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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2677 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-03-18 17:37:50 +00:00
parent d32f0a53f2
commit f7b4f5747a
6 changed files with 139 additions and 6 deletions
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13
doc/Section_commands.html
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@ -319,12 +319,13 @@ of each style or click on the style itself for a full description:
<DIV ALIGN=center><TABLE BORDER=1 >
<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_atom.html">ave/atom</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_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</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><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</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><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD></TR>
<TR ALIGN="center"><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_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD></TR>
<TR ALIGN="center"><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_nve_sphere.html">nve/sphere</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_nvt_sphere.html">nvt/sphere</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_press_berendsen.html">press/berendsen</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_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><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>
<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</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><TD ><A HREF = "fix_langevin.html">langevin</A></TD></TR>
<TR ALIGN="center"><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_npt_sphere.html">npt/sphere</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_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</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_nvt_sphere.html">nvt/sphere</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_press_berendsen.html">press/berendsen</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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><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_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -392,6 +392,7 @@ of each style or click on the style itself for a full description:
"dt/reset"_fix_dt_reset.html,
"efield"_fix_efield.html,
"enforce2d"_fix_enforce2d.html,
"evaporate"_fix_evaporate.html,
"freeze"_fix_freeze.html,
"gravity"_fix_gravity.html,
"gyration"_fix_gyration.html,

1
doc/fix.html
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@ -120,6 +120,7 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_dt_reset.html">dt/reset</A> - reset the timestep based on velocity, forces
<LI><A HREF = "fix_efield.html">efield</A> - impose electric field on system
<LI><A HREF = "fix_enforce2d.html">enforce2d</A> - zero out z-dimension velocity and force
<LI><A HREF = "fix_evaporate.html">evaporate</A> - remove atoms from simulation periodically
<LI><A HREF = "fix_freeze.html">freeze</A> - freeze atoms in a granular simulation
<LI><A HREF = "fix_gravity.html">gravity</A> - add gravity to atoms in a granular simulation
<LI><A HREF = "fix_gyration.html">gyration</A> - compute radius of gyration

1
doc/fix.txt
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@ -117,6 +117,7 @@ list of fix styles available in LAMMPS:
"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
"efield"_fix_efield.html - impose electric field on system
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
"freeze"_fix_freeze.html - freeze atoms in a granular simulation
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"gyration"_fix_gyration.html - compute radius of gyration

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doc/fix_evaporate.html Normal file
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@ -0,0 +1,65 @@
<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 evaporate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID evaporate N M region-ID seed
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>evaporate = style name of this fix command
<LI>N = delete atoms every this many timesteps
<LI>M = number of atoms to delete each time
<LI>region-ID = ID of region within which to perform deletions
<LI>seed = random number seed to use for choosing atoms to delete
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 solvent evaporate 1000 10 surface 49892
</PRE>
<P><B>Description:</B>
</P>
<P>Remove M atoms from the simulation every N steps. This can be used,
for example, to model evaporation of a solvent or drying of a system.
Every N steps, the number of atoms in the fix group and within the
specifed region are counted. M of these are chosen at random and
deleted. If there are less than M eligible particles, then all of
them are deleted.
</P>
<P>Note that neighbor lists are re-built on timesteps that atoms are
removed. Thus you should not remove atoms too frequently or you will
incur overhead due to the cost of building neighbor lists.
</P>
<P><B>Restart, fix_modify, 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.
</P>
<P>The cummulative number of deleted atoms is stored as a scalar quantity
by this fix. This quantity can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar value is "intensive",
meaning it is independent of the number of atoms in the simulation.
</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. 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_deposit.html">fix deposit</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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doc/fix_evaporate.txt Normal file
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@ -0,0 +1,64 @@
"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 evaporate command :h3
[Syntax:]
fix ID group-ID evaporate N M region-ID seed :pre
ID, group-ID are documented in "fix"_fix.html command
evaporate = style name of this fix command
N = delete atoms every this many timesteps
M = number of atoms to delete each time
region-ID = ID of region within which to perform deletions
seed = random number seed to use for choosing atoms to delete :ul
[Examples:]
fix 1 solvent evaporate 1000 10 surface 49892 :pre
[Description:]
Remove M atoms from the simulation every N steps. This can be used,
for example, to model evaporation of solvent particles (i.e. drying)
of a system. Every N steps, the number of atoms in the fix group and
within the specifed region are counted. M of these are chosen at
random and deleted. If there are less than M eligible particles, then
all of them are deleted.
Note that you cannot currently delete solvent molecules with this
command, only individual atoms. If you delete only one atom in a
molecule, an error will result.
Note that neighbor lists are re-built on timesteps that atoms are
removed. Thus you should not remove atoms too frequently or you will
incur overhead due to the cost of building neighbor lists.
[Restart, fix_modify, 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.
The cummulative number of deleted atoms is stored as a scalar quantity
by this fix. This quantity can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar value is "intensive",
meaning it is independent of the number of atoms in the simulation.
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 deposit"_fix_deposit.html
[Default:] none