forked from lijiext/lammps
218 lines
8.9 KiB
HTML
218 lines
8.9 KiB
HTML
<HTML>
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<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>
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<HR>
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<H3>fix property/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID property/atom vec1 vec2 ... keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>property/atom = style name of this fix command
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<LI>vec1,vec2,... = <I>mol</I> or <I>q</I> or <I>i_name</I> or <I>d_name</I>
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<PRE> <I>mol</I> = molecule IDs
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<I>q</I> = charge
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<I>i_name</I> = new integer vector referenced by name
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<I>d_name</I> = new floating-point vector referenced by name
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</PRE>
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<LI>zero of more keyword/value pairs may be appended
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<LI>keyword = <I>ghost</I>
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<PRE> <I>ghost</I> value = <I>no</I> or <I>yes</I> for whether ghost atom info in communicated
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all property/atom mol
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fix 1 all property/atom i_myflag1 i_myflag2
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fix 1 all property/atom d_sx d_sy d_sz
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Create one or more additional per-atom vectors to store information
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about atoms and to use during a simulation. The specified <I>group-ID</I>
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is ignored by this fix.
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</P>
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<P>The atom style used for a simulation defines a set of per-atom
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properties, as explained on the <A HREF = "atom_style.html">atom_style</A> and
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<A HREF = "read_data.html">read_data</A> doc pages. The latter command allows these
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properties to be defined for each atom in the system when a data file
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is read. This fix will augment the set of properties with new custom
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ones.
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</P>
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<P>This can be useful in at least two scenarios.
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</P>
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<P>If the atom style does not define molecule IDs or per-atom charge,
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they can be added using the <I>mol</I> or <I>q</I> keywords. This can be
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useful, e.g, to define "molecules" to use as rigid bodies with the
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<A HREF = "fix_rigid.html">fix rigid</A> command, or just to carry around an extra
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flag with the atoms (stored as a molecule ID). An alternative is to
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use an atom style that does define molecule IDs or charge or to use a
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hybrid atom style that combines two styles to allow for molecule IDs
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or charge, but that has 2 practical drawbacks. First it typically
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necessitates changing the format of the data file. And it may define
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additional properties that aren't needed such as bond lists, which has
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some overhead when there are no bonds.
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</P>
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<P>In the future, we may add additional per-atom properties similar to
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<I>mol</I> or <I>q</I>, which "turn-on" specific properties defined by some atom
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styles, so they can be used by atom styles that don't define them.
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</P>
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<P>More generally, the <I>i_name</I> and <I>d_name</I> vectors allow one or more
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new custom per-atom properties to be defined. Each name must be
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unique and can use alphanumeric or underscore characters. These
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vectors can store whatever values you decide are useful in your
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simulation. As explained below there are several ways to initialize
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and access and output these values, both via input script commands and
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in new code that you add to LAMMPS.
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</P>
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<P>This is effectively a simple way to add per-atom properties to a model
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without needing to write code for a new <A HREF = "atom_style.html">atom style</A>
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that defines the properties. Note however that implementing a new
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atom style allows new atom properties to be more tightly and
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seamlessly integrated with the rest of the code.
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</P>
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<P>The new atom properties encode values that migrate with atoms to new
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processors and are written to restart files. If you want the new
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properties to also be defined for ghost atoms, then use the <I>ghost</I>
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keyword with a value of <I>yes</I>. This will invoke extra communication
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when ghost atoms are created (at every re-neighboring) to insure the
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new properties are also defined for the ghost atoms.
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</P>
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<P>IMPORTANT NOTE: The properties for ghost atoms are not updated every
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timestep, but only once every few steps when neighbor lists are
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re-built. Thus the <I>ghost</I> keyword is suitable for static properties,
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like molecule IDs, but not for dynamic properties that change every
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step. For the latter, the code you add to LAMMPS to change the
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properties will also need to communicate their new values to/from
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ghost atoms, an operation that can be invoked from within a <A HREF = "pair_style.html">pair
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style</A> or <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A>
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that you write.
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</P>
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<HR>
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<P>This fix is one of a small number that can be defined in an input
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script before the simulation box is created or atoms are defined.
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This is so it can be used with the <A HREF = "read_data.html">read_data</A> command
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as described below.
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</P>
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<P>Per-atom properties that are defined by the <A HREF = "atom_style.html">atom
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style</A> are initialized when atoms are created, e.g. by
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the <A HREF = "read_data.html">read_data</A> or <A HREF = "create_atoms.html">create_atoms</A>
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commands. The per-atom properaties defined by this fix are not. So
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you need to initialize them explicitly. This can be done by the
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<A HREF = "read_data.html">read_data</A> command, using its <I>fix</I> keyword and
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passing it the fix-ID of this fix.
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</P>
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<P>Thus these commands:
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</P>
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<PRE>fix prop all property/atom mol d_flag
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read_data data.txt fix prop NULL Molecules
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</PRE>
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<P>would allow a data file to have a section like this:
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</P>
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<PRE>Molecules
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</PRE>
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<PRE>1 4 1.5
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2 4 3.0
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3 10 1.0
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4 10 1.0
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5 10 1.0
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...
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N 763 4.5
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</PRE>
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<P>where N is the number of atoms, and the first field on each line is
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the atom-ID, followed by a molecule-ID and a floating point value that
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will be stored in a new property called "flag". Note that the list of
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per-atom properties can be in any order.
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</P>
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<P>Another way of initializing the new properties is via the
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<A HREF = "set.html">set</A> command. For example, if you wanted molecules
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defined for every set of 10 atoms, based on their atom-IDs,
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these commands could be used:
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</P>
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<PRE>fix prop all property/atom mol
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variable cluster atom ((id-1)/10)+1
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set id * mol v_cluster
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</PRE>
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<P>The <A HREF = "variable.html">atom-style variable</A> will create values for atoms
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with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the
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<A HREF = "set.html">set</A> commands assigns them to the molecule ID for each atom,
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they will be truncated to an integer value, so atoms 31-40 will all be
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assigned a molecule ID of 4.
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</P>
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<P>Note that <A HREF = "variable.html">atomfile-style variables</A> can also be used in
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place of atom-style variables, which means in this case that the
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molecule IDs could be read-in from a separate file and assinged by the
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<A HREF = "set.html">set</A> command. This allows you to initialize new per-atom
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properties in a completely general fashion.
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</P>
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<HR>
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<P>For new atom properties specified as <I>i_name</I> or <I>d_name</I>, the
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<A HREF = "compute_property_atom.html">compute property/atom</A> command can access
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their values. This means that the values can be output via the <A HREF = "dump.html">dump
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custom</A> command, accessed by fixes like <A HREF = "fix_ave_atom.html">fix
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ave/atom</A>, accessed by other computes like <A HREF = "compute_reduce.html">compute
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reduce</A>, or used in <A HREF = "variables">atom-style
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variables</A>.
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</P>
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<P>For example, these commands will output two new properties to a custom
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dump file:
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</P>
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<PRE>fix prop all property/atom i_flag1 d_flag2
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compute 1 all property/atom i_flag1 d_flag2
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dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
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</PRE>
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<HR>
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<P>If you wish to add new <A HREF = "pair_style.html">pair styles</A>,
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<A HREF = "fix.html">fixes</A>, or <A HREF = "compute.html">computes</A> that use the per-atom
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properties defined by this fix, see <A HREF = "Section_modify.html#mod_1">Section
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modify</A> of the manual which has some details
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on how the properties can be accessed from added classes.
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</P>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>This fix writes the per-atom values it stores to <A HREF = "restart.html">binary restart
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files</A>, so that the values can be restored when a
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simulation is restarted. See the <A HREF = "read_restart.html">read_restart</A>
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command for info on how to re-specify a fix in an input script that
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reads a restart file, so that the operation of the fix continues in an
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uninterrupted fashion.
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
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commands</A>. No parameter of this fix can
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be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
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This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "read_data.html">read_data</A>, <A HREF = "set.html">set</A>, <A HREF = "compute_property_atom.html">compute
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property/atom</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The default keyword values are ghost = no.
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</P>
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</HTML>
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