CELL

Input parameters needed to set up the simulation cell. Simple products and fractions combined with functions of a single number can be used like 2/3, 0.3*COS(60) or -SQRT(3)/2. The functions COS, EXP, LOG, LOG10, SIN, SQRT, and TAN are available.

Cell settings are parsed in the following precedence order:

  1. The external file set by CELL_FILE_NAME with a CELL_FILE_FORMAT;

  2. The lengths and angles of cell vectors set by ABC and ALPHA_BETA_GAMMA;

  3. The vectors set by A, B, C together;

  4. If none above exist, the external file set by TOPOLOGY/COORD_FILE_NAME with certain TOPOLOGY/COORD_FILE_FORMAT may also be parsed. [Edit on GitHub]

Subsections

Keywords

Keyword descriptions

A: real[3] = [angstrom]

Usage: A 10.000 0.000 0.000

Specify the Cartesian components for the cell vector A. This defines the first column of the h matrix. Ignored if the keywords ABC or CELL_FILE_NAME are used. [Edit on GitHub]

ABC: real[3] = [angstrom]

Usage: ABC 10.000 10.000 10.000

Specify the lengths of the cell vectors A, B, and C, which defines the diagonal elements of h matrix for an orthorhombic cell. For non-orthorhombic cells it is possible either to specify the angles ALPHA, BETA, GAMMA via ALPHA_BETA_GAMMA keyword or alternatively use the keywords A, B, and C. The convention is that A lies along the X-axis, B is in the XY plane. Ignored if CELL_FILE_NAME is used. [Edit on GitHub]

ALPHA_BETA_GAMMA: real[3] = 9.00000000E+001 9.00000000E+001 9.00000000E+001 [deg]

Aliases: ANGLES

Usage: ALPHA_BETA_GAMMA [deg] 90.0 90.0 120.0

Specify the angles between the vectors A, B and C when using the ABC keyword. The convention is that A lies along the X-axis, B is in the XY plane. ALPHA is the angle between B and C, BETA is the angle between A and C and GAMMA is the angle between A and B. [Edit on GitHub]

B: real[3] = [angstrom]

Usage: B 0.000 10.000 0.000

Specify the Cartesian components for the cell vector B. This defines the second column of the h matrix. Ignored if the keywords ABC or CELL_FILE_NAME are used. [Edit on GitHub]

C: real[3] = [angstrom]

Usage: C 0.000 0.000 10.000

Specify the Cartesian components for the cell vector C. This defines the third column of the h matrix. Ignored if the keywords ABC or CELL_FILE_NAME are used. [Edit on GitHub]

CELL_FILE_FORMAT: enum = CP2K

Usage: CELL_FILE_FORMAT (CP2K|CIF|XSC|EXTXYZ|XYZ|PDB)

Valid values:

  • CP2K Cell info in the CP2K native format

  • CIF Cell info from CIF file (from fields _cell_length_a or _cell.length_a, etc)

  • XSC Cell info in the XSC format (NAMD)

  • EXTXYZ Cell info as lattice=... field in the comment line of Extended XYZ format

  • XYZ Alias for Extended XYZ

  • PDB Cell info in the CRYST1 record of PDB format

Format of the external file from which cell is parsed. If the format specifies a cell by lengths and angles of three vectors, then a cell matrix is constructed with the convention that A lies along the X-axis, B is in the XY plane. ALPHA is the angle between B and C, BETA is the angle between A and C, and GAMMA is the angle between A and B. [Edit on GitHub]

CELL_FILE_NAME: string

Usage: CELL_FILE_NAME

The external file from which cell is parsed [Edit on GitHub]

MULTIPLE_UNIT_CELL: integer[3] = 1 1 1

Usage: MULTIPLE_UNIT_CELL 1 1 1

Specifies the numbers of repetition in space (X, Y, Z) of the defined cell, assuming it as a unit cell. This keyword affects only the CELL specification. The same keyword in SUBSYS%TOPOLOGY%MULTIPLE_UNIT_CELL should be modified in order to affect the coordinates specification. [Edit on GitHub]

PERIODIC: enum = NONE

Usage: PERIODIC (x|y|z|xy|xz|yz|xyz|none)

Valid values:

  • X

  • Y

  • Z

  • XY

  • XZ

  • YZ

  • XYZ

  • NONE

Specify the directions for which periodic boundary conditions (PBC) will be applied. Important notice: This applies to the generation of the pair lists as well as to the application of the PBCs to positions. See the POISSON section to specify the periodicity used for the electrostatics. Typically the settings should be the same. [Edit on GitHub]

SYMMETRY: enum = NONE

Usage: SYMMETRY monoclinic

Valid values:

  • NONE No cell symmetry

  • TRICLINIC Triclinic (a ≠ b ≠ c ≠ a, α ≠ β ≠ γ ≠ α ≠ 90°)

  • MONOCLINIC Monoclinic (a ≠ b ≠ c, α = γ = 90°, β ≠ 90°)

  • MONOCLINIC_GAMMA_AB Monoclinic (a = b ≠ c, α = β = 90°, γ ≠ 90°)

  • ORTHORHOMBIC Orthorhombic (a ≠ b ≠ c, α = β = γ = 90°)

  • TETRAGONAL_AB Tetragonal (a = b ≠ c, α = β = γ = 90°)

  • TETRAGONAL_AC Tetragonal (a = c ≠ b, α = β = γ = 90°)

  • TETRAGONAL_BC Tetragonal (a ≠ b = c, α = β = γ = 90°)

  • TETRAGONAL Tetragonal (alias for TETRAGONAL_AB)

  • RHOMBOHEDRAL Rhombohedral (a = b = c, α = β = γ ≠ 90°)

  • HEXAGONAL Hexagonal (alias for HEXAGONAL_GAMMA_60)

  • HEXAGONAL_GAMMA_60 Hexagonal (a = b ≠ c, α = β = 90°, γ = 60°)

  • HEXAGONAL_GAMMA_120 Hexagonal (a = b ≠ c, α = β = 90°, γ = 120°)

  • CUBIC Cubic (a = b = c, α = β = γ = 90°)

Imposes an initial cell symmetry, according to the convention that A lies along the X-axis, B is in the XY plane. After the input cell information is parsed, the symmetry is enforced by reconstructing the cell matrix from lengths and angles of the cell vectors, taking averages if necessary. This process does not affect input atomic coordinates; in case a space group is to be detected and preserved for an optimization task, atomic coordinates should correspond to cell vectors already obeying the convention mentioned above. [Edit on GitHub]