cubegen

Gaussian includes a standalone utility for generating cubes from the data in a formatted checkpoint file (equivalent to the previous Cube keyword). The utility is named cubegen, and it has the following syntax:

cubegen memory kind fchkfile cubefile npts format

All parameters are optional; cubegen will prompt for fchkfile if necessary. The default command is:

cubegen 0 density=scf test.cube 0 h

The parameters, which are not case-sensitive, have the following meanings:

memory
Previously this parameter was used to specify the amount of memory to allocate. It is now ignored, and the GAUSS_MEMDEF environment variable is used.

kind
A keyword specifying the type of cube to generate:

MO=n   Molecular orbital n. The keywords Homo, Lumo, All, OccA (all alpha occupied), OccB (all beta occupied), Valence (all valence orbitals) and Virtuals (all virtual orbitals) may also be used in place of a specific orbital number. There is no default for n, and an error will occur if it is omitted. AMO and BMO can be similarly used to select only alpha or beta orbitals (respectively). For open shell systems, Homo selects both alpha and beta orbitals.
Density=type   Total density of the specified type. The type keyword is one of the single density selection options that are valid with the Density keyword: SCF, MP2, CI, QCI, and so on (note that Current is not supported). The FDensity= variation requests the use of the full instead of the frozen core density. The default type keyword is SCF.
Spin=type   Spin density (difference between α and β densities) of the specified type.
Alpha=type   Alpha spin density of the specified type. FAlpha= requests the use of the full instead of the frozen core density.
Beta=type   Beta spin density of the specified type. FBeta= requests the use of the full instead of the frozen core density.
Potential=type   Electrostatic potential using the density of the specified type.
Gradient   Compute the density and gradient.
Laplacian   Compute the Laplacian of the density (∇2ρ).
NormGradient   Compute the norm of the density gradient at each point.
CurrentDensity=I   Magnitude of the magnetically-induced (GIAO) current density, where I is the applied magnetic field direction (X, Y or Z).
ShieldingDensity=IJN   Magnetic shielding densit}. I is the direction of the applied magnetic field, J is the direction of the induced field (X, Y or Z), and N is the number of the nucleus for which the shielding density (GIAO) is to be calculated.

fchkfile
Name of the formatted checkpoint file. cubegen will prompt for this filename if it is not specified.

cubefile
Name of the output cube file; test.cube is the default if it is not explicitly specified (i.e., specifying the name of the checkpoint file does not change the default cube filename).

npts
Number of points per side in the cube. A value of 0 selects the default value of 803 points distributed evenly over a rectangular grid generated automatically by the program (not necessarily a cube). Positive values of npts similarly specify the number of points per “side”; e.g., 100 specified a grid of 1,000,000 (1003) points.

The values -2, -3 and -4 correspond to the keywords Coarse, Medium and Fine and to values of 3 points/Bohr, 6 points/Bohr and 12 points/Bohr (respectively). Negative values of npts ≤-5 specify spacing of npts*10-3 Angstroms between points in the grid.

A value of -1 says to read the cube specification from the input stream, according to the following format:

IFlag, X0, Y0, Z0        Output unit number and initial point.
N1, X1, Y1, Z1 Number of points and step-size in the X-direction.
N2, X2, Y2, Z2 Number of points and step-size in the Y-direction.
N3, X3, Y3, Z3 Number of points and step-size in the Z-direction.
IFlag is the output unit number. If IFlag is less than 0, then a formatted file will be produced; otherwise, an unformatted file will be written.

If N1<0 the input cube coordinates are assumed to be in Bohr, otherwise, they are interpreted as Angstroms. |N1| is used as the number of X-direction points in any case; N2 and N3 specify the number of points in the Y and Z directions, respectively. Note that the three axes are used exactly as specified; they are not orthogonalized, so the grid need not be rectangular.

The value -5 says to read in an arbitrary list of points from standard input. If you enter this input by hand, terminate the input with an end-of-file (i.e., Ctrl-D under Unix). Alternatively, you can redirect standard input to a file containing the list of points (do not place a blank line or Ctrl-D at the end of the file).

format
Format of formatted output files: h means include header (this is the default); n means don’t include header. This parameter is ignored when unformatted cube files are produced.

cubefile2
If specified, the size for the generated cube is taken from this file. This option is useful when creating cubes for later arithmetic operations such as difference densities.

In order for the cube dimensions to be taken from the specified cube file, the npts parameters must be -1 and the specified file must have been crated with a header.

OUTPUT FILE FORMATS

All values in the cube file are in atomic units, regardless of the input units.

For density and potential grids, unformatted files have one row per record (i.e., N1*N2 records each of length N3). For formatted output, each row is written out in format (6E13.5). In this case, if N3 is not a multiple of six, then there may be blank space in some lines.

The norm of the density gradient and the Laplacian are also scalar (i.e., one value per point), and are written out in the same manner. Density+Gradient grids are similar, but with two writes for each row (of lengths N3 and 3*N3). Density+Gradient+Laplacian grids have 3 writes per row (of lengths N3, 3*N3, and N3).

For example, for a density cube, the output file looks like this:

NAtoms, X-Origin, Y-Origin, Z-Origin
N1, X1, Y1, Z1               # of increments in the slowest running direction
N2, X2, Y2, Z2
N3, X3, Y3, Z3               # of increments in the fastest running direction
IA1, Chg1, X1, Y1, Z1        Atomic number, charge, and coordinates of the first atom
…
IAn, Chgn, Xn, Yn, Zn        Atomic number, charge, and coordinates of the last atom
(N1*N2) records, each of length N3 Values of the density at each point in the grid

Note that a separate write is used for each record.

For molecular orbital output, NAtoms will be less than zero, and an additional record follows the data for the final atom (in format 10I5 if the file is formatted):

NMO, (MO(I),I=1,NMO)   Number of MOs and their numbers

If NMO orbitals were evaluated, then each record is NMO*N3 long and has the values for all orbitals at each point together.

READING CUBE FILES WITH FORTRAN PROGRAMS

If one wishes to read the values of the density, Laplacian, or potential back into an array dimensioned X(N3,N2,N1), code like the following Fortran loop may be used:

      Do 10 I1 = 1, N1
      Do 10 I2 = 1, N2
         Read(n,'(6E13.5)') (X(I3,I2,I1),I3=1,N3)
      10 Continue

where n is the unit number corresponding to the cube file.

If the origin is (X0,Y0,Z0), and the increment is (X1,Y1,Z1), then point (I1,I2,I3) has the coordinates:

X-coordinate: X0+(I1-1)*X1+(I2-1)*X2+(I3-1)*X3

Y-coordinate: Y0+(I1-1)*Y1+(I2-1)*Y2+(I3-1)*Y3

Z-coordinate: Z0+(I1-1)*Z1+(I2-1)*Z2+(I3-1)*Z3

The output is similar if the gradient or gradient and Laplacian of the charge density are also requested, except that in these cases there are two or three records, respectively, written for each pair of I1, I2 values. Thus, if the density and gradient are to be read into arrays D(N3,N2,N1), G(3,N3,N2,N1), RL(N3,N2,N1), a correct set of Fortran loops would be:

      Do 10 I1 = 1, N1
      Do 10 I2 = 1, N2
         Read(n,'(6F13.5)')  (D(I3,I2,I1),I3=1,N3)
         Read(n,'(6F13.5)')  ((G(IXYZ,I3,I2,I1),IXYZ=1,3), I3=1,N3)
 10   Continue

where again n is the unit number corresponding to the cube file.

 


Last update: 23 April 2013