A number of utility programs are included with Gaussian 09W. They are accessible via the various items on the Utilities menu in the program’s main window. We will consider them here in the same order as they appear in that menu, beginning with the NewZMat facility.
The NewZMat File Conversion window controls file conversions. It is reached via the NewZMat item on the Utilities menu. By default, it converts files to Gaussian 09W input files (.GJF files). It is an interface to the standard NewZMat utility which is included with Gaussian 09.
The Generated Filename field is used to specify the name of the converted file. The default is the filename of the file to be converted with the extension GJF.
The Convert button begins the conversion of the designated file, using currently set options.
The Cancel button returns you to the Job Processing window without converting any file.
The Load button (appears as a file folder icon) can be used to load a different input file to be converted.
Load Converted File as Job
If checked, load the converted job into memory. The default is checked if the
selected file is not a .GJF file.
Edit Generated File
If checked, edit the new input file after converting using the Job Edit window
(default is unchecked).
Ext. Editor → Generated File
If checked, edit the new input file after conversion using the designated external
editor (default is unchecked).
Input Options
Opens the NewZMat Input Options window.
Output Options
Opens the NewZMat Output Options window.
Other Options
Opens the Other Options window.
Template Options
This option is not implemented in the current version of Gaussian 09W.
The radio buttons on this window specify the format of the file to be converted:
| Radio Button | NewZMat Option |
|---|---|
| Biograf internal file format (BGF) | -ibgf |
| Brookhaven data format (PDB) Brookhaven protein data bank format. |
-ibkv |
| Z-matrix in Checkpoint file Extract a Z-matrix from a Gaussian 09 checkpoint file, from the optimization step indicated in the Checkpt Geom Opt. Step field. |
-ichk |
| .CON data file from QUIPU | -icon |
| MacroModel file | -immodel |
| Model/MM2 | -imodel |
| MOPAC format | -imopac |
| Unformatted MacroModel file | -iummodel |
| Cartesian Coords. w/ Atomic Type | -ixyz |
| Z-matrix (this is the default) | -izmat |
| PC-Model Format (PCM) | -ipcm |
Distances in Bohr
If checked (unchecked is the default), distances in the file to be converted
are assumed to be in Bohr rather than angstroms (-ubohr).
Angles in Radians
If checked (unchecked is the default), angles in the file to be converted are
assumed to be in radians rather than degrees (-urad).
The radio buttons on this window specify the format of the generated file:
Radio
Button |
NewZMat Option(s) |
|---|---|
| MacroModel Format 1 | -ommodel -mof1 |
| MacroModel Format 2 | -ommodel -mof2 |
| Brookhaven data format (PDB) |
-opdb |
| Biograf internal format | -obgf |
| CaChe molecule file | -ocache |
| Z-matrix to Checkpoint file Output a Z-matrix within a checkpoint file. |
-ochk |
| MOPAC data file | -omopac |
| Output for Any PPP Program Format for a Pople-Paiser-Parr program. |
-oppp |
| ZIndo format | -ozindo |
| Z-matrix format (this is the default) | -ozmat |
| PC-model Format (PCM) | -opcm |
This window is used to set other conversion options. The corresponding NewZMat command line options are indicated in parentheses.
Use symmetry
If checked (default), then use symmetry information in converting the input.
(The unchecked state corresponds to -nosymm.)
Use loose cutoffs for determining symmetry
Assume molecular symmetry more easily (-lsymm).
Use tight cutoffs for determining symmetry
This is the default (-tsymm).
No averaging of input coordinates
Don’t average input coordinates (-nosymav). This is the
default.
Average coordinates using approx. symmetry operations
Average input coordinates using approximate symmetry operations to achieve exact
symmetry (-symav).
Round Z-matrix parameters to 0.01 Å and 1-degree
Round parameters before assigning symmetry (-round).
Assume all atoms bonded for connectivity generation
This is the default.
Generate connectivity using internal radii
Corresponds to the -gencon option.
Keep atom order as close to input order as possible
Corresponds to the -order option.
The options in this area are available only when the input file type is checkpoint and the output file type is a CaChe molecule file.
Generate natural orbitals for density
Generate natural orbitals for the orbital specified in the N field (-density).
Density N - density M, and convert to natural orbitals
Subtract generalized density in field M from the density in field N, and then
convert to natural orbitals (-mdensity).
Build a new Z-matrix rather than use the read-in matrix
Also implies generating connectivity from internal radii (-rebuildzmat).
Debug Level
Set NewZMat internal debug level. The default is 0 (-d, one
or more times).
This utility creates a cube file from the information stored in a Gaussian 09W checkpoint file, in a manner similar to the Cube keyword. It prompts you for the required information:
Property [Density]? MO=LUMO
Formatted Checkpoint file? water
Cube file [ ]? w_lumo.cub
Approximate points per side [0]? 75
Header in cube file [H]? N
The desired kind of cube is specified via one of the following keywords at the first prompt:
MO=n
Molecular orbital n. The keywords Homo, Lumo, All, OccA (all α occupied), OccB, Valence and Virtuals may
also be used in place of a specific orbital number.
Density=type
Total density of the specified type (see below). The FDensity form
requests the use of full instead of frozen core densities.
Spin=type
Spin density (α − β) of the specified type.
Alpha=type
Alpha spin density of the specified type. The FAlpha form requests
the use of full instead of frozen core densities.
Beta=type
Beta spin density of the specified type. The FBeta form requests
the use of full instead of frozen core densities.
Potential=type
Electrostatic potential of the specified type.
type is one of the single density selection options that are valid with the Gaussian 09W Density keyword: HF, MP2, CI, QCI, and so on (Current is not supported).
The Approximate points per side prompt specifies the grid size: a rectangular grid of n3 evenly distributed points, which may or may not be a cube. The default is 80 if 0 is specified for this prompt. If the value of -1 is given in response to the prompt, then the grid specifications will be accepted after the final prompt, as with Cube=Cards. The keywords Coarse, Medium and Fine may also be used to specify values of 40, 80 and 100, respectively.
The cubman program manipulates cubes of values of electron density and electrostatic potential as produced by Gaussian. The program prompts for an operation to perform, and then the names of the necessary files. The possible operations and their associated subcommands are:
All operation subcommands can be abbreviated to the shortest unique form.
Here are two annotated sample runs with cubman (user input is shown in boldface
type, and output has been condensed
slightly due to space considerations):
Action [Add, Copy, Difference, Props, SUbtract, SCale]? p Input file? b.cube Is it formatted [no,yes,old]? y Gaussian cube files are formatted Opened special file b.cube. Input file titles: First excited state of propellane Title line from the job CI Total Density Contents of cube file
SumAP= 13.39263 SumAN= .00000 SumA= 13.39263 Stats about cube CAMax= 3.35320 XYZ= .18898 -1.32280 .000004 CAMin= .00000 XYZ= -9999.00000 -9999.00000 -9999.00000 DipAE= -.8245357658 .7624198057 .1127178115 DipAN= -.0000060000 -.0000060000 .0000000000 DipA= -.8245417658 .7624138057 .1127178115 Action [Add, Copy, Difference, Props, SUbtract, SCale]? su First input? b.cube
Is it formatted [no,yes,old]? y
Opened special file b.cube.
Second input? a.cube
Is it formatted [no,yes,old]? y
Opened special file a.cube.
Output file? c.cube File to hold the new cube
Should it be formatted [no,yes,old]? y
Opened special file c.cube.
Input file titles:
First excited state of propellane Title from first file
CI Total Density Contents of first cube
Input file titles:
Propellane HF/6-31G* Title from second file
SCF Total Density Contents of second cube
Output file titles: Title used for new file
First excited state of propellane || Propellane HF/6-31G*
CI Total Density - SCF Total Density Difference to be computed
SumAP= 13.39263 SumAN= .00000 SumA= 13.39263 Stats for 1st cube
CAMax= 3.35320 XYZ= .18898 -1.32280 .000004
CAMin= .00000 XYZ= -9999.00000 -9999.00000 -9999.00000
SumBP= 13.38168 SumBN= .00000 SumB= 13.38168 Stats for 2nd cube
CBMax= 3.39683 CBMin= .00000
SumOP= .63453 SumON=-.62358 SumO= .01094 Stats for new cube
COMax= .49089 COMin=-.39885
DipAE= -.8245357658 .7624198057 .1127178115
DipAN= -.0000060000 -.0000060000 .0000000000
DipA= -.8245417658 .7624138057 .1127178115
DipBE= -.8306292172 .5490287046 .1243830393
DipBN= -.0000060000 -.0000060000 .0000000000
DipB= -.8306352172 .5490227046 .1243830393
DipOE= .0060934514 .2133911011 -.0116652278
DipON= -.0000060000 -.0000060000 .0000000000
DipO= .0060874514 .2133851011 -.0116652278
In the output. the input cubes are denoted as A and B, and the output cube is designated by O. Other code letters are N for “negative values” or for “nuclear,” depending on the context, P for “positive values,” E for “electronic,” C for “charge,” Dip for “dipole,” Sum for “sum,” Max for “maximum,” and Min for “minimum.” Thus, SumAN is the sum over the first input cube, taking the negative values only, and DipON is the nuclear contribution to the dipole moment for the output cube. Similarly, CBMax is the maximum charge for the second input cube, and SumO is the sum of the values in the output cube, including both positive and negative values.
FreqChk is used to generate frequency and thermochemistry data from a checkpoint file. Here is an example of its use in this mode:
Checkpoint file? water
Write Hyperchem files? N
Temperature (K)? [0=>298.15] 300 Specify desired temperature.
Pressure (Atm)? [0=>1 atm] 0 Specified desired pressure.
Scale factor for frequencies during thermochemistry? [0=>1/1.12] 0.9613 Specify scale
factor for thermochemical calculation.
Do you want to use the principal isotope masses? [Y]: N
Use this feature to substitute other isotopes for the standard (most abundant) ones.
For each atom, give the integer mass number.
In each case, the default is the principal isotope.
Atom number 1, atomic number 8: [16] 16
Atom number 2, atomic number 1: [1] 2
Atom number 3, atomic number 1: [1] 2
------------------------------------------------------------
Center Atomic Coordinates (Angstroms)
Number Number X Y Z
------------------------------------------------------------
1 8 0.000000 0.000000 0.058070
2 1 0.000000 0.407058 -0.232281
3 1 0.000000 -0.407058 -0.232281
------------------------------------------------------------
Atom 1 has atomic number 8 and mass 15.99491
Atom 2 has atomic number 1 and mass 2.01410
Atom 3 has atomic number 1 and mass 2.01410
...
1 2
A1 A1
Frequencies — 2170.0510 4142.4280
Red. masses — 1.0785 1.0491
Frc consts — 2.9923 10.6067
IR Inten — 7.2428 44.3099
Raman Activ — 9.2625 47.7624
Depolar — .7245 .1791
Atom AN X Y Z X Y Z
1 8 .00 .00 .07 .00 .00 .05
2 1 .00 -.45 -.54 .00 .57 -.42
3 1 .00 .45 -.54 .00 -.57 -.42
-------------------
- Thermochemistry -
-------------------
Temperature 300.000 Kelvin. Pressure 1.00000 Atm.
Thermochemistry will use frequencies scaled by 0.9613.
Molecular mass: 20.02312 amu.
Zero-point correction= 0.060789
Thermal correction to Energy= 0.063639
Thermal correction to Enthalpy= 0.064589
Thermal correction to Gibbs Free Energy= 0.043825
...
Note that when a scale factor is included, the frequencies are scaled only when they are used to perform the thermochemistry analysis. The displayed frequencies themselves are not scaled.
This utility produces an ASCII formatted checkpoint file from a Gaussian 09W checkpoint file. Formatted checkpoint files are the recommended method for transferring data to graphics and other post-processing programs (see the Gaussian 09 Programmer’s Reference for further details).
Here is an example use of FormChk:
Checkpoint file? water Read checkpoint file water.chk Write formatted file water.fch
Note that formatted checkpoint files have the extension .FCH in the Windows environment.
This utility is the opposite number to FormChk. It converts a formatted checkpoint file to a binary Gaussian 09W checkpoint file:
Formatted Checkpoint file? water Read formatted file water.fch Write checkpoint file water.chk
This utility displays the route and title sections corresponding to a checkpoint file and indicates other information that is present within it:
Checkpoint file? water Checkpoint file water.chk: Title: Water frequencies Route: #T B3LYP/6-31G* Freq Test Atomic coordinates present. Z-matrix present with variables. MO coefficients present. Cartesian force constants present. Internal force constants may be present.
This utility converts binary checkpoint files between the formats used by Gaussian 09W and previous program versions. Note that the output from C8609 is not intended to be readable. Use the FormChk utility to produce human- and program-readable formatted checkpoint files.