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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@830 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2007-09-05 16:05:47 +00:00
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8
doc/Section_commands.html
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@ -321,10 +321,10 @@ description:
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>

1
doc/Section_commands.txt
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@ -403,6 +403,7 @@ description:
"nve/asphere"_fix_nve_asphere.html,
"nve/dipole"_fix_nve_dipole.html,
"nve/gran"_fix_nve_gran.html,
"nve/limit"_fix_nve_limit.html,
"nve/noforce"_fix_nve_noforce.html,
"nvt"_fix_nvt.html,
"nvt/asphere"_fix_nvt_asphere.html,

1
doc/fix.html
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@ -99,6 +99,7 @@ for individual fixes for info on which ones can be restarted.
<LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A> - NVT for aspherical particles
<LI><A HREF = "fix_nve_dipole.html">fix nve/dipole</A> - NVE for point dipolar particles
<LI><A HREF = "fix_nve_gran.html">fix nve/gran</A> - NVE for granular particles
<LI><A HREF = "fix_nve_limit.html">fix nve/limit</A> - NVE with limited step length
<LI><A HREF = "fix_nve_noforce.html">fix nve/noforce</A> - NVE without forces (v only)
<LI><A HREF = "fix_nvt.html">fix nvt</A> - constant NVT time integration via Nose/Hoover
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A> - NVT for aspherical particles

1
doc/fix.txt
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@ -98,6 +98,7 @@ Here is an alphabetic list of fix styles available in LAMMPS:
"fix nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles
"fix nve/dipole"_fix_nve_dipole.html - NVE for point dipolar particles
"fix nve/gran"_fix_nve_gran.html - NVE for granular particles
"fix nve/limit"_fix_nve_limit.html - NVE with limited step length
"fix nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"fix nvt"_fix_nvt.html - constant NVT time integration via Nose/Hoover
"fix nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles

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doc/fix_nve_limit.html Normal file
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@ -0,0 +1,72 @@
<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 nve/limit command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve/limit xmax
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve = style name of this fix command
<LI>xmax = maximum distance an atom can move in one timestep (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve/limit 0.1
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE updates of position and velocity for atoms in the
group each timestep. A limit is imposed on the maximum distance an
atom can move in one timestep. This is useful when starting a
simulation with a configuration containing highly overlapped atoms.
Normally this would generate huge forces which would blow atoms out of
the simulation box, causing LAMMPS to stop with an error.
</P>
<P>Using this fix can overcome that problem. Forces on atoms must still
be computable (which typically means 2 atoms must have a separation
distance > 0.0). But large velocities generated by large forces are
reset to a value that corresponds to a displacement of length <I>xmax</I>
in a single timestep. <I>Xmax</I> is specified in distance units; see the
<A HREF = "units.html">units</A> command for details. The value of <I>xmax</I> should be
consistent with the neighbor skin distance and the frequency of
neighbor list re-building, so that pairwise interactions are not
missed on successive timesteps as atoms move. See the
<A HREF = "neighbor.html">neighbor</A> and <A HREF = "neigh_modify.html">neigh_modify</A> commands
for details.
</P>
<P>Note that if a velocity reset occurs the integrator will not conserve
energy. On steps where no velocity resets occur, this integrator is
exactly like the <A HREF = "fix_nve.html">fix nve</A> command. Since forces are
unaltered, pressures computed by thermodynamic output will still be
very large for overlapped configurations.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_noforce.html">fix nve/noforce</A>,
<A HREF = "pair_soft.html">pair_style soft</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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doc/fix_nve_limit.txt Normal file
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@ -0,0 +1,67 @@
"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
fix nve/limit command :h3
[Syntax:]
fix ID group-ID nve/limit xmax :pre
ID, group-ID are documented in "fix"_fix.html command
nve = style name of this fix command
xmax = maximum distance an atom can move in one timestep (distance units) :ul
[Examples:]
fix 1 all nve/limit 0.1 :pre
[Description:]
Perform constant NVE updates of position and velocity for atoms in the
group each timestep. A limit is imposed on the maximum distance an
atom can move in one timestep. This is useful when starting a
simulation with a configuration containing highly overlapped atoms.
Normally this would generate huge forces which would blow atoms out of
the simulation box, causing LAMMPS to stop with an error.
Using this fix can overcome that problem. Forces on atoms must still
be computable (which typically means 2 atoms must have a separation
distance > 0.0). But large velocities generated by large forces are
reset to a value that corresponds to a displacement of length {xmax}
in a single timestep. {Xmax} is specified in distance units; see the
"units"_units.html command for details. The value of {xmax} should be
consistent with the neighbor skin distance and the frequency of
neighbor list re-building, so that pairwise interactions are not
missed on successive timesteps as atoms move. See the
"neighbor"_neighbor.html and "neigh_modify"_neigh_modify.html commands
for details.
Note that if a velocity reset occurs the integrator will not conserve
energy. On steps where no velocity resets occur, this integrator is
exactly like the "fix nve"_fix_nve.html command. Since forces are
unaltered, pressures computed by thermodynamic output will still be
very large for overlapped configurations.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"fix nve"_fix_nve.html, "fix nve/noforce"_fix_nve_noforce.html,
"pair_style soft"_pair_soft.html
[Default:] none

5
doc/pair_soft.html
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@ -33,7 +33,8 @@ pair_coeff 1 1 0.0 60.0 3.0
blow up as r goes to 0. A is a pre-factor that varies in time from
the start to the end of the run. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs. Rc is the
cutoff.
cutoff. See the <A HREF = "fix_nve_limit.html">fix nve/limit</A> command for
another way to push apart overlapping atoms.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
@ -86,7 +87,7 @@ to be specified in an input script that reads a restart file.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_limit.html">fix nve/limit</A>
</P>
<P><B>Default:</B> none
</P>

5
doc/pair_soft.txt
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@ -30,7 +30,8 @@ It is useful for pushing apart overlapping atoms, since it does not
blow up as r goes to 0. A is a pre-factor that varies in time from
the start to the end of the run. The "run"_run.html command documents
how to make the ramping take place across multiple runs. Rc is the
cutoff.
cutoff. See the "fix nve/limit"_fix_nve_limit.html command for
another way to push apart overlapping atoms.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -83,6 +84,6 @@ to be specified in an input script that reads a restart file.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_coeff"_pair_coeff.html, "fix nve/limit"_fix_nve_limit.html
[Default:] none