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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2820 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-05-19 14:57:46 +00:00
parent 65317f1486
commit b1ac804d3c
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56
doc/fix_write_reax_bonds.txt
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@ -1,56 +0,0 @@
"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 write/reax/bonds command :h3
[Syntax:]
fix ID group-ID write/reax/bonds Nevery filename :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
write/reax/bonds = style name of this fix command :l
Nevery = output interval in timesteps :l
filename = naem of output file
[Examples:]
fix 1 all write/reax/bonds 100 bonds.tatb
[Description:]
Write out the bond information computed by the
ReaxFF potential ("pair_style reax"_pair_reax.html).
During dynamics runs, the bond information is written
to {filename} on timesteps that are multiples of
{Nevery}, including timestep 0. No output is generated
during minimization runs.
:line
[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. This fix does not provide any compute
quantities.
[Restrictions:]
This fix requires that the "pair_style reax"_pair_reax.html be invoked.
This fix is part of the "reax" package. It is only enabled if
LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"pair_style reax"_pair_reax.html
[Default:]
none

29
doc/mass.html
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@ -26,10 +26,10 @@ mass 2* 62.5
</PRE>
<P><B>Description:</B>
</P>
<P>Set the mass for all atoms of one or more atom types. Mass values can
also be set in the <A HREF = "read_data.html">read_data</A> data file using the
"Masses" keyword. See the <A HREF = "units.html">units</A> command for what mass
units to use.
<P>Set the mass for all atoms of one or more atom types. Per-type mass
values can also be set in the <A HREF = "read_data.html">read_data</A> data file
using the "Masses" keyword. See the <A HREF = "units.html">units</A> command for
what mass units to use.
</P>
<P>The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the 1st example above. Or a wild-card
@ -50,13 +50,14 @@ line that corresponds to the 1st example above would be listed as
<PRE>1 1.0
</PRE>
<P>Note that the mass command can only be used if the <A HREF = "atom_style.html">atom
style</A> requires per-type atom mass to be set, which
most do. Exceptions are <A HREF = "atom_style.html">atom_style granular</A> or
<A HREF = "atom_style.html">atom_style peri</A>, which require mass to be set for
individual particles, not types. Per-atom masses are defined in the
data file read by the <A HREF = "read_data.html">read_data</A> command, or set to
default values by the <A HREF = "create_atoms.html">create_atoms</A> command, or set
to new values by the <A HREF = "set.html">set density</A> command.
style</A> requires per-type atom mass to be set.
Currently, all but the <I>granular</I> and <I>peri</I> styles do. They require
mass to be set for individual particles, not types. Per-atom masses
are defined in the data file read by the <A HREF = "read_data.html">read_data</A>
command, or set to default values by the
<A HREF = "create_atoms.html">create_atoms</A> command. Per-atom masses can also be
set to new values by the <A HREF = "set.html">set diameter</A> or <A HREF = "set.html">set
density</A> command.
</P>
<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> defines the masses of
atom types in the EAM potential file, in which case the mass command
@ -64,9 +65,9 @@ is normally not used.
</P>
<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
(or more) sub-styles which require per-type mass and one (or more)
sub-styles which require per-atom mass, then you must define both.
However, the per-type mass is ignored in this case; only the per-atom
mass is used.
sub-styles which require per-atom mass, then you must define both. In
this case the per-type mass will be ignored; only the per-atom mass is
used by LAMMPS.
</P>
<P><B>Restrictions:</B>
</P>

29
doc/mass.txt
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@ -23,10 +23,10 @@ mass 2* 62.5 :pre
[Description:]
Set the mass for all atoms of one or more atom types. Mass values can
also be set in the "read_data"_read_data.html data file using the
"Masses" keyword. See the "units"_units.html command for what mass
units to use.
Set the mass for all atoms of one or more atom types. Per-type mass
values can also be set in the "read_data"_read_data.html data file
using the "Masses" keyword. See the "units"_units.html command for
what mass units to use.
The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the 1st example above. Or a wild-card
@ -47,13 +47,14 @@ line that corresponds to the 1st example above would be listed as
1 1.0 :pre
Note that the mass command can only be used if the "atom
style"_atom_style.html requires per-type atom mass to be set, which
most do. Exceptions are "atom_style granular"_atom_style.html or
"atom_style peri"_atom_style.html, which require mass to be set for
individual particles, not types. Per-atom masses are defined in the
data file read by the "read_data"_read_data.html command, or set to
default values by the "create_atoms"_create_atoms.html command, or set
to new values by the "set density"_set.html command.
style"_atom_style.html requires per-type atom mass to be set.
Currently, all but the {granular} and {peri} styles do. They require
mass to be set for individual particles, not types. Per-atom masses
are defined in the data file read by the "read_data"_read_data.html
command, or set to default values by the
"create_atoms"_create_atoms.html command. Per-atom masses can also be
set to new values by the "set diameter"_set.html or "set
density"_set.html command.
Also note that "pair_style eam"_pair_eam.html defines the masses of
atom types in the EAM potential file, in which case the mass command
@ -61,9 +62,9 @@ is normally not used.
If you define a "hybrid atom style"_atom_style.html which includes one
(or more) sub-styles which require per-type mass and one (or more)
sub-styles which require per-atom mass, then you must define both.
However, the per-type mass is ignored in this case; only the per-atom
mass is used.
sub-styles which require per-atom mass, then you must define both. In
this case the per-type mass will be ignored; only the per-atom mass is
used by LAMMPS.
[Restrictions:]

13
doc/set.html
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@ -145,12 +145,17 @@ xy plane are generated.
<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A>
being used must support the use of dipoles or quaternions.
</P>
<P>Keyword <I>diameter</I> sets the size of all selected particles.
<P>Keyword <I>diameter</I> sets the size of all selected particles. If the
particles have a per-atom mass and density, then it also sets their
mass.
</P>
<P>Keyword <I>density</I> sets the density of all selected particles, which
combined with its density determines their mass.
<P>Keyword <I>density</I> sets the density of all selected particles. If the
particles have a per-atom mass and diameter, then it also sets their
mass. If the particles have a per-atom mass and volume (as defined by
PeriDynamics), then it also sets their mass.
</P>
<P>Keyword <I>volume</I> sets the effective size of all selected particles.
<P>Keyword <I>volume</I> sets the volume of all selected particles, as defined
by PeriDynamics.
</P>
<P>Keyword <I>image</I> sets which image of the simulation box the atom is
considered to be in. It is only applied to periodic dimensions. An

13
doc/set.txt
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@ -140,12 +140,17 @@ xy plane are generated.
For the {dipole} and {quat} keywords, the "atom style"_atom_style.html
being used must support the use of dipoles or quaternions.
Keyword {diameter} sets the size of all selected particles.
Keyword {diameter} sets the size of all selected particles. If the
particles have a per-atom mass and density, then it also sets their
mass.
Keyword {density} sets the density of all selected particles, which
combined with its density determines their mass.
Keyword {density} sets the density of all selected particles. If the
particles have a per-atom mass and diameter, then it also sets their
mass. If the particles have a per-atom mass and volume (as defined by
PeriDynamics), then it also sets their mass.
Keyword {volume} sets the effective size of all selected particles.
Keyword {volume} sets the volume of all selected particles, as defined
by PeriDynamics.
Keyword {image} sets which image of the simulation box the atom is
considered to be in. It is only applied to periodic dimensions. An