2006-09-22 00:22:34 +08:00
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<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>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 value ...
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</PRE>
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<UL><LI>ID = user-assigned name for the region
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2010-01-01 05:08:23 +08:00
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<LI>style = <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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2006-09-22 00:22:34 +08:00
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2009-07-13 23:55:54 +08:00
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<PRE> <I>block</I> args = xlo xhi ylo yhi zlo zhi
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2009-06-24 01:19:47 +08:00
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xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
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2009-07-13 23:55:54 +08:00
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<I>cone</I> args = dim c1 c2 radlo radhi lo hi
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2009-06-24 01:19:47 +08:00
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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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2006-09-22 00:22:34 +08:00
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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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2010-01-01 05:08:23 +08:00
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<I>plane</I> args = px py pz nx ny nz
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2010-01-09 06:54:29 +08:00
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px,py,pz = point on the plane (distance units)
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2010-01-01 05:08:23 +08:00
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nx,ny,nz = direction normal to plane (distance units)
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2007-03-08 09:01:08 +08:00
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<I>prism</I> args = xlo xhi ylo yhi zlo zhi xy xz yz
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2009-06-24 01:19:47 +08:00
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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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2006-10-13 04:46:30 +08:00
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<I>sphere</I> args = x y z radius
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2009-06-24 01:19:47 +08:00
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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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2006-09-22 00:22:34 +08:00
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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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2007-07-03 04:04:44 +08:00
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<LI>zero or more keyword/value pairs may be appended
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2006-09-22 00:22:34 +08:00
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2010-01-12 04:54:59 +08:00
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<LI>keyword = <I>side</I> or <I>units</I> or <I>vel</I> or <I>wiggle</I> or <I>rotate</I>
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2006-09-22 00:22:34 +08:00
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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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2010-01-12 04:54:59 +08:00
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<I>box</I> = the geometry is defined in simulation box units
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<I>vel</I> args = Vx Vy Vz
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Vx,Vy,Vz = components of velocity vector (velocity units)
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<I>wiggle</I> args = Ax Ay Az period
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Ax,Ay,Az = components of amplitude vector (distance units)
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period = period of oscillation (time units)
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<I>rotate</I> args = Px Py Pz Rx Ry Rz period
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Px,Py,Pz = origin point of axis of rotation (distance units)
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Rx,Ry,Rz = axis of rotation vector
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period = period of rotation (time units)
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2006-09-22 00:22:34 +08:00
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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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2009-01-09 07:18:29 +08:00
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region void cylinder y 2 3 5 -5.0 EDGE units box
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2006-10-13 04:37:55 +08:00
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region 1 prism 0 10 0 10 0 10 2 0 0
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2010-01-12 04:54:59 +08:00
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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 wiggle 1 1 0 10
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2006-09-22 00:22:34 +08:00
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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 the atoms
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in the region can be identified as a group via the <A HREF = "group.html">group</A>
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command, or deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command.
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2010-01-09 06:54:29 +08:00
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Or the surface of the region can be used as a boundary wall via the
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<A HREF = "fix_wall_region.html">fix wall/region</A> command.
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2006-09-22 00:22:34 +08:00
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</P>
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2010-01-12 04:54:59 +08:00
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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>vel</I> or <I>wiggle</I> or
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<I>rotate</I> keyword is used, as described below, the region becomes
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"dynamic", meaning it's location or orientation changes with time.
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This may be useful, for example, when thermostatting a region, via the
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compute temp/region command, or when the fix wall/region command uses
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a region surface as a bounding wall on particle motion, i.e. a
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rotating container.
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</P>
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2009-06-24 01:19:47 +08:00
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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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2007-08-07 21:47:11 +08:00
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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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2010-01-09 06:54:29 +08:00
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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 is the 2d geometric object you want.
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2006-09-22 00:22:34 +08:00
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</P>
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2009-06-24 01:19:47 +08:00
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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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2010-01-09 06:54:29 +08:00
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defined. Either of the radii (but not both) can be 0.0.
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2009-06-24 01:19:47 +08:00
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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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2006-09-22 00:22:34 +08:00
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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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2010-01-09 06:54:29 +08:00
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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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2007-03-08 09:01:08 +08:00
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<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
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2008-03-01 09:13:20 +08:00
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parallelepiped in an input script!). Think of the parallelepiped as
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2007-03-08 09:01:08 +08:00
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initially an axis-aligned orthogonal box with the same xyz lo/hi
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parameters as region style <I>block</I> would define. Then, while holding
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2007-04-02 22:26:01 +08:00
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the (xlo,ylo,zlo) corner point fixed, the box is "skewed" or "tilted"
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in 3 directions. First, for the lower xy face of the box, the <I>xy</I>
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factor is how far the upper y edge is shifted in the x direction. The
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lower xy face is now a parallelogram. A plus or minus value for <I>xy</I>
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can be specified; 0.0 means no tilt. Then, the upper xy face of the
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box is translated in the x and y directions by <I>xz</I> and <I>yz</I>. This
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results in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3
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edge vectors starting from its origin given by a = (xhi-xlo,0,0); b =
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2007-03-08 09:01:08 +08:00
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(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
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2006-10-13 04:37:55 +08:00
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</P>
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2007-06-20 20:56:17 +08:00
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<P>A prism region used with the <A HREF = "create_box.html">create_box</A> command must
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have tilt factors (xy,xz,yz) that do not skew the box more than half
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the distance of 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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equivalent.
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</P>
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2006-09-22 00:22:34 +08:00
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<P>The <I>union</I> style creates a region consisting of the volume of all the
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2008-03-01 09:13:20 +08:00
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listed regions combined. The <I>intersect</I> style creates a region
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2006-09-22 00:22:34 +08:00
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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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2010-01-12 04:54:59 +08:00
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<HR>
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2006-09-22 00:22:34 +08:00
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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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2010-01-09 06:54:29 +08:00
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to define the region for any argument above listed as having distance
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2010-01-12 04:54:59 +08:00
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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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2010-01-09 06:54:29 +08:00
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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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2010-01-12 04:54:59 +08:00
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<HR>
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<P>If the <I>vel</I> or <I>wiggle</I> or <I>rotate</I> keywords are used, the region
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is "dynamic", meaning its location or orientation changes with time.
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No more than one of these keywords can be used at a time. These
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keywords cannot be used with a <I>union</I> or <I>intersect</I> style region.
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Instead, the keywords should be used to define the individual
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sub-regions of the <I>union</I> or <I>intersect</I> region. Normally, each
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sub-region should be "dynamic" in the same manner (e.g. rotate around
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the same point), though this is not a requirement.
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</P>
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<P>The <I>vel</I> style moves the region at a constant velocity, so that its
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position <I>X</I> = (x,y,z) as a function of time is given in vector
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notation as
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</P>
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<PRE>X(t) = X0 + V * delta
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</PRE>
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<P>where <I>X0</I> = (x0,y0,z0) is its position at the time the region is
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specified, <I>V</I> is the specified velocity vector with components
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(Vx,Vy,Vz), and <I>delta</I> is the time elapsed since the region was
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specified.
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</P>
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<P>The <I>wiggle</I> style moves the region in an oscillatory fashion, so that
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its position <I>X</I> = (x,y,z) as a function of time is given in vector
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notation as
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</P>
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<PRE>X(t) = X0 + A sin(omega*delta)
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</PRE>
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<P>where <I>X0</I> = (x0,y0,z0) is its position at the time the region is
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specified, <I>A</I> is the specified amplitude vector with components
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(Ax,Ay,Az), <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the time
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elapsed since the region was specified.
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</P>
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<P>The <I>rotate</I> style 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 <I>period</I> of
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the rotation is also specified. The direction of rotation for the
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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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2007-03-09 08:00:06 +08:00
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<P><B>Restrictions:</B>
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2006-09-22 00:22:34 +08:00
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</P>
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2006-10-13 04:37:55 +08:00
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<P>A prism cannot be of 0.0 thickness in any dimension; use a small z
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2007-03-08 09:01:08 +08:00
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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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2006-10-13 04:37:55 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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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>
|
2010-01-12 04:56:22 +08:00
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<P>The option defaults are side = in, units = lattice, and no
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velocity, wiggling, or rotation.
|
2006-09-22 00:22:34 +08:00
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</P>
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</HTML>
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