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rLAMMPS lammps
lattice.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>
lattice command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
lattice style scale keyword values ...
</PRE>
<UL><LI>
style =
<I>
none
</I>
or
<I>
sc
</I>
or
<I>
bcc
</I>
or
<I>
fcc
</I>
or
<I>
diamond
</I>
or
<I>
sq
</I>
or
<I>
sq2
</I>
or
<I>
hex
</I>
or
<I>
custom
</I>
<LI>
scale = scale factor between lattice and simulation box
<PRE>
for style
<I>
none
</I>
:
scale is not specified (nor any optional args)
for all other styles:
scale = reduced density rho* (for LJ units)
scale = lattice constant in Angstroms (for real or metal units)
</PRE>
<LI>
zero or more keyword/value pairs may be appended
<LI>
keyword =
<I>
origin
</I>
or
<I>
orient
</I>
or
<I>
spacing
</I>
or
<I>
a1
</I>
or
<I>
a2
</I>
or
<I>
a3
</I>
or
<I>
basis
</I>
<PRE>
<I>
origin
</I>
values = x y z
x,y,z = fractions of a unit cell (0
<
= x,y,z
< 1
)
<
I
>
orient
</I>
values = dim i j k
dim =
<I>
x
</I>
or
<I>
y
</I>
or
<I>
z
</I>
i,j,k = integer lattice directions
<I>
spacing
</I>
values = dx dy dz
dx,dy,dz = lattice spacings in the x,y,z box directions
<I>
a1
</I>
,
<I>
a2
</I>
,
<I>
a3
</I>
values = x y z
x,y,z = primitive vector components that define unit cell
<I>
basis
</I>
values = x y z
x,y,z = fractional coords of a basis atom (0
<
= x,y,z
< 1
)
</
PRE
>
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
lattice fcc 3.52
lattice hex 0.85
lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5
&
basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
lattice none
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Define a lattice for use by other commands. In LAMMPS, a lattice is
simply a set of points in space, determined by a unit cell with basis
atoms, that is replicated infinitely in all dimensions. The arguments
of the lattice command can be used to define a wide variety of
crystallographic lattices.
</P>
<P>
A lattice is used by LAMMPS in two ways. First, the
<A
HREF =
"create_atoms.hmtl"
>
create_atoms
</A>
command creates atoms on the lattice
points inside the simulation box. Note that the
<A
HREF =
"create_atoms.html"
>
create_atoms
</A>
command allows different atom types
to be assigned to different basis atoms of the lattice. Second, the
lattice spacing in the x,y,z dimensions implied by the lattice, can be
used by other commands as distance units
(e.g.
<A
HREF =
"create_box.html"
>
create_box
</A>
,
<A
HREF =
"region.html"
>
region
</A>
and
<A
HREF =
"velocity.html"
>
velocity
</A>
), which are often convenient to use when the
underlying problem geometry is atoms on a lattice.
</P>
<P>
The lattice style must be consistent with the dimension of the
simulation - see the
<A
HREF =
"dimension.html"
>
dimension
</A>
command. Styles
<I>
sc
</I>
or
<I>
bcc
</I>
or
<I>
fcc
</I>
or
<I>
diamond
</I>
are for 3d problems. Styles
<I>
sq
</I>
or
<I>
sq2
</I>
or
<I>
hex
</I>
are for 2d problems. Style
<I>
custom
</I>
can be used for
either 2d or 3d problems.
</P>
<P>
A lattice consists of a unit cell, a set of basis atoms within that
cell, and a set of transformation parameters (scale, origin, orient)
that map the unit cell into the simulation box. The vectors a1,a2,a3
are the edge vectors of the unit cell. This is the nomenclature for
"primitive" vectors in solid-state crystallography, but in LAMMPS the
unit cell they determine does not have to be a "primitive cell" of
minimum volume.
</P>
<HR>
<P>
Lattices of style
<I>
sc
</I>
,
<I>
fcc
</I>
,
<I>
bcc
</I>
, and
<I>
diamond
</I>
are 3d lattices
that define a cubic unit cell with edge length = 1.0. This means a1 =
1.0 0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0. The placement of
the basis atoms within the unit cell are described in any solid-state
physics text. A
<I>
sc
</I>
lattice has 1 basis atom at the
lower-left-bottom corner of the cube. A
<I>
bcc
</I>
lattice has 2 basis
atoms, one at the corner and one at the center of the cube. A
<I>
fcc
</I>
lattice has 4 basis atoms, one at the corner and 3 at the cube face
centers. A
<I>
diamond
</I>
lattice has 8 basis atoms.
</P>
<P>
Lattices of style
<I>
sq
</I>
and
<I>
sq2
</I>
are 2d lattices that define a square
unit cell with edge length = 1.0. This means a1 = 1.0 0.0 0.0 and a2
= 0.0 1.0 0.0. A
<I>
sq
</I>
lattice has 1 basis atom at the lower-left
corner of the square. A
<I>
sq2
</I>
lattice has 2 basis atoms, one at the
corner and one at the center of the square. A
<I>
hex
</I>
style is also a
2d lattice, but the unit cell is rectangular, with a1 = 1.0 0.0 0.0
and a2 = 0.0 sqrt(3.0) 0.0. It has 2 basis atoms, one at the corner
and one at the center of the rectangle.
</P>
<P>
A lattice of style
<I>
custom
</I>
allows you to specify a1, a2, a3, and a
list of basis atoms to put in the unit cell. By default, a1,a2,a3 are
3 orthogonal unit vectors (edges of a unit cube). But you can specify
them to be of any length and non-orthogonal to each other, so that
they describe a tilted parallelepiped. Via the
<I>
basis
</I>
keyword you
add atoms, one at a time, to the unit cell. Its arguments are
fractional coordinates (0.0
<
= x,y,z
< 1
.
0
),
so
that
a
value
of
0
.
5
means
a
position
half-way
across
the
unit
cell
in
that
dimension
.
</
P
>
<HR>
<P>
This sub-section discusses the arguments that determine how the
idealized unit cell is transformed into a lattice of points within the
simulation box.
</P>
<P>
The
<I>
scale
</I>
argument determines how the size of the unit cell will be
scaled when mapping it into the simulation box. I.e. it determines a
multiplicative factor to apply to the unit cell, to convert it to a
lattice of the desired size and distance units in the simulation box.
The meaning of the
<I>
scale
</I>
argument depends on the
<A
HREF =
"unit.html"
>
units
</A>
being used in your simulation.
</P>
<P>
For unit style
<I>
real
</I>
or
<I>
metal
</I>
, the scale argument is in Angstroms.
For example, if the unit cell is a unit cube with edge length 1.0,
setting scale = 3.52 would create a cubic lattice with a spacing of
3.52 Angstroms.
</P>
<P>
For unit style
<I>
lj
</I>
, the scale argument is the Lennard-Jones reduced
density, typically written as rho*. LAMMPS converts this value into
the multiplicative factor via the formula "factor^dim = rho/rho*",
where rho = N/V with V = the volume of the lattice unit cell and N =
the number of basis atoms in the unit cell (described below), and dim
= 2 or 3 for the dimensionality of the simulation. Effectively, this
means that if LJ particles of size sigma = 1.0 are used in the
simulation, the lattice of particles will be at the desired reduced
density.
</P>
<P>
The
<I>
origin
</I>
option specifies how the unit cell will be shifted or
translated when mapping it into the simulation box. The x,y,z values
are fractional values (0.0
<
= x,y,z
< 1
.
0
)
meaning
shift
the
lattice
by
a
fraction
of
the
lattice
spacing
in
each
dimension
.
The
meaning
of
"
lattice
spacing
"
is
discussed
below
.
</
P
>
<P>
The
<I>
orient
</I>
option specifies how the unit cell will be rotated when
mapping it into the simulation box. The
<I>
dim
</I>
argument is one of the
3 coordinate axes in the simulation box. The other 3 arguments are
the crystallographic direction in the lattice that you want to orient
along that axis, specified as integers. E.g. "orient x 2 1 0" means
the x-axis in the simulation box will be the [210] lattice
direction. The 3 lattice directions you specify must be mutually
orthogonal and obey the right-hand rule, i.e. (X cross Y) points in
the Z direction. Note that this description is really only valid for
orthogonal lattices. if you are using the more general lattice style
<I>
custom
</I>
with non-orthogonal a1,a2,a3 vectors, then think of the 3
<I>
orient
</I>
options as creating a 3x3 rotation matrix which is applied to
a1,a2,a3 to rotate the original unit cell to a new orientation in the
simulation box.
</P>
<HR>
<P>
Several LAMMPS commands have the option to use distance units that are
inferred from "lattice spacing" in the x,y,z box directions. E.g. the
<A
HREF =
"region.html"
>
region
</A>
command can create a block of size 10x20x20,
where 10 means 10 lattice spacings in the x direction.
</P>
<P>
The
<I>
spacing
</I>
option sets the 3 lattice spacings directly. All must
be non-zero (use 1.0 for dz in a 2d simulation). The specified values
are multiplied by the multiplicative factor described above that is
associated with the scale factor. Thus a spacing of 1.0 means one
unit cell independent of the scale factor. This option can be useful
if the spacings LAMMPS computes are inconvenient to use in subsequent
commands, which can be the case for non-orthogonal or rotated
lattices.
</P>
<P>
If the
<I>
spacing
</I>
option is not specified, the lattice spacings are
computed by LAMMPS in the following way. A unit cell of the lattice
is mapped into the simulation box (scaled, shifted, rotated), so that
it now has (perhaps) a modified shape and orientation. The lattice
spacing in X is defined as the difference between the min/max extent
of the x coordinates of the 8 corner points of the modified unit cell.
Similarly, the Y and Z lattice spacings are defined as the difference
in the min/max of the y and z coordinates.
</P>
<P>
Note that if the unit cell is orthogonal with axis-aligned edges (not
rotated via the
<I>
orient
</I>
keyword), then the lattice spacings in each
dimension are simply the scale factor (described above) multiplied by
the length of a1,a2,a3. Thus a
<I>
hex
</I>
style lattice with a scale
factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
3*sqrt(3.0) in y.
</P>
<P>
IMPORTANT NOTE: For non-orthogonal unit cells and/or when a rotation
is applied via the
<I>
orient
</I>
keyword, then the lattice spacings may be
less intuitive. In particular, in these cases, there is no guarantee
that the lattice spacing is an integer multiple of the periodicity of
the lattice in that direction. Thus, if you create an orthogonal
periodic simulation box whose size in a dimension is a multiple of the
lattice spacing, and then fill it with atoms via the
<A
HREF =
"create_atoms.html"
>
create_atoms
</A>
command, you will NOT necessarily
create a periodic system. I.e. atoms may overlap incorrectly at the
faces of the simulation box.
</P>
<P>
Regardless of these issues, the values of the lattice spacings LAMMPS
calculates are printed out, so their effect in commands that use the
spacings should be decipherable.
</P>
<HR>
<P>
The command "lattice none" can be used to turn off a previous lattice
definition. Any command that attempts to use the lattice directly
(
<A
HREF =
"create_atoms.html"
>
create_atoms
</A>
) or associated lattice spacings will
then generate an error. No additional arguments need be used with
"lattice none".
</P>
<HR>
<P><B>
Restrictions:
</B>
</P>
<P>
The
<I>
a1,a2,a3,basis
</I>
keywords can only be used with style
<I>
custom
</I>
.
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"dimension.html"
>
dimension
</A>
,
<A
HREF =
"create_atoms.html"
>
create_atoms
</A>
,
<A
HREF =
"region.html"
>
region
</A>
</P>
<P><B>
Default:
</B>
</P>
<PRE>
lattice none
</PRE>
<P>
For other lattice styles, the option defaults are origin = 0.0 0.0
0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1.0
0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0.
</P>
</HTML>
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