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< title > region command — LAMMPS 15 May 2015 version documentation< / title >
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2006-09-22 00:22:34 +08:00
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
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< li > region command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< div class = "section" id = "region-command" >
< span id = "index-0" > < / span > < h1 > region command< a class = "headerlink" href = "#region-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > region ID style args keyword arg ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID = user-assigned name for the region< / li >
< li > style = < em > delete< / em > or < em > block< / em > or < em > cone< / em > or < em > cylinder< / em > or < em > plane< / em > or < em > prism< / em > or < em > sphere< / em > or < em > union< / em > or < em > intersect< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > delete< / em > = no args
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< em > block< / em > args = xlo xhi ylo yhi zlo zhi
xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
< em > cone< / em > args = dim c1 c2 radlo radhi lo hi
dim = < em > x< / em > or < em > y< / em > or < em > z< / em > = axis of cone
c1,c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
< em > cylinder< / em > args = dim c1 c2 radius lo hi
dim = < em > x< / em > or < em > y< / em > or < em > z< / em > = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
radius = cylinder radius (distance units)
radius can be a variable (see below)
lo,hi = bounds of cylinder in dim (distance units)
< em > plane< / em > args = px py pz nx ny nz
px,py,pz = point on the plane (distance units)
nx,ny,nz = direction normal to plane (distance units)
< em > prism< / em > 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)
< em > sphere< / em > args = x y z radius
x,y,z = center of sphere (distance units)
radius = radius of sphere (distance units)
radius can be a variable (see below)
< em > union< / em > 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
< em > intersect< / em > 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
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< / pre >
< ul class = "simple" >
< li > zero or more keyword/arg pairs may be appended< / li >
< li > keyword = < em > side< / em > or < em > units< / em > or < em > move< / em > or < em > rotate< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > side< / em > value = < em > in< / em > or < em > out< / em >
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< em > in< / em > = the region is inside the specified geometry
< em > out< / em > = the region is outside the specified geometry
< em > units< / em > value = < em > lattice< / em > or < em > box< / em >
< em > lattice< / em > = the geometry is defined in lattice units
< em > box< / em > = the geometry is defined in simulation box units
< em > move< / em > args = v_x v_y v_z
v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
< em > rotate< / em > args = v_theta Px Py Pz Rx Ry Rz
v_theta = equal-style variable for rotaton of region over time (in radians)
Px,Py,Pz = origin for axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < 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
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< 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 class = "reference internal" href = "create_atoms.html" > < em > create_atoms< / em > < / 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 class = "reference internal" href = "create_box.html" > < em > create_box< / em > < / a > command. Or the atoms in the region
can be identified as a group via the < a class = "reference internal" href = "group.html" > < em > group< / em > < / a > command, or
deleted via the < a class = "reference internal" href = "delete_atoms.html" > < em > delete_atoms< / em > < / a > command. Or the
surface of the region can be used as a boundary wall via the < a class = "reference internal" href = "fix_wall_region.html" > < em > fix wall/region< / em > < / a > command.< / p >
< 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
exactly on the region boundary are considered to be interior to the
region. This means, for example, for a spherical region, an atom on
the sphere surface would be part of the region if the sphere were
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defined with the < em > side in< / em > keyword, but would not be part of the
region if it were defined using the < em > side out< / em > keyword. See more
details on the < em > side< / em > keyword below.< / p >
< p > Normally, regions in LAMMPS are “ static” , meaning their geometric
extent does not change with time. If the < em > move< / em > or < em > rotate< / em > keyword
is used, as described below, the region becomes “ dynamic” , meaning
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
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.< / p >
< p > The < em > delete< / em > 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
this, unless you are defining and discarding large numbers of regions
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in your input script.< / p >
< p > The lo/hi values for < em > block< / em > or < em > cone< / em > or < em > cylinder< / em > or < em > prism< / em > styles
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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
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region is defined before the simulation box has been created (via
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< a class = "reference internal" href = "create_box.html" > < em > create_box< / em > < / a > or < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > or
< a class = "reference internal" href = "read_restart.html" > < em > read_restart< / em > < / a > commands), then an EDGE or INF
parameter cannot be used. For a < em > prism< / em > region, a non-zero tilt
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factor in any pair of dimensions cannot be used if both the lo/hi
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.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > Regions in LAMMPS do not get wrapped across periodic
boundaries, as specified by the < a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > command. For
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example, a spherical region that is defined so that it overlaps a
periodic boundary is not treated as 2 half-spheres, one on either side
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of the simulation box.< / p >
< / div >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > Regions in LAMMPS are always 3d geometric objects,
regardless of whether the < a class = "reference internal" href = "dimension.html" > < em > dimension< / em > < / a > of a simulation
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is 2d or 3d. Thus when using regions in a 2d simulation, you should
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.< / p >
< / div >
< p > For style < em > cone< / em > , an axis-aligned cone is defined which is like a
< em > cylinder< / em > except that two different radii (one at each end) can be
defined. Either of the radii (but not both) can be 0.0.< / p >
< p > For style < em > cone< / em > and < em > cylinder< / em > , the c1,c2 params are coordinates in
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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
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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.< / p >
< p > For style < em > plane< / em > , 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 < em > side< / em > option below.< / p >
< p > For style < em > prism< / em > , 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). < em > Xy,xz,yz< / em > can be 0.0 or positive or negative values
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.< / p >
< p > A prism region that will be used with the < a class = "reference internal" href = "create_box.html" > < em > create_box< / em > < / a >
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command to define a triclinic simulation box must have tilt factors
(xy,xz,yz) that do not skew the box more than half the distance of
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
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
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geometrically equivalent.< / p >
< p > The < em > radius< / em > value for style < em > sphere< / em > and < em > cylinder< / em > can be specified
as an equal-style < a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > . If the value is a
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variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
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its value used to determine the radius of the region.< / p >
< p > Equal-style variables can specify formulas with various mathematical
functions, and include < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent radius.< / p >
< p > See < a class = "reference internal" href = "Section_howto.html#howto-12" > < span > Section_howto 12< / span > < / a > of the doc pages
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for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
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triclinic representations.< / p >
< p > The < em > union< / em > style creates a region consisting of the volume of all the
listed regions combined. The < em > intersect< / em > style creates a region
consisting of the volume that is common to all the listed regions.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > The < em > union< / em > and < em > intersect< / em > regions operate by
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invoking methods from their list of sub-regions. Thus you cannot
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delete the sub-regions after defining the < em > union< / em > or < em > intersection< / em >
region.< / p >
< / div >
< hr class = "docutils" / >
< p > The < em > side< / em > 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 < em > union< / em > and < em > intersect< / em > 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 < em > union< / em > style with < em > side< / em > = out was
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constructed listing the region-IDs of the 2 spheres, the resulting
region would be all the volume in the simulation box that was outside
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both of the spheres.< / p >
< p > The < em > units< / em > 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 < em > vel< / em > keyword, the amplitude vector specified with the
< em > wiggle< / em > keyword, and the rotation point specified with the < em > rotate< / em >
keyword, since they each involve a distance metric.< / p >
< p > A < em > box< / em > value selects standard distance units as defined by the
< a class = "reference internal" href = "units.html" > < em > units< / em > < / a > command, e.g. Angstroms for units = real or metal.
A < em > lattice< / em > value means the distance units are in lattice spacings.
The < a class = "reference internal" href = "lattice.html" > < em > lattice< / em > < / a > command must have been previously used to
define the lattice spacings which are used as follows:< / p >
< ul class = "simple" >
< li > For style < em > block< / em > , 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.< / li >
< li > For style < em > cone< / em > , the lattice spacing in argument < em > dim< / em > is applied to
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lo and hi. The spacings in the two radial dimensions are applied to
c1 and c2. The two cone radii are scaled by the lattice
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spacing in the dimension corresponding to c1.< / li >
< li > For style < em > cylinder< / em > , the lattice spacing in argument < em > dim< / em > is applied
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to lo and hi. The spacings in the two radial dimensions are applied
to c1 and c2. The cylinder radius is scaled by the lattice
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spacing in the dimension corresponding to c1.< / li >
< li > For style < em > plane< / em > , 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.< / li >
< li > For style < em > prism< / em > , 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
in dimension x is applied to xy and xz, and the spacing in dimension y
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to yz.< / li >
< li > For style < em > sphere< / em > , 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.< / li >
< / ul >
< hr class = "docutils" / >
< p > If the < em > move< / em > or < em > rotate< / em > 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 < em > union< / em > or < em > intersect< / em > style region. Instead,
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the keywords should be used to make the individual sub-regions of the
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< em > union< / em > or < em > intersect< / em > region dynamic. Normally, each sub-region
should be “ dynamic” in the same manner (e.g. rotate around the same
point), though this is not a requirement.< / p >
< p > The < em > move< / em > keyword allows one or more < a class = "reference internal" href = "variable.html" > < em > equal-style variables< / em > < / 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
specified as v_name, where name is the variable name. Any of the
three variables can be specified as NULL, in which case no
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displacement is calculated in that dimension.< / p >
< p > Note that equal-style variables can specify formulas with various
mathematical functions, and include < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a >
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command keywords for the simulation box parameters and timestep and
elapsed time. Thus it is easy to specify a region displacement that
change as a function of time or spans consecutive runs in a continuous
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fashion. For the latter, see the < em > start< / em > and < em > stop< / em > keywords of the
< a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command and the < em > elaplong< / em > keyword of < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / a > for details.< / p >
< 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:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > variable dx equal ramp(0,10)
region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
< / pre > < / div >
< / div >
< p > Note that the initial displacemet is 0.0, though that is not required.< / p >
< p > Either of these varaibles would “ wiggle” the region back and forth in
the y direction:< / p >
< div class = "highlight-python" > < div class = "highlight" > < 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
< / pre > < / div >
< / div >
< p > The < em > rotate< / em > keyword rotates the region around a rotation axis < em > R< / em > =
(Rx,Ry,Rz) that goes thru a point < em > P< / em > = (Px,Py,Pz). The rotation
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angle is calculated, presumably as a function of time, by a variable
specified as v_theta, where theta is the variable name. The variable
should generate its result in radians. The direction of rotation for
the region around the rotation axis is consistent with the right-hand
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rule: if your right-hand thumb points along < em > R< / em > , then your fingers
wrap around the axis in the direction of rotation.< / p >
< p > The < em > move< / em > and < em > rotate< / em > keywords can be used together. In this case,
the displacement specified by the < em > move< / em > keyword is applied to the < em > P< / em >
point of the < em > rotate< / em > keyword.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< 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.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "lattice.html" > < em > lattice< / em > < / a > , < a class = "reference internal" href = "create_atoms.html" > < em > create_atoms< / em > < / a > ,
< a class = "reference internal" href = "delete_atoms.html" > < em > delete_atoms< / em > < / a > , < a class = "reference internal" href = "group.html" > < em > group< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The option defaults are side = in, units = lattice, and no move or
rotation.< / p >
< / div >
< / div >
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