Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/region.html
1138cacffd62lammps-icms

Last Change
Raw File

region.html
View Options

<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>region command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>region ID style args keyword value ...
</PRE>
<UL><LI>ID = user-assigned name for the region
<LI>style = <I>block</I> or <I>cylinder</I> or <I>prism</I> or <I>sphere</I> or <I>union</I> or <I>intersect</I>
<PRE> <I>block</I> args = xlo xhi ylo yhi zlo zhi
xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all
dimensions (distance units)
<I>cylinder</I> args = dim c1 c2 radius lo hi
dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
radius = cylinder radius (distance units)
lo,hi = bounds of cylinder in dim (distance units)
<I>prism</I> args = xlo xhi ylo yhi zlo zhi xy xz yz
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
xy = distance to tilt y in x direction (distance units)
xz = distance to tilt z in x direction (distance units)
yz = distance to tilt z in y direction (distance units)
<I>sphere</I> args = x y z radius
x,y,z = center of sphere (distance units)
radius = radius of sphere (distance units)
<I>union</I> args = N reg-ID1 reg-ID2 ...
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to join together
<I>intersect</I> args = N reg-ID1 reg-ID2 ...
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to intersect
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>side</I> or <I>units</I>
<PRE> <I>side</I> value = <I>in</I> or <I>out</I>
<I>in</I> = the region is inside the specified geometry
<I>out</I> = the region is outside the specified geometry
<I>units</I> value = <I>lattice</I> or <I>box</I>
<I>lattice</I> = the geometry is defined in lattice units
<I>box</I> = the geometry is defined in simulation box units
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>region 1 block -3.0 5.0 INF 10.0 INF INF
region 2 sphere 0.0 0.0 0.0 5 side out
region void cylinder y 2 3 5 -5.0 INF units box
region 1 prism 0 10 0 10 0 10 2 0 0
region outside union 4 side1 side2 side3 side4
</PRE>
<P><B>Description:</B>
</P>
<P>This command defines a geometric region of space. Various other
commands use regions. For example, the region can be filled with
atoms via the <A HREF = "create_atoms.html">create_atoms</A> command. Or the atoms
in the region can be identified as a group via the <A HREF = "group.html">group</A>
command, or deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command.
</P>
<P>The lo/hi values for <I>block</I> or <I>cylinder</I> or <I>prism</I> styles can be
specified as EDGE or INF. EDGE means they extend all the way to the
global simulation box boundary. Note that this is the current box
boundary; if the box changes size during a simulation the region does
not. INF means a large negative or positive number (1.0e20), so it
should encompass the simulation box even if it changes size. If a
region is defined before the simulation box has been created (via
<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> commands), then an EDGE or INF
parameter cannot be used.
</P>
<P>For style <I>cylinder</I>, the c1,c2 params are coordinates in the 2 other
dimensions besides the cylinder axis dimension. For dim = x, c1/c2 =
y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. Thus the
third example above specifies a cylinder with its axis in the
y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
extending in the y-direction from -5.0 to the upper box boundary.
</P>
<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
parallelepiped in an input script!). Think of the parallelepiped as
initially an axis-aligned orthogonal box with the same xyz lo/hi
parameters as region style <I>block</I> would define. Then, while holding
the (xlo,ylo,zlo) corner point fixed, the box is "skewed" or "tilted"
in 3 directions. First, for the lower xy face of the box, the <I>xy</I>
factor is how far the upper y edge is shifted in the x direction. The
lower xy face is now a parallelogram. A plus or minus value for <I>xy</I>
can be specified; 0.0 means no tilt. Then, the upper xy face of the
box is translated in the x and y directions by <I>xz</I> and <I>yz</I>. This
results in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3
edge vectors starting from its origin given by a = (xhi-xlo,0,0); b =
(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
</P>
<P>A prism region used with the <A HREF = "create_box.html">create_box</A> command must
have tilt factors (xy,xz,yz) that do not skew the box more than half
the distance of the parallel box length. For example, if xlo = 2 and
xhi = 12, then the x box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
equivalent.
</P>
<P>The <I>union</I> style creates a region consisting of the volume of all the
listed regions combined. The <I>intersect</I> style creates a region
consisting of the volume that is common to all the listed regions.
</P>
<P>The <I>side</I> keyword determines whether the region is considered to be
inside or outside of the specified geometry. Using this keyword in
conjunction with <I>union</I> and <I>intersect</I> regions, complex geometries
can be built up. For example, if the interior of two spheres were
each defined as regions, and a <I>union</I> style with <I>side</I> = out was
constructed listing the region-IDs of the 2 spheres, the resulting
region would be all the volume in the simulation box that was outside
both of the spheres.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
to define the region. A <I>box</I> value selects standard distance units
as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for units
= real or metal. A <I>lattice</I> value means the distance units are in
lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have been
previously used to define the lattice spacing.
</P>
<P><B>Restrictions:</B>
</P>
<P>A prism cannot be of 0.0 thickness in any dimension; use a small z
thickness for 2d simulations. For 2d simulations, the xz and yz
parameters must be 0.0.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "lattice.html">lattice</A>, <A HREF = "create_atoms.html">create_atoms</A>,
<A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "group.html">group</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are side = in and units = lattice.
</P>
</HTML>
c4science · Help