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Sat, Nov 16, 13:29
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rLAMMPS lammps
region.html
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<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>
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