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310 lines
15 KiB
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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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<H3>region command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>region ID style args keyword arg ...
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</PRE>
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<UL><LI>ID = user-assigned name for the region
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<LI>style = <I>delete</I> or <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>plane</I> or <I>prism</I> or <I>sphere</I> or <I>union</I> or <I>intersect</I>
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<PRE> <I>delete</I> = no args
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<I>block</I> args = xlo xhi ylo yhi zlo zhi
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xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
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<I>cone</I> args = dim c1 c2 radlo radhi lo hi
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dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cone
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c1,c2 = coords of cone axis in other 2 dimensions (distance units)
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radlo,radhi = cone radii at lo and hi end (distance units)
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lo,hi = bounds of cone in dim (distance units)
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<I>cylinder</I> args = dim c1 c2 radius lo hi
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dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cylinder
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c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
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radius = cylinder radius (distance units)
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lo,hi = bounds of cylinder in dim (distance units)
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<I>plane</I> args = px py pz nx ny nz
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px,py,pz = point on the plane (distance units)
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nx,ny,nz = direction normal to plane (distance units)
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<I>prism</I> args = xlo xhi ylo yhi zlo zhi xy xz yz
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xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
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xy = distance to tilt y in x direction (distance units)
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xz = distance to tilt z in x direction (distance units)
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yz = distance to tilt z in y direction (distance units)
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<I>sphere</I> args = x y z radius
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x,y,z = center of sphere (distance units)
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radius = radius of sphere (distance units)
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<I>union</I> args = N reg-ID1 reg-ID2 ...
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N = # of regions to follow, must be 2 or greater
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reg-ID1,reg-ID2, ... = IDs of regions to join together
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<I>intersect</I> args = N reg-ID1 reg-ID2 ...
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N = # of regions to follow, must be 2 or greater
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reg-ID1,reg-ID2, ... = IDs of regions to intersect
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</PRE>
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<LI>zero or more keyword/arg pairs may be appended
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<LI>keyword = <I>side</I> or <I>units</I> or <I>move</I> or <I>rotate</I>
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<PRE> <I>side</I> value = <I>in</I> or <I>out</I>
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<I>in</I> = the region is inside the specified geometry
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<I>out</I> = the region is outside the specified geometry
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<I>units</I> value = <I>lattice</I> or <I>box</I>
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<I>lattice</I> = the geometry is defined in lattice units
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<I>box</I> = the geometry is defined in simulation box units
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<I>move</I> args = v_x v_y v_z
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v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
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<I>rotate</I> args = v_theta Px Py Pz Rx Ry Rz
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v_theta = equal-style variable for rotaton of region over time (in radians)
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Px,Py,Pz = origin for axis of rotation (distance units)
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Rx,Ry,Rz = axis of rotation vector
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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>region 1 block -3.0 5.0 INF 10.0 INF INF
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region 2 sphere 0.0 0.0 0.0 5 side out
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region void cylinder y 2 3 5 -5.0 EDGE units box
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region 1 prism 0 10 0 10 0 10 2 0 0
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region outside union 4 side1 side2 side3 side4
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region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This command defines a geometric region of space. Various other
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commands use regions. For example, the region can be filled with
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atoms via the <A HREF = "create_atoms.html">create_atoms</A> command. Or a bounding
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box around the region, can be used to define the simulation box via
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the <A HREF = "create_box.html">create_box</A> command. Or the atoms in the region
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can be identified as a group via the <A HREF = "group.html">group</A> command, or
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deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command. Or the
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surface of the region can be used as a boundary wall via the <A HREF = "fix_wall_region.html">fix
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wall/region</A> command.
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</P>
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<P>Commands which use regions typically test whether an atom's position
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is contained in the region or not. For this purpose, coordinates
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exactly on the region boundary are considered to be interior to the
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region. This means, for example, for a spherical region, an atom on
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the sphere surface would be part of the region if the sphere were
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defined with the <I>side in</I> keyword, but would not be part of the
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region if it were defined using the <I>side out</I> keyword. See more
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details on the <I>side</I> keyword below.
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</P>
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<P>Normally, regions in LAMMPS are "static", meaning their geometric
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extent does not change with time. If the <I>move</I> or <I>rotate</I> keyword
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is used, as described below, the region becomes "dynamic", meaning
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it's location or orientation changes with time. This may be useful,
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for example, when thermostatting a region, via the compute temp/region
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command, or when the fix wall/region command uses a region surface as
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a bounding wall on particle motion, i.e. a rotating container.
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</P>
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<P>The <I>delete</I> style removes the named region. Since there is little
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overhead to defining extra regions, there is normally no need to do
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this, unless you are defining and discarding large numbers of regions
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in your input script.
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</P>
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<P>The lo/hi values for <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>prism</I> styles
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can be specified as EDGE or INF. EDGE means they extend all the way
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to the global simulation box boundary. Note that this is the current
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box boundary; if the box changes size during a simulation, the region
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does not. INF means a large negative or positive number (1.0e20), so
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it should encompass the simulation box even if it changes size. If a
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region is defined before the simulation box has been created (via
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<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
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<A HREF = "read_restart.html">read_restart</A> commands), then an EDGE or INF
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parameter cannot be used. For a <I>prism</I> region, a non-zero tilt
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factor in any pair of dimensions cannot be used if both the lo/hi
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values in either of those dimensions are INF. E.g. if the xy tilt is
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non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi.
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</P>
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<P>IMPORTANT NOTE: Regions in LAMMPS do not get wrapped across periodic
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boundaries, as specified by the <A HREF = "boundary.html">boundary</A> command. For
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example, a spherical region that is defined so that it overlaps a
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periodic boundary is not treated as 2 half-spheres, one on either side
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of the simulation box.
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</P>
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<P>IMPORTANT NOTE: Regions in LAMMPS are always 3d geometric objects,
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regardless of whether the <A HREF = "dimension.html">dimension</A> of a simulation
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is 2d or 3d. Thus when using regions in a 2d simulation, you should
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be careful to define the region so that its intersection with the 2d
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x-y plane of the simulation has the 2d geometric extent you want.
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</P>
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<P>For style <I>cone</I>, an axis-aligned cone is defined which is like a
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<I>cylinder</I> except that two different radii (one at each end) can be
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defined. Either of the radii (but not both) can be 0.0.
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</P>
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<P>For style <I>cone</I> and <I>cylinder</I>, the c1,c2 params are coordinates in
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the 2 other dimensions besides the cylinder axis dimension. For dim =
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x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y.
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Thus the third example above specifies a cylinder with its axis in the
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y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
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extending in the y-direction from -5.0 to the upper box boundary.
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</P>
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<P>For style <I>plane</I>, a plane is defined which contain the point
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(px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does
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not have to be of unit length. The "inside" of the plane is the
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half-space in the direction of the normal vector; see the discussion
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of the <I>side</I> option below.
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</P>
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<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
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parallelepiped in an input script!). The parallelepiped has its
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"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
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from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
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(xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
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and are called "tilt factors" because they are the amount of
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displacement applied to faces of an originally orthogonal box to
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transform it into the parallelepiped.
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</P>
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<P>A prism region that will be used with the <A HREF = "create_box.html">create_box</A>
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command to define a triclinic simulation box must have tilt factors
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(xy,xz,yz) that do not skew the box more than half the distance of
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corresponding the parallel box length. For example, if xlo = 2 and
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xhi = 12, then the x box length is 10 and the xy tilt factor must be
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between -5 and 5. Similarly, both xz and yz must be between
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-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
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since if the maximum tilt factor is 5 (as in this example), then
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configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
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geometrically equivalent.
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</P>
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<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
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geometric description of triclinic boxes, as defined by LAMMPS, and
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how to transform these parameters to and from other commonly used
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triclinic representations.
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</P>
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<P>The <I>union</I> style creates a region consisting of the volume of all the
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listed regions combined. The <I>intersect</I> style creates a region
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consisting of the volume that is common to all the listed regions.
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</P>
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<HR>
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<P>The <I>side</I> keyword determines whether the region is considered to be
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inside or outside of the specified geometry. Using this keyword in
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conjunction with <I>union</I> and <I>intersect</I> regions, complex geometries
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can be built up. For example, if the interior of two spheres were
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each defined as regions, and a <I>union</I> style with <I>side</I> = out was
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constructed listing the region-IDs of the 2 spheres, the resulting
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region would be all the volume in the simulation box that was outside
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both of the spheres.
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</P>
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<P>The <I>units</I> keyword determines the meaning of the distance units used
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to define the region for any argument above listed as having distance
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units. It also affects the scaling of the velocity vector specfied
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with the <I>vel</I> keyword, the amplitude vector specified with the
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<I>wiggle</I> keyword, and the rotation point specified with the <I>rotate</I>
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keyword, since they each involve a distance metric.
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</P>
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<P>A <I>box</I> value selects standard distance units as defined by the
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<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
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A <I>lattice</I> value means the distance units are in lattice spacings.
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The <A HREF = "lattice.html">lattice</A> command must have been previously used to
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define the lattice spacings which are used as follows:
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</P>
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<UL><LI>For style <I>block</I>, the lattice spacing in dimension x is applied to
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xlo and xhi, similarly the spacings in dimensions y,z are applied to
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ylo/yhi and zlo/zhi.
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<LI>For style <I>cone</I>, the lattice spacing in argument <I>dim</I> is applied to
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lo and hi. The spacings in the two radial dimensions are applied to
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c1 and c2. The two cone radii are scaled by the lattice
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spacing in the dimension corresponding to c1.
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<LI>For style <I>cylinder</I>, the lattice spacing in argument <I>dim</I> is applied
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to lo and hi. The spacings in the two radial dimensions are applied
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to c1 and c2. The cylinder radius is scaled by the lattice
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spacing in the dimension corresponding to c1.
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<LI>For style <I>plane</I>, the lattice spacing in dimension x is applied to
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px and nx, similarly the spacings in dimensions y,z are applied to
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py/ny and pz/nz.
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<LI>For style <I>prism</I>, the lattice spacing in dimension x is applied to
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xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing
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in dimension x is applied to xy and xz, and the spacing in dimension y
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to yz.
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<LI>For style <I>sphere</I>, the lattice spacing in dimensions x,y,z are
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applied to the sphere center x,y,z. The spacing in dimension x is
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applied to the sphere radius.
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</UL>
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<HR>
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<P>If the <I>move</I> or <I>rotate</I> keywords are used, the region is "dynamic",
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meaning its location or orientation changes with time. These keywords
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cannot be used with a <I>union</I> or <I>intersect</I> style region. Instead,
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the keywords should be used to make the individual sub-regions of the
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<I>union</I> or <I>intersect</I> region dynamic. Normally, each sub-region
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should be "dynamic" in the same manner (e.g. rotate around the same
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point), though this is not a requirement.
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</P>
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<P>The <I>move</I> keyword allows one or more <A HREF = "variable.html">equal-style
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variables</A> to be used to specify the x,y,z displacement
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of the region, typically as a function of time. A variable is
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specified as v_name, where name is the variable name. Any of the
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three variables can be specified as NULL, in which case no
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displacement is calculated in that dimension.
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</P>
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<P>Note that equal-style variables can specify formulas with various
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mathematical functions, and include <A HREF = "thermo_style.html">thermo_style</A>
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command keywords for the simulation box parameters and timestep and
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elapsed time. Thus it is easy to specify a region displacement that
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change as a function of time or spans consecutive runs in a continuous
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fashion. For the latter, see the <I>start</I> and <I>stop</I> keywords of the
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<A HREF = "run.html">run</A> command and the <I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style
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custom</A> for details.
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</P>
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<P>For example, these commands would displace a region from its initial
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position, in the positive x direction, effectively at a constant
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velocity:
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</P>
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<PRE>variable dx equal ramp(0,10)
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region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
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</PRE>
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<P>Note that the initial displacemet is 0.0, though that is not required.
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</P>
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<P>Either of these varaibles would "wiggle" the region back and forth in
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the y direction:
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</P>
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<PRE>variable dy equal swiggle(0,5,100)
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variable dysame equal 5*sin(2*PI*elaplong*dt/100)
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region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
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</PRE>
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<P>The <I>rotate</I> keyword rotates the region around a rotation axis <I>R</I> =
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(Rx,Ry,Rz) that goes thru a point <I>P</I> = (Px,Py,Pz). The rotation
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angle is calculated, presumably as a function of time, by a variable
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specified as v_theta, where theta is the variable name. The variable
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should generate its result in radians. The direction of rotation for
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the region around the rotation axis is consistent with the right-hand
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rule: if your right-hand thumb points along <I>R</I>, then your fingers
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wrap around the axis in the direction of rotation.
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</P>
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<P>The <I>move</I> and <I>rotate</I> keywords can be used together. In this case,
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the displacement specified by the <I>move</I> keyword is applied to the <I>P</I>
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point of the <I>rotate</I> keyword.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>A prism cannot be of 0.0 thickness in any dimension; use a small z
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thickness for 2d simulations. For 2d simulations, the xz and yz
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parameters must be 0.0.
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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 = "lattice.html">lattice</A>, <A HREF = "create_atoms.html">create_atoms</A>,
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<A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "group.html">group</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 option defaults are side = in, units = lattice, and no move or
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rotation.
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</P>
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</HTML>
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