\(\renewcommand{\AA}{\text{Å}}\)

create_box command

Syntax

create_box N region-ID keyword value ...
create_box N NULL alo ahi blo bhi clo chi keyword value ...

  • N = # of atom types to use in this simulation

  • region-ID = ID of region to use as simulation domain or NULL for general triclinic box

  • alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc”lattice <lattice> command (only when region-ID = NULL)

  • zero or more keyword/value pairs may be appended

  • keyword = bond/types or angle/types or dihedral/types or improper/types or extra/bond/per/atom or extra/angle/per/atom or extra/dihedral/per/atom or extra/improper/per/atom or extra/special/per/atom

    bond/types value = # of bond types
angle/types value = # of angle types
dihedral/types value = # of dihedral types
improper/types value = # of improper types
extra/bond/per/atom value = # of bonds per atom
extra/angle/per/atom value = # of angles per atom
extra/dihedral/per/atom value = # of dihedrals per atom
extra/improper/per/atom value = # of impropers per atom
extra/special/per/atom value = # of special neighbors per atom

Examples

# orthogonal or restricted triclinic box using regionID = mybox
create_box 2 mybox
create_box 2 mybox bond/types 2 extra/bond/per/atom 1

# 2d general triclinic box using primitive cell for 2d hex lattice
lattice       custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
              a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
create_box    1 NULL 0 5 0 5 -0.5 0.5

# 3d general triclinic box using primitive cell for 3d fcc lattice
lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general
create box 1 NULL -5 5 -10 10 0 20

Description

This command creates a simulation box. It also partitions the box into a regular 3d grid of smaller sub-boxes, one per processor (MPI task). The geometry of the partitioning is based on the size and shape of the simulation box, the number of processors being used and the settings of the processors command. The partitioning can later be changed by the balance or fix balance commands.

Simulation boxes in LAMMPS can be either orthogonal or triclinic in shape. Orthogonal boxes are a brick in 3d (rectangle in 2d) with 6 faces that are each perpendicular to one of the standard xyz coordinate axes. Triclinic boxes are a parallelepiped in 3d (parallelogram in 2d) with opposite pairs of faces parallel to each other. LAMMPS supports two forms of triclinic boxes, restricted and general, which differ in how the box is oriented with respect to the xyz coordinate axes. See the Howto triclinic for a detailed description of all 3 kinds of simulation boxes.

The argument N is the number of atom types that will be used in the simulation.

Orthogonal and restricted triclinic boxes are created by specifying a region ID previously defined by the region command. General triclinic boxes are discussed below.

If the region is not of style prism, then LAMMPS encloses the region (block, sphere, etc.) with an axis-aligned orthogonal bounding box which becomes the simulation domain. For a 2d simulation, the zlo and zhi values of the simulation box must straddle zero.

If the region is of style prism, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. As defined by the region prism command, the parallelepiped has an “origin” at (xlo,ylo,zlo) and three edge vectors starting from the origin given by \(\vec a = (x_\text{hi}-x_\text{lo},0,0)\); \(\vec b = (xy,y_\text{hi}-y_\text{lo},0)\); and \(\vec c = (xz,yz,z_\text{hi}-z_\text{lo})\). In LAMMPS lingo, this is a restricted triclinic box because the three edge vectors cannot be defined in arbitrary (general) directions. The parameters xy, xz, and yz can be 0.0 or positive or negative values and are called “tilt factors” because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. For a 2d simulation, the zlo and zhi values of the simulation box must straddle zero.

Typically a prism region used with the create_box command should have tilt factors \((xy,xz,yz)\) that do not skew the box more than half the distance of the parallel box length. For example, if \(x_\text{lo} = 2\) and \(x_\text{hi} = 12\), 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 \(-(x_\text{hi}-x_\text{lo})/2\) and \(+(y_\text{hi}-y_\text{lo})/2\). Note that this is not a limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt \(= \dots, -15\), \(-5\), \(5\), \(15\), \(25, \dots\) are all geometrically equivalent.

LAMMPS will issue a warning if the tilt factors of the created box do not meet this criterion. This is because simulations with large tilt factors may run inefficiently, since they require more ghost atoms and thus more communication. With very large tilt factors, LAMMPS may eventually produce incorrect trajectories and stop with errors due to lost atoms or similar issues.

See the Howto triclinic page for geometric descriptions of triclinic boxes and tilt factors, as well as how to transform the restricted triclinic parameters to and from other commonly used triclinic representations.

When a prism region is used, the simulation domain should normally be periodic in the dimension that the tilt is applied to, which is given by the second dimension of the tilt factor (e.g., \(y\) for \(xy\) tilt). This is so that pairs of atoms interacting across that boundary will have one of them shifted by the tilt factor. Periodicity is set by the boundary command. For example, if the \(xy\) tilt factor is non-zero, then the \(y\) dimension should be periodic. Similarly, the \(z\) dimension should be periodic if \(xz\) or \(yz\) is non-zero. LAMMPS does not require this periodicity, but you may lose atoms if this is not the case.

Note that if your simulation will tilt the box (e.g., via the fix deform command), the simulation box must be created as triclinic, even if the tilt factors are initially 0.0. You can also change an orthogonal box to a triclinic box or vice versa by using the change box command with its ortho and triclinic options.

Note

If the system is non-periodic (in a dimension), then you should not make the lo/hi box dimensions (as defined in your region command) radically smaller/larger than the extent of the atoms you eventually plan to create (e.g., via the create_atoms command). For example, if your atoms extend from 0 to 50, you should not specify the box bounds as \(-10000\) and \(10000\). This is because as described above, LAMMPS uses the specified box size to lay out the 3d grid of processors. A huge (mostly empty) box will be sub-optimal for performance when using “fixed” boundary conditions (see the boundary command). When using “shrink-wrap” boundary conditions (see the boundary command), a huge (mostly empty) box may cause a parallel simulation to lose atoms the first time that LAMMPS shrink-wraps the box around the atoms.

As noted above, general triclinic boxes in LAMMPS allow the box to have arbitrary edge vectors A, B, C. The only restrictions are that the three vectors be distinct, non-zero, and not co-planar. They must also define a right-handed system such that (A x B) points in the direction of C. Note that a left-handed system can be converted to a right-handed system by simply swapping the order of any pair of the A, B, C vectors.

To create a general triclinic boxes, the region is specified as NULL and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three edge vectors A, B, C using additional information previously defined by the lattice command.

The lattice must be of style custom and use its triclinic/general option. This insures the lattice satisfies the restrictions listed above. The a1, *a2, a3 settings of the lattice command define the edge vectors of a unit cell of the general triclinic lattice. This command uses them to define the three edge vectors and origin of the general triclinic box as:

  • A = (ahi-alo) * a1

  • B = (bhi-blo) * a2

  • C = (chi-clo) * a3

  • origin = (alo*a1 + blo*a2 + clo*a3)

For 2d general triclinic boxes, clo = -0.5 and chi = 0.5 is required.

Note

LAMMPS allows specification of general triclinic 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 defined by this command and per-atom information (e.g. coordinates, velocities) defined by the create_atoms command are converted (rotated) from general to restricted triclinic form when the two commands are invoked. The <Howto_triclinic>` doc page also discusses other LAMMPS commands which can input/output general triclinic representations of the simulation box and per-atom data.

The optional keywords can be used to create a system that allows for bond (angle, dihedral, improper) interactions, or for molecules with special 1–2, 1–3, or 1–4 neighbors to be added later. These optional keywords serve the same purpose as the analogous keywords that can be used in a data file which are recognized by the read_data command when it sets up a system.

Note that if these keywords are not used, then the create_box command creates an atomic (non-molecular) simulation that does not allow bonds between pairs of atoms to be defined, or a bond potential to be specified, or for molecules with special neighbors to be added to the system by commands such as create_atoms mol, fix deposit or fix pour.

As an example, see the examples/deposit/in.deposit.molecule script, which deposits molecules onto a substrate. Initially there are no molecules in the system, but they are added later by the fix deposit command. The create_box command in the script uses the bond/types and extra/bond/per/atom keywords to allow this. If the added molecule contained more than one special bond (allowed by default), an extra/special/per/atom keyword would also need to be specified.

Restrictions

An atom_style and region must have been previously defined to use this command.

Default

none