>
<P>The option defaults are min = 0.1 0.1 40 50, no temp setting, vel =
geom gaussian, and time = step.
geom gaussian, and time = steps.
</P>
<HR>

3
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View File

@ -559,6 +559,7 @@ of analysis.
<TR><TD >meso</TD><TD > atom-ID atom-type rho e cv x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
<TR><TD >smd</TD><TD > atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z</TD></TR>
<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >template</TD><TD > atom-ID molecule-ID template-index template-atom atom-type x y z</TD></TR>
<TR><TD >tri</TD><TD > atom-ID molecule-ID atom-type triangleflag density x y z</TD></TR>
@ -591,6 +592,8 @@ of analysis.
<LI>eradius = electron radius (or fixed-core radius)
<LI>etag = integer ID of electron that each wavepacket belongs to
<LI>cs_re,cs_im = real/imaginary parts of wavepacket coefficients
<LI>kernel_radius = ??? (distance units)
<LI>contact_radius = ??? (distance units)
</UL>
<P>The units for these quantities depend on the unit style; see the
<A HREF = "units.html">units</A> command for details.

27
doc/doc2/set.html
View File

@ -23,7 +23,7 @@
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat</I> or <I>quat/random</I> or <I>diameter</I> or <I>shape</I> or <I>length</I> or <I>tri</I> or <I>theta</I> or <I>angmom</I> or <I>mass</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
<I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or
<I>meso_e</I> or <I>meso_cv</I> or <I>meso_rho</I> or <I>i_name</I> or <I>d_name</I>
<I>meso_e</I> or <I>meso_cv</I> or <I>meso_rho</I> or <I>smd_contact_radius</I> or <I>smd_mass_density</I> or <I>i_name</I> or <I>d_name</I>
<PRE> <I>type</I> value = atom type
value can be an atom-style variable (see below)
@ -83,10 +83,12 @@
value can be an atom-style variable (see below)
<I>meso_rho</I> value = density of SPH particles (need units)
value can be an atom-style variable (see below)
<I>i_name</I> value = value for custom integer vector with name
value can be an atom-style variable (see below)
<I>d_name</I> value = value for custom floating-point vector with name
<I>smd_contact_radius</I> = radius for short range interactions, i.e. contact and friction
value can be an atom-style variable (see below)
<I>smd_mass_density</I> = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
<I>i_name</I> value = value for custom integer vector with name
<I>d_name</I> value = value for custom floating-point vector with name
</PRE>
</UL>
@ -316,6 +318,20 @@ assumed to be in mass/distance^2 units). If none of these cases are
valid, then the mass is set to the density value directly (the input
density is assumed to be in mass units).
</P>
<P>Keyword <I>smd_mass_density</I> also sets the mass of all selected
particles, but it is only applicable to the Smooth Mach Dynamics
package USER-SMD. This command assumes that the particle volume has
already been correctly set and calculates particle mass from the
provided mass density value.
</P>
<P>Keyword <I>smd_contact_radius</I> only applies to simulations with the
Smooth Mach Dynamics package USER-SMD. This command sets an
interaction radius for computing short-range interactions,
e.g. repulsive forces to prevent different individual physical bodies
from penetrating each other. Note that the SPH smoothing kernel
diameter used for computing long range, nonlocal interactions, is set
using the <I>diameter</I> keyword.
</P>
<P>Keyword <I>volume</I> sets the volume of all selected particles.
Currently, only the <A HREF = "atom_style.html">atom_style peri</A> command defines
particles with a volume attribute. Note that this command does not
@ -331,8 +347,7 @@ the simulation. The flags can be output with atom snapshots via the
nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 can be
specified. This keyword does not allow use of atom-style variables.
</P>
<P>This command can be useful after a system has been equilibrated and
This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion