forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11483 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -17,7 +17,7 @@
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</PRE>
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<UL><LI>ID = user-defined name of the group
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<LI>style = <I>delete</I> or <I>region</I> or <I>type</I> or <I>id</I> or <I>molecule</I> or <I>variable</I> or <I>subtract</I> or <I>union</I> or <I>intersect</I>
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<LI>style = <I>delete</I> or <I>region</I> or <I>type</I> or <I>id</I> or <I>molecule</I> or <I>variable</I> or <I>subtract</I> or <I>union</I> or <I>intersect</I> or <I>dynamic</I> or <I>static</I>
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<PRE> <I>delete</I> = no args
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<I>region</I> args = region-ID
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@ -32,10 +32,17 @@
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args = logical value1 value2
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logical = "<>"
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value1,value2 = atom types or atom IDs or molecule IDs (depending on <I>style</I>)
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<I>variable</I> args = variable-ID
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<I>variable</I> args = variable-name
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<I>subtract</I> args = two or more group IDs
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<I>union</I> args = one or more group IDs
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<I>intersect</I> args = two or more group IDs
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<I>intersect</I> args = two or more group IDs
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<I>dynamic</I> args = parent-ID keyword value ...
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one or more keyword/value pairs may be appended
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keyword = <I>region</I> or <I>var</I> or <I>every</I>
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<I>region</I> value = region-ID
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<I>var</I> value = name of variable
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<I>every</I> value = N = update group every this many timesteps
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<I>static</I> = no args
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</PRE>
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</UL>
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@ -52,7 +59,8 @@ group hienergy variable eng
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group boundary subtract all a2 a3
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group boundary union lower upper
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group boundary intersect upper flow
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group boundary delete
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group boundary delete
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group mine dynamic all region myRegion every 100
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -64,6 +72,18 @@ to act on those atoms together.
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<P>If the group ID already exists, the group command adds the specified
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atoms to the group.
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</P>
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<P>IMPORTANT NOTE: By default groups are static, meaning the atoms are
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permanently assigned to the group. For example, if the <I>region</I> style
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is used to assign atoms to a group, the atoms will remain in the group
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even if they later move out of the region. As explained below, the
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<I>dynamic</I> style can be used to make a group dynamic so that a periodic
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determination is made as to which atoms are in the group. Since many
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LAMMPS commands operate on groups of atoms, you should think carefully
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about whether making a group dynamic makes sense for your model.
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</P>
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<P>A group with the ID <I>all</I> is predefined. All atoms belong to this
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group. This group cannot be deleted, or made dynamic.
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</P>
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<P>The <I>delete</I> style removes the named group and un-assigns all atoms
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that were assigned to that group. Since there is a restriction (see
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below) that no more than 32 groups can be defined at any time, the
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@ -156,14 +176,63 @@ added to the specified group.
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as arguments. Atoms that belong to every one of the listed groups are
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added to the specified group.
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</P>
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<P>A group with the ID <I>all</I> is predefined. All atoms belong to this
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group. This group cannot be deleted.
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<HR>
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<P>The <I>dynamic</I> style flags an existing or new group as dynamic. This
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means atoms will be (re)assigned to the group periodically as a
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simulation runs. This is in contrast to static groups where atoms are
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permanently assigned to the group. The way the assignment occurs is
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as follows. Only atoms in the group specified as the parent group via
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the parent-ID are initially assigned to the dynamic group. If the
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<I>region</I> keyword is used, atoms not in the specified region are
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removed from the dynamic group. If the <I>var</I> keyword is used, the
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variable name must be an atom-style or atomfile-style variable. The
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variable is evaluated and atoms whose per-atom values are 0.0, are
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removed from the dynamic group.
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</P>
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<P>The assignment of atoms to a dynamic group is done at the beginning of
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each run and on every timestep that is a multiple of <I>N</I>, which is the
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argument for the <I>every</I> keyword (N = 1 is the default). For an
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energy minimization, via the <A HREF = "minimize.html">minimize</A> command, an
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assignement is made at the beginning of the minimization, but not
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during the iterations of the minimizer.
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</P>
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<P>The point in the timestep at which atoms are assigned to a dynamic
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group is after the initial stage of velocity Verlet time integration
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has been performed, and before neighbor lists or forces are computed.
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This is the point in the timestep where atom positions have just
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changed due to the time integration, so the region criterion should be
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accurate, if applied.
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</P>
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<P>Here is an example of using a dynamic group to shrink the set of atoms
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being integrated by using a spherical region with a variable radius
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(shrinking from 18 to 5 over the course of the run). This could be
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used to model a quench of the system, freezing atoms outside the
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shrinking sphere, then converting the remaining atoms to a static
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group and running further.
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</P>
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<PRE>variable nsteps equal 5000
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variable rad equal 18-(step/v_nsteps)*(18-5)
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region ss sphere 20 20 0 v_rad
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group mobile dynamic all region ss
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fix 1 mobile nve
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run $<I>nsteps</I>
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group mobile static
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run $<I>nsteps</I>
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</PRE>
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<P>The <I>static</I> style removes the setting for a dynamic group, converting
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it to a static group (the default). The atoms in the static group are
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those currently in the dynamic group.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>There can be no more than 32 groups defined at one time, including
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"all".
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</P>
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<P>The parent group of a dynamic group cannot itself be a dynamic group.
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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 = "dump.html">dump</A>, <A HREF = "fix.html">fix</A>, <A HREF = "region.html">region</A>,
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@ -14,7 +14,7 @@ group ID style args :pre
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ID = user-defined name of the group :ulb,l
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style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
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{subtract} or {union} or {intersect} :l
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{subtract} or {union} or {intersect} or {dynamic} or {static} :l
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{delete} = no args
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{region} args = region-ID
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{type} or {id} or {molecule}
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@ -28,10 +28,17 @@ style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
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args = logical value1 value2
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logical = "<>"
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value1,value2 = atom types or atom IDs or molecule IDs (depending on {style})
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{variable} args = variable-ID
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{variable} args = variable-name
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{subtract} args = two or more group IDs
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{union} args = one or more group IDs
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{intersect} args = two or more group IDs :pre
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{intersect} args = two or more group IDs
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{dynamic} args = parent-ID keyword value ...
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one or more keyword/value pairs may be appended
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keyword = {region} or {var} or {every}
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{region} value = region-ID
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{var} value = name of variable
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{every} value = N = update group every this many timesteps
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{static} = no args :pre
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:ule
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[Examples:]
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@ -47,7 +54,9 @@ group hienergy variable eng
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group boundary subtract all a2 a3
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group boundary union lower upper
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group boundary intersect upper flow
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group boundary delete :pre
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group boundary delete
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group mine dynamic all region myRegion every 100 :pre
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[Description:]
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@ -59,6 +68,18 @@ to act on those atoms together.
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If the group ID already exists, the group command adds the specified
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atoms to the group.
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IMPORTANT NOTE: By default groups are static, meaning the atoms are
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permanently assigned to the group. For example, if the {region} style
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is used to assign atoms to a group, the atoms will remain in the group
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even if they later move out of the region. As explained below, the
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{dynamic} style can be used to make a group dynamic so that a periodic
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determination is made as to which atoms are in the group. Since many
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LAMMPS commands operate on groups of atoms, you should think carefully
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about whether making a group dynamic makes sense for your model.
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A group with the ID {all} is predefined. All atoms belong to this
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group. This group cannot be deleted, or made dynamic.
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The {delete} style removes the named group and un-assigns all atoms
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that were assigned to that group. Since there is a restriction (see
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below) that no more than 32 groups can be defined at any time, the
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@ -151,14 +172,63 @@ The {intersect} style takes a list of two or more existing group names
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as arguments. Atoms that belong to every one of the listed groups are
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added to the specified group.
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A group with the ID {all} is predefined. All atoms belong to this
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group. This group cannot be deleted.
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:line
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The {dynamic} style flags an existing or new group as dynamic. This
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means atoms will be (re)assigned to the group periodically as a
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simulation runs. This is in contrast to static groups where atoms are
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permanently assigned to the group. The way the assignment occurs is
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as follows. Only atoms in the group specified as the parent group via
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the parent-ID are initially assigned to the dynamic group. If the
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{region} keyword is used, atoms not in the specified region are
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removed from the dynamic group. If the {var} keyword is used, the
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variable name must be an atom-style or atomfile-style variable. The
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variable is evaluated and atoms whose per-atom values are 0.0, are
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removed from the dynamic group.
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The assignment of atoms to a dynamic group is done at the beginning of
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each run and on every timestep that is a multiple of {N}, which is the
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argument for the {every} keyword (N = 1 is the default). For an
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energy minimization, via the "minimize"_minimize.html command, an
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assignement is made at the beginning of the minimization, but not
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during the iterations of the minimizer.
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The point in the timestep at which atoms are assigned to a dynamic
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group is after the initial stage of velocity Verlet time integration
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has been performed, and before neighbor lists or forces are computed.
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This is the point in the timestep where atom positions have just
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changed due to the time integration, so the region criterion should be
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accurate, if applied.
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Here is an example of using a dynamic group to shrink the set of atoms
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being integrated by using a spherical region with a variable radius
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(shrinking from 18 to 5 over the course of the run). This could be
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used to model a quench of the system, freezing atoms outside the
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shrinking sphere, then converting the remaining atoms to a static
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group and running further.
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variable nsteps equal 5000
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variable rad equal 18-(step/v_nsteps)*(18-5)
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region ss sphere 20 20 0 v_rad
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group mobile dynamic all region ss
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fix 1 mobile nve
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run ${nsteps}
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group mobile static
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run ${nsteps} :pre
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The {static} style removes the setting for a dynamic group, converting
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it to a static group (the default). The atoms in the static group are
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those currently in the dynamic group.
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:line
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[Restrictions:]
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There can be no more than 32 groups defined at one time, including
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"all".
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The parent group of a dynamic group cannot itself be a dynamic group.
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[Related commands:]
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"dump"_dump.html, "fix"_fix.html, "region"_region.html,
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Loading…
Reference in New Issue