Graphical representations: points, lines, planes, grids

Points (POINT)

POINT [x.r y.r z.r|file.s] [ALL] [FIELD {id.s|"expr.s"}]

Calculates the value of the reference field or an arithmetic expression at point (x.r, y.r, z.r) in crystallographic coordinates (if the structure is a CRYSTAL) or molecular Cartesian coordinates (if a MOLECULE). For the latter, the default units are angstrom unless changed by the UNITS keyword. If a file name is passed instead (file.s), calculate the same quantities at all the points specified by the file. All non-blank lines in the file that do not start with a comment symbol (#) represent a point, and only the first three real numbers from each line are read.

If ALL is used, all loaded fields are evaluated. In addition, all arithmetic expressions that have been registered using the POINTPROP keyword are also calculated. The POINTPROP keyword combined with POINT is useful to evaluate chemical functions at arbitrary points in space.

If FIELD is used and followed by an integer or field identifier (id.s), then only that field is evaluated. FIELD followed by an arithmetic expression calculates the value of that expression at the point.

Lines (LINE)

LINE x0.r y0.r z0.r x1.r y1.r z1.r npts.i [FILE file.s]
     [FIELD id.s|"expr.s"] [GX|GY|GZ|GMOD|HXX|HXY|HXZ|HYX|HYY|

Calculate a line from (x0.r, y0.r, z0.r) to (x1.r, y1.r, z1.r) with npts.i points. The units for the two endpoints (x0 and x1) are crystallographic coordinates in crystals and molecular Cartesian coordinates in molecules. The latter are angstrom by default (unless UNITS is used).

By default, the result is written to the standard output, but it can be redirected to a file using FILE. The reference field is used unless a FIELD keyword is given, in which case the field id.s or the expression expr.s are evaluated. Together with the value of the field, an additional quantity can be evaluated: the components of the gradient (GX,GY,GZ), the norm of the gradient (GMOD), the components of the Hessian (HXX,…) and the Laplacian of the reference (or the id.s) field.

Planes and Contour Plots (PLANE)

PLANE x0.r y0.r z0.r x1.r y1.r z1.r x2.r y2.r z2.r nx.i ny.i
      [SCALE sx.r sy.r] [EXTENDX zx0.r zx1.r] [EXTENDY zy0.r zy1.r]
      [FILE file.s] [FIELD id.s/"expr"]
      [CONTOUR {LOG niso.i [zmin.r zmax.r]|ATAN niso.i [zmin.r zmax.r]|
      BADER|LIN niso.i [rini.r rend.r]|i1.r i2.r ...}] [COLORMAP [LOG|ATAN]]
      [RELIEF zmin.r zmax.r] [LABELZ labelz.r]

Calculate the value (or derivatives) of the reference field on a plane. The results are written to a file, with default name <root>_plane.dat. The geometry of the plane is specified by three points: the origin (x0.r, y0.r, z0.r), the end of the x-axis (x1.r, y1.r, z1.r), and the end of the y-axis (x2.r, y2.r, z2.r). The number of points calculated on each axis are given by nx.i (x-axis) and ny.i (y-axis). The units are crystallographic coordinates in a crystal, and molecular Cartesian coordinates in a molecule (default: angstrom unless the UNITS keyword is used). The two axes of the plane can be scaled using the SCALE keyword. If sx.r (sy.r) is given, the total length of the x-axis (y-axis) is scaled by sx.r (sy.r). If EXTENDX is used, extend the x-axis by zx0.r (initial point of the x-axis) and zx1.r (end point). The keyword EXTENDY performs the equivalent operation on the y-axis. The units for EXTENDX and EXTENDY are bohr (crystals) or angstrom (molecules) unless changed by the UNITS keyword.

The name of the output file can be changed with FILE. Using FIELD, one of the loaded fields (id.s) or an expression (expr.s) can be evaluated. In addition to the field value, a second property can be evaluated: the field again (F), its derivatives (Gx), its second derivatives (Hxx), the gradient norm (GMOD) or the Laplacian (LAP).

The keyword CONTOUR writes a contour map representation of the plane: two contour line files (.iso and .neg.iso) and a gnuplot script (.gnu). The distribution of contour values can be: logarithmic (LOG, with niso.i contours), arctangent (ATAN, with niso.i contours), same as in the aimpac program (BADER, {1,2,4,8}x10^{-3,-2,-1,0,1}), linear (LIN, niso.i contours from r0.r to r1.r), or the user can specify the contour values manually (no keyword). In LOG, ATAN, and LIN, the default contour values range from the minimum to the maximum value of the field in the plot. These quantities can be changed by passing the optional zmin.r and zmax.r parameters to LOG/ATAN. The field or any of its derivatives, selected with the [F|GX|…] keyword, is used for the contour plot. The GRDVEC keyword performs the same task as PLANE with the CONTOUR option, and more (e.g. tracing gradient paths), but is more complex to use.

The RELIEF keyword writes a gnuplot template for a three-dimensional relief plot using the data calculated by PLANE. The default suffix is -relief.gnu. The mandatory arguments zmin.r and zmax.r set the range of the z axis in the plot.

The COLORMAP keyword writes a template for a colormap plot of the field on the plane. If the LOG or ATAN keywords are given, the logarithm or the arctangent of the field are represented in the colormap.

For the plots that display atomic or critical point labels, LABELZ controls how many labels are represented. Any atom or critical point that is at a distance less than labelz.r (default: 0.1 bohr) is shown as a label in the plot.

Grids (CUBE)

CUBE x0.r y0.r z0.r x1.r y1.r z1.r nx.i ny.i nz.i [FILE file.s] [FIELD id.s/"expr"]
CUBE x0.r y0.r z0.r x1.r y1.r z1.r lpp.r ...
CUBE CELL {lpp.r|nx.i ny.i nz.i} ...
CUBE GRID [SHIFT ix.i iy.i iz.i] ...
CUBE MLWF ibnd.i nRx.i nRy.i nRz.i [SPIN ispin.i] ...
CUBE WANNIER ibnd.i nRx.i nRy.i nRz.i [SPIN ispin.i] ...
CUBE UNK ibnd.i ik.i [SPIN ispin.i] ...
CUBE PSINK ibnd.i ik.i nRx.i nRy.i nRz.i [SPIN ispin.i] ...
CUBE ... FILE bleh.cube
CUBE ... FILE bleh.bincube
CUBE ... FILE bleh.xsf

The CUBE keyword writes a three-dimensional grid in Gaussian cube, binary cube, VASP CHGCAR, and xsf formats. The limits of the grid can be set in three ways. By giving the end-points (x0.r, y0.r, z0.r) and (x1.r, y1.r, z1.r) it is possible to build a grid from a fragment of the system (this is only possible using the cube and bincube formats). In crystals, this fragment has the same shape as the unit cell. To write an orthogonal fragment, use the additional ORTHO keyword. In molecules, it is always an orthogonal fragment. The CELL keyword calculates a grid spanning the entire unit cell. GRID, MLWF, WANNIER, UNK, and PSIK has the same effect as CELL regarding the output grid geometry.

If the end-points are given, they must be in crystallographic coordinates if the system is a periodic crystal (the structure was read using the CRYSTAL keyword) or molecular Cartesian coordinates if the system is a molecule (read with the MOLECULE keyword). The units in the latter default to angstrom unless changed using the UNITS keyword.

The number of points in the grid can also be controlled in several ways. If the grid limits are given explicitly or using CELL, then the number of points on each axis can be indicated by giving three integers (nx.i, ny.i, and nz.i) corresponding to the number of points in the x-, y-, and z-axis respectively. If a single number (lpp.r) is found, then the number of points is the length of the axis divided by lpp.r (lpp means “length per point”). The units for lpp.r are angstrom for molecules and bohr for crystals unless the UNITS keyword is used.

The GRID keyword can be used to write a given grid to a grid file directly. If FIELD is used in combination with GRID, then the indicated field or expression is used; otherwise, the reference field is used. The GRID keyword is useful when combined with LOAD and arithmetic operations to read, manipulate, and then save grids to an external file. If GRID is used, both the geometry of the grid and the number of points are taken from the parent grid field. The SHIFT keyword is used for shifting the origin of the grid to a different point. The origin of the shifted grid is the position of point ix.i, iy.i, iz.i in the old grid.

The MLWF, WANNIER, UNK, and PSINK keywords are similar to GRID in that they dump a scalar field on a grid to a file directly. These keywords only work with Quantum ESPRESSO pwc files, which contain the information about the Bloch states in a periodic solid. The meaning of these keywords is:

  • MLWF writes the maximally-localized Wannier function for band ibnd.i and lattice vector given by the integers nRx.i, nRy.i, and nRz.i (). Requires the Wannier checkpoint file for the Bloch coefficient rotation.

  • WANNIER writes a Wannier function calculated without rotation of the Bloch coefficients, for band ibnd.i and lattice vector given by the integers nRx.i, nRy.i, and nRz.i (). Requires that the k-point list corresponds to a uniform Monkhorst-Pack grid (i.e. no symmetry).

  • UNK writes the periodic part of the Bloch state with band index ibnd.i and k-point ik.i (). The k-point identifier can be found from the output when the .pwc file is loaded. Does not require a Wannier checkpoint file.

  • PSINK writes the Bloch state with band index ibnd.i and k-point ik.i at lattice vector nRx.i, nRy.i, and nRz.i (). The k-point identifier can be found from the output when the .pwc file is loaded. Does not require a Wannier checkpoint file.

In a spin-polarized calculation, the spin channel can be selected using the SPIN keyword (1 for spin-up and 2 for spin-down).

Independently on how the grid is set up, several options control the behavior of CUBE. FILE sets the name of the output file (default: <root>.cube). critic2 uses different formats depending on the extension: binary cube (.bincube), cube (.cube), xsf (.xsf), and VASP-style CHGCAR (everything else). The HEADER keyword writes only the header to the output file. FIELD sets the field to be used by the field number or alias (id.s). Alternatively, an arithmetic expression can be used. Finally, a derivative of the scalar field (gradient, Hessian, Laplacian) can be selected instead of the value of the field itself (F) to build the grid.