create_box command — LAMMPS documentation

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# create_box command

## Syntax

    create_box N region-ID keyword value ...

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

- region-ID = ID of region to use as simulation domain

- 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

    create_box 2 mybox
    create_box 2 mybox bond/types 2 extra/bond/per/atom 1

## Description

This command creates a simulation box based on the specified region. Thus a region command must first be used to define a geometric domain. It also partitions the simulation box into a regular 3d grid of rectangular bricks, one per processor, based on 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.

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

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.

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 its “origin” at (xlo,ylo,zlo) and is defined by 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 \(\vec c = (xz,yz,z_\text{hi}-z_\text{lo})\). 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.

By default, a prism region used with the create_box command must 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. Simulations with large tilt factors will run inefficiently, since they require more ghost atoms and thus more communication. With very large tilt factors, LAMMPS will eventually produce incorrect trajectories and stop with errors due to lost atoms or similar.

See the Howto triclinic page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these 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 set up to be 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.

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.

## Related commands

read_data, create_atoms, region

## Default

none