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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix write/reax/bonds command :h3
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[Syntax:]
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fix ID group-ID write/reax/bonds Nevery filename :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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write/reax/bonds = style name of this fix command :l
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Nevery = output interval in timesteps :l
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filename = naem of output file
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[Examples:]
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fix 1 all write/reax/bonds 100 bonds.tatb
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[Description:]
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Write out the bond information computed by the
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ReaxFF potential ("pair_style reax"_pair_reax.html).
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During dynamics runs, the bond information is written
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to {filename} on timesteps that are multiples of
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{Nevery}, including timestep 0. No output is generated
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during minimization runs.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. This fix does not provide any compute
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quantities.
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[Restrictions:]
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This fix requires that the "pair_style reax"_pair_reax.html be invoked.
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This fix is part of the "reax" package. It is only enabled if
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LAMMPS was built with that package, which also requires the REAX
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library be built and linked with LAMMPS. See the "Making
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LAMMPS"_Section_start.html#2_3 section for more info.
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[Related commands:]
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"pair_style reax"_pair_reax.html
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[Default:]
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none
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@ -26,10 +26,10 @@ mass 2* 62.5
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Set the mass for all atoms of one or more atom types. Mass values can
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also be set in the <A HREF = "read_data.html">read_data</A> data file using the
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"Masses" keyword. See the <A HREF = "units.html">units</A> command for what mass
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units to use.
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<P>Set the mass for all atoms of one or more atom types. Per-type mass
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values can also be set in the <A HREF = "read_data.html">read_data</A> data file
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using the "Masses" keyword. See the <A HREF = "units.html">units</A> command for
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what mass units to use.
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</P>
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<P>The I index can be specified in one of two ways. An explicit numeric
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value can be used, as in the 1st example above. Or a wild-card
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@ -50,13 +50,14 @@ line that corresponds to the 1st example above would be listed as
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<PRE>1 1.0
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</PRE>
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<P>Note that the mass command can only be used if the <A HREF = "atom_style.html">atom
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style</A> requires per-type atom mass to be set, which
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most do. Exceptions are <A HREF = "atom_style.html">atom_style granular</A> or
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<A HREF = "atom_style.html">atom_style peri</A>, which require mass to be set for
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individual particles, not types. Per-atom masses are defined in the
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data file read by the <A HREF = "read_data.html">read_data</A> command, or set to
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default values by the <A HREF = "create_atoms.html">create_atoms</A> command, or set
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to new values by the <A HREF = "set.html">set density</A> command.
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style</A> requires per-type atom mass to be set.
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Currently, all but the <I>granular</I> and <I>peri</I> styles do. They require
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mass to be set for individual particles, not types. Per-atom masses
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are defined in the data file read by the <A HREF = "read_data.html">read_data</A>
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command, or set to default values by the
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<A HREF = "create_atoms.html">create_atoms</A> command. Per-atom masses can also be
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set to new values by the <A HREF = "set.html">set diameter</A> or <A HREF = "set.html">set
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density</A> command.
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</P>
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<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> defines the masses of
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atom types in the EAM potential file, in which case the mass command
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@ -64,9 +65,9 @@ is normally not used.
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</P>
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<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
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(or more) sub-styles which require per-type mass and one (or more)
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sub-styles which require per-atom mass, then you must define both.
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However, the per-type mass is ignored in this case; only the per-atom
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mass is used.
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sub-styles which require per-atom mass, then you must define both. In
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this case the per-type mass will be ignored; only the per-atom mass is
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used by LAMMPS.
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</P>
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<P><B>Restrictions:</B>
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</P>
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29
doc/mass.txt
29
doc/mass.txt
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[Description:]
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Set the mass for all atoms of one or more atom types. Mass values can
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also be set in the "read_data"_read_data.html data file using the
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"Masses" keyword. See the "units"_units.html command for what mass
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units to use.
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Set the mass for all atoms of one or more atom types. Per-type mass
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values can also be set in the "read_data"_read_data.html data file
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using the "Masses" keyword. See the "units"_units.html command for
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what mass units to use.
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The I index can be specified in one of two ways. An explicit numeric
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value can be used, as in the 1st example above. Or a wild-card
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@ -47,13 +47,14 @@ line that corresponds to the 1st example above would be listed as
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1 1.0 :pre
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Note that the mass command can only be used if the "atom
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style"_atom_style.html requires per-type atom mass to be set, which
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most do. Exceptions are "atom_style granular"_atom_style.html or
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"atom_style peri"_atom_style.html, which require mass to be set for
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individual particles, not types. Per-atom masses are defined in the
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data file read by the "read_data"_read_data.html command, or set to
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default values by the "create_atoms"_create_atoms.html command, or set
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to new values by the "set density"_set.html command.
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style"_atom_style.html requires per-type atom mass to be set.
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Currently, all but the {granular} and {peri} styles do. They require
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mass to be set for individual particles, not types. Per-atom masses
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are defined in the data file read by the "read_data"_read_data.html
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command, or set to default values by the
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"create_atoms"_create_atoms.html command. Per-atom masses can also be
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set to new values by the "set diameter"_set.html or "set
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density"_set.html command.
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Also note that "pair_style eam"_pair_eam.html defines the masses of
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atom types in the EAM potential file, in which case the mass command
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@ -61,9 +62,9 @@ is normally not used.
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If you define a "hybrid atom style"_atom_style.html which includes one
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(or more) sub-styles which require per-type mass and one (or more)
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sub-styles which require per-atom mass, then you must define both.
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However, the per-type mass is ignored in this case; only the per-atom
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mass is used.
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sub-styles which require per-atom mass, then you must define both. In
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this case the per-type mass will be ignored; only the per-atom mass is
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used by LAMMPS.
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[Restrictions:]
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13
doc/set.html
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doc/set.html
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<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A>
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being used must support the use of dipoles or quaternions.
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</P>
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<P>Keyword <I>diameter</I> sets the size of all selected particles.
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<P>Keyword <I>diameter</I> sets the size of all selected particles. If the
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particles have a per-atom mass and density, then it also sets their
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mass.
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</P>
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<P>Keyword <I>density</I> sets the density of all selected particles, which
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combined with its density determines their mass.
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<P>Keyword <I>density</I> sets the density of all selected particles. If the
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particles have a per-atom mass and diameter, then it also sets their
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mass. If the particles have a per-atom mass and volume (as defined by
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PeriDynamics), then it also sets their mass.
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</P>
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<P>Keyword <I>volume</I> sets the effective size of all selected particles.
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<P>Keyword <I>volume</I> sets the volume of all selected particles, as defined
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by PeriDynamics.
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</P>
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<P>Keyword <I>image</I> sets which image of the simulation box the atom is
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considered to be in. It is only applied to periodic dimensions. An
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13
doc/set.txt
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doc/set.txt
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For the {dipole} and {quat} keywords, the "atom style"_atom_style.html
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being used must support the use of dipoles or quaternions.
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Keyword {diameter} sets the size of all selected particles.
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Keyword {diameter} sets the size of all selected particles. If the
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particles have a per-atom mass and density, then it also sets their
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mass.
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Keyword {density} sets the density of all selected particles, which
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combined with its density determines their mass.
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Keyword {density} sets the density of all selected particles. If the
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particles have a per-atom mass and diameter, then it also sets their
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mass. If the particles have a per-atom mass and volume (as defined by
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PeriDynamics), then it also sets their mass.
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Keyword {volume} sets the effective size of all selected particles.
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Keyword {volume} sets the volume of all selected particles, as defined
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by PeriDynamics.
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Keyword {image} sets which image of the simulation box the atom is
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considered to be in. It is only applied to periodic dimensions. An
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