Gaussian 03 Online Manual
The following options from early revisions of Gaussian 03 have been removed in revision D.1:
The following table lists obsolete keywords used by previous versions of Gaussian. While all of them are still supported by Gaussian 03, we strongly recommend converting to the up-to-date equivalents given in the table.
The chkmove utility, which converted checkpoint files to and from binary and text formats for transfer between different computer architectures, is no longer provided. Its functionality is now handled by formchk and unfchk.
All: Write everything to the formatted
LST and LSTCyc
Note that an LST calculation does not actually locate a proper transition state. However, the structure resulting from an LST calculation may be suitable as input for a subsequent Opt=TS. In general, however, the LST method has been superseded by Opt=QST2.
Description of Cube
The Cube properties keyword can be used to evaluate molecular orbitals, the electrostatic potential, the electron density, density gradient, the norm of the density gradient, and Laplacian of the density over a 3 dimensional grid (cube) of points. Its use is deprecated in favor of the cubegen utility.
By default, Cube evaluates the electron density (corresponding to the Density option). Which density is used is controlled by the Density keyword; use Density=Current to evaluate the cube over the density from a correlated or CI-Singles wavefunction instead of the default Hartree-Fock density.
Note that only one of the available quantities can be evaluated within any one job step. Save the checkpoint file (using %Chk), and include Guess=(Read,Only) Density=Checkpoint in the route section of a subsequent job (or job step) in order to evaluate a different quantity without repeating any of the other steps of the calculation.
Gaussian provides reasonable defaults for grids, so Cube does not require that the cube be specified by the user. However, the output filename must always be provided (see below).
Alternatively, Cube may be given a parameter specifying the number of points to use per "side" (the default is 80). For example, Cube=100 specifies a grid of 1,000,000 points (1003), evenly distributed over the rectangular grid generated by the program (which is not necessarily a cube). In addition, the input format used by earlier versions of Gaussian is still supported; Cube=Cards indicates that a grid will be input. It may be used to specify a grid of arbitrary size and shape.
The options Coarse, Medium and Fine may also be specified as the parameter to Cube. They correspond to densities of 3, 6 and 12 points/Bohr, respectively. These options are designed to facilitate uniform quality in grid sampling across the range of molecular sizes.
The files created by Cube can be manipulated using the cubman utility.
Note that Pop=None will inhibit cube file creation.
When the user elects to provide it, the grid information is read from the input stream. The first line-required for all Cube jobs-gives a file name for the cube file. Subsequent lines, which are included only with Cube=Cards, must conform to format (I5,3F12.6), according to the following syntax:
Output-file-name Required in all Cube jobs. 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 (this keyword is not affected by the setting of the Units keyword). |N1| is used as the number of X-direction points in any case. Note that the three axes are used exactly as specified; they are not orthogonalized, so the grid need not be rectangular.
If the Orbitals option is selected, the cube filename (or cube filename and cube specification input) is immediately followed by a list of the orbitals to evaluate, in free-format, terminated by a blank line. In addition to numbers for the orbitals (with β orbitals numbered starting at N+1), the following abbreviations can appear in the list:
See the examples section for sample input files.
OUTPUT FILE FORMATS
All values in the cube file are in atomic units, regardless of the input units.
Using the default input to Cube produces an unformatted output file (you can use the cubman utility to convert it to a formatted version if you so desire). When the Cards option is specified, then the IFlag parameter's sign determines the output file type. If IFlag>0, the output is unformatted. If IFlag<0, the output is formatted. 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:
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.
CUBE CONTENTS OPTIONS
The following job will create a cube file named orbitals.cube containing the HOMO and LUMO.
#n rhf/6-31g* 5d scf=tight cube=(orbitals) test HOMO and LUMO in default cube 0,1 O H,1,R2 F,1,R3,2,A3 Variables: R2=0.96 R3=1.42 A3=109.47122063 orbitals.cube homo lumo
The following cube file illustrates the method for defining your own cube via Cube=Cards:
# rhf/6-31g* 5d scf=tight cube=(density,cards) test Density cube with user-defined cube 0,1 O H,1,R2 F,1,R3,2,A3 Variables: R2=0.96 R3=1.42 A3=109.47122063 density.cube -51 -2.0 -2.0 -1.0 40 0.1 0.0 0.0 40 0.0 0.1 0.0 20 0.0 0.0 0.1
Description of Massage
The Massage keyword requests that the molecule specification and basis set data be modified after it is generated. This keyword is deprecated in favor of ExtraBasis, Charge, Counterpoise and other keywords.
The Massage keyword thus makes it possible to add additional uncontracted basis functions to a standard basis set. Common polarization or diffuse functions can be added in this way to standard basis sets for which these functions are not internally defined. For example, diffuse functions could be added to the 3-21G basis set to form 3-21+G. Similarly, polarization functions might be added to 6-311G to form a 6-311G(5d3f) basis, which is larger than the largest internally stored 6-311G-based basis set, 6-311G(3d1f).
The standard basis functions are assigned to atoms before Massage alterations take place, while the number of electrons is computed from the atomic numbers after the modifications.
Calculations with massaged basis set data cannot generate archive entries, and do not take advantage of molecular symmetry. Some of this functionality of Massage has been superceded by the ExtraBasis keyword. Point charges may also be specified for single point energy calculations using Charge.
Massage may also be used for counterpoise calculations and BSSE (see the examples).
Massage requires one or more lines of input in the following format:
center, func, exp, [cX, cY, cZ ]
where center is the center number (numbering follows the ordering of the molecule specification section), func is a code indicating the type of modification (see below), exp is the exponent of Gaussian or new nuclear charge (a value of 0 says to add a ghost atom), and cX,cY,cZ are the coordinates of the point charge in Angstroms when func is -1 (see below). A blank line terminates this input section.
func can take
on these values:
0 or Nuc
1 or SP
3 or P
4 or S
-1 or Ch
Note that this keyword is not affected by the setting of the Units keyword, and its input is always interpreted as Angstroms.
Adding Point Charges. The following input file adds point charges to a calculation on water using the Massage keyword. Note: This is usually done with the Charge keyword and input.
# RHF/6-31G(d) Massage Test Water with point charges 0 1 O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0 0 ch 2.0 1.0 1.0 1.0 0 ch 2.5 1.0 -1.0 1.0
Adding Basis Functions. The following input adds functions to the D95 basis set (in order to reproduce a calculation from the literature that used a non-standard basis set). Note: This is usually done with the ExtraBasis keyword and input.
# RQCISD(Full)/D95 Freq=Numer Massage Test H2O Frequencies at QCISD(Full)/DZP 0 1 O H 1 R H 1 R 2 A R=0.961882 A=104.612551 1 D 0.85 2 P 1.0 3 P 1.0
Computing Counterpoise Corrections Manually. The following input file performs a counterpoise calculation. Note the the Massage keyword is not used. The atoms to be removed are simply designated with the ghost atom suffix (Bq). Note: The Counterpoise keyword is now used to perform this type of calculation.
# b3lyp/3-21G** nosymm scf=tight test HBr + H2O manual counterpoise calculation, H2O removed 0 1 H 0.685176 -0.004924 -0.026973 Br -0.771917 0.000050 0.001967 O-Bq 2.536864 -0.000136 -0.051401 H-Bq 3.015128 0.789231 0.184042 H-Bq 3.021888 -0.784986 0.185282