lattice command — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# lattice command

## Syntax

    lattice style scale keyword values ...

- style = none or sc or bcc or fcc or hcp or diamond or sq or sq2 or hex or custom

- scale = scale factor between lattice and simulation box

      scale = reduced density rho* (for LJ units)
      scale = lattice constant in distance units (for all other units)

- zero or more keyword/value pairs may be appended

- keyword = origin or orient or spacing or a1 or a2 or a3 or basis or triclinic/general

      origin values = x y z
        x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
      orient values = dim i j k
        dim = x or y or z
        i,j,k = integer lattice directions
      spacing values = dx dy dz
        dx,dy,dz = lattice spacings in the x,y,z box directions
      a1,a2,a3 values = x y z
        x,y,z = primitive vector components that define unit cell
      basis values = x y z
        x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1)
      triclinic/general values = no values

## Examples

    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 triclinic/general
    lattice none 2.0

## Description

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.

A lattice is used by LAMMPS in two ways. First, the create_atoms command creates atoms on the lattice points inside the simulation box. Note that the create_atoms 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. create_box, region and velocity), which are often convenient to use when the underlying problem geometry is atoms on a lattice.

The lattice style must be consistent with the dimension of the simulation - see the dimension command. Styles sc or bcc or fcc or hcp or diamond are for 3d problems. Styles sq or sq2 or hex are for 2d problems. Style custom can be used for either 2d or 3d problems.

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.

Note that the lattice command can be used multiple times in an input script. Each time it is invoked, the lattice attributes are re-defined and are used for all subsequent commands (that use lattice attributes). For example, a sequence of lattice, region, and create_atoms commands can be repeated multiple times to build a poly-crystalline model with different geometric regions populated with atoms in different lattice orientations.

A lattice of style none does not define a unit cell and basis set, so it cannot be used with the create_atoms command. However it does define a lattice spacing via the specified scale parameter. As explained above the lattice spacings in x,y,z can be used by other commands as distance units. No additional keyword/value pairs can be specified for the none style. By default, a “lattice none 1.0” is defined, which means the lattice spacing is the same as one distance unit, as defined by the units command.

Lattices of style sc, fcc, bcc, and diamond are 3d lattices that define a cubic unit cell with edge length = 1.0. This means a1 = 1 0 0, a2 = 0 1 0, and a3 = 0 0 1. Style hcp has a1 = 1 0 0, a2 = 0 sqrt(3) 0, and a3 = 0 0 sqrt(8/3). The placement of the basis atoms within the unit cell are described in any solid-state physics text. A sc lattice has 1 basis atom at the lower-left-bottom corner of the cube. A bcc lattice has 2 basis atoms, one at the corner and one at the center of the cube. A fcc lattice has 4 basis atoms, one at the corner and 3 at the cube face centers. A hcp lattice has 4 basis atoms, two in the z = 0 plane and 2 in the z = 0.5 plane. A diamond lattice has 8 basis atoms.

Lattices of style sq and sq2 are 2d lattices that define a square unit cell with edge length = 1.0. This means a1 = 1 0 0 and a2 = 0 1 0. A sq lattice has 1 basis atom at the lower-left corner of the square. A sq2 lattice has 2 basis atoms, one at the corner and one at the center of the square. A hex style is also a 2d lattice, but the unit cell is rectangular, with a1 = 1 0 0 and a2 = 0 sqrt(3) 0. It has 2 basis atoms, one at the corner and one at the center of the rectangle.

A lattice of style custom allows you to specify a1, a2, a3, and a list of basis atoms to put in the unit cell. By default, a1 and a2 and 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 basis keyword you add atoms, one at a time, to the unit cell. Its arguments are fractional coordinates (0.0 <= x,y,z < 1.0). For 2d simulations, the fractional z coordinate for any basis atom must be 0.0.

The position vector x of a basis atom within the unit cell is a linear combination of the unit cell’s 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, where bx,by,bz are the 3 values specified for the basis keyword.

This subsection discusses the arguments that determine how the idealized unit cell is transformed into a lattice of points within the simulation box.

The scale 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 scale argument depends on the units being used in your simulation.

For all unit styles except lj, the scale argument is specified in the distance units defined by the unit style. For example, in real or metal units, if the unit cell is a unit cube with edge length 1.0, specifying scale = 3.52 would create a cubic lattice with a spacing of 3.52 Angstroms. In cgs units, the spacing would be 3.52 cm.

For unit style lj, 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.

The origin 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. For 2d simulations, the origin z value must be 0.0.

The orient option specifies how the unit cell will be rotated when mapping it into the simulation box. The dim 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, and similarly for y and z. The 3 lattice directions you specify do not have to be unit vectors, but they must be mutually orthogonal and obey the right-hand rule, i.e. (X cross Y) points in the Z direction. For 2d simulations, the orient x and y vectors must define 0 for their 3rd component. Similarly the orient z vector must define 0 for its 1st and 2nd components.

Note

The preceding paragraph describing lattice directions is only valid for orthogonal cubic unit cells (or square in 2d). If you are using a hcp or hex lattice or the more general lattice style custom with non-orthogonal a1,a2,a3 vectors, then you should think of the 3 orient vectors 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.

The triclinic/general option specifies that the defined lattice is for use with a general triclinic simulation box, as opposed to an orthogonal or restricted triclinic box. The Howto triclinic doc page explains all 3 kinds of simulation boxes LAMMPS supports.

If this option is specified, a custom lattice style must be used. The a1, a2, a3 vectors should define the edge vectors of a single unit cell of the lattice with one or more basis atoms. They edge vectors can be arbitrary so long as they are non-zero, distinct, and not co-planar. In addition, they must define a right-handed system, such that (a1 cross a2) points in the direction of a3. Note that a left-handed system can be converted to a right-handed system by simply swapping the order of any pair of the a1, a2, a3 vectors. For 2d simulations, the a3 vector must be specified as (0.0,0.0,1.0), which is its default value.

If this option is used, the origin and orient settings must have their default values. Namely (0.0,0.0,0.0) for the origin and (100), (010), (001) for the orient vectors.

The create_box command can be used to create a general triclinic box that replicates the a1, a2, a3 unit cell vectors in each direction to create the 3 arbitrary edge vectors of the overall simulation box. It requires a lattice with the triclinic/general option.

Likewise, the create_atoms command can be used to add atoms (or molecules) to a general triclinic box which lie on the lattice points defined by a1, a2, a3 and the unit cell basis atoms. To do this, it also requires a lattice with the triclinic/general option.

Note

LAMMPS allows specification of general triclinic lattices and simulation boxes as a convenience for users who may be converting data from solid-state crystallographic representations or from DFT codes for input to LAMMPS. However, as explained on the Howto_triclinic doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means the box and per-atom information (e.g. coordinates, velocities) defined by the create_box and create_atoms commands are converted from general to restricted triclinic form when the two commands are invoked. It also means that any other commands which use lattice spacings from this command (e.g. the region command), will be operating on a restricted triclinic simulation box, even if the triclinic/general option was used to define the lattice. See the next section for details.

Several LAMMPS commands have the option to use distance units that are inferred from “lattice spacings” in the x,y,z box directions. E.g. the region command can create a block of size 10x20x20, where 10 means 10 lattice spacings in the x direction.

Note

Though they are called lattice spacings, all the commands that have a “units lattice” option, simply use the 3 values as scale factors on the distance units defined by the units command. Thus if you do not like the lattice spacings computed by LAMMPS (e.g. for a non-orthogonal or rotated unit cell), you can define the 3 values to be whatever you wish, via the spacing option.

If the spacing 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 and rotated), so that it now has (perhaps) a modified size 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 (4 in 2d). Similarly, the Y and Z lattice spacings are defined as the difference in the min/max of the y and z coordinates.

Note

If the triclinic/general option is specified, the unit cell defined by a1, a2, a3 edge vectors is first converted to a restricted triclinic orientation, which is a rotation operation. The min/max extent of the 8 corner points is then determined, as described in the preceding paragraph, to set the lattice spacings. As explained for the triclinic/general option above, this is because any use of the lattice spacings by other commands will be for a restricted triclinic simulation box, not a general triclinic box.

Note that if the unit cell is orthogonal with axis-aligned edges (no rotation via the orient 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 hex 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.

Note

For non-orthogonal unit cells and/or when a rotation is applied via the orient keyword, then the lattice spacings computed by LAMMPS are typically less intuitive. In particular, in these cases, there is no guarantee that a particular 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 create_atoms command, you will NOT necessarily create a periodic system. I.e. atoms may overlap incorrectly at the faces of the simulation box.

The spacing 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 edge length independent of the scale factor. As mentioned above, 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.

Note that whenever the lattice command is used, the values of the lattice spacings LAMMPS calculates are printed out. Thus their effect in commands that use the spacings should be decipherable.

Example commands for generating a Wurtzite crystal. The lattice constants approximate those of CdSe. The \(\sqrt{3}\times 1\) orthorhombic supercell is used with the x, y, and z directions oriented along \([\bar{1}\bar{2}30]\), \([10\bar{1}0]\), and \([0001]\), respectively.

    variable a equal  4.34
    variable b equal  $a*sqrt(3.0)
    variable c equal  $a*sqrt(8.0/3.0)

    variable third equal 1.0/3.0
    variable five6 equal 5.0/6.0

    lattice custom    1.0     &
            a1      $b       0.0     0.0     &
            a2      0.0      $a      0.0     &
            a3      0.0      0.0     $c      &
            basis   0.0      0.0     0.0     &
            basis   0.5      0.5     0.0     &
            basis   ${third} 0.0     0.5     &
            basis   ${five6} 0.5     0.5     &
            basis   0.0      0.0     0.625   &
            basis   0.5      0.5     0.625   &
            basis   ${third} 0.0     0.125   &
            basis   ${five6} 0.5     0.125

    region myreg block 0 1 0 1 0 1
    create_box      2 myreg
    create_atoms    1 box      &
            basis   5       2       &
            basis   6       2       &
            basis   7       2       &
            basis   8       2

## Restrictions

The a1,a2,a3,basis keywords can only be used with style custom.

## Related commands

dimension, create_atoms, region

## Default

    lattice none 1.0

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, a2 = 0 1 0, and a3 = 0 0 1.