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:
add
Add two cubes to produce a new one.
copy
Copy a cube, possibly converting it from formatted to unformatted or vice versa.
diff
Compute properties of the difference between two cubes, without writing out a new cube.
prop
Computes the properties of a single cube.
subtract
Subtracts two cubes to produce a new cube.
scale
Scale a cube by a constant factor, producing a new cube.
square
Multiply a cube by itself to produce a new cube.
All operation subcommands can be abbreviated to the shortest unique form.
Here are some annotated sample runs with cubman (user input is shown in boldface type, and output has been condensed slightly due to space considerations):
$ cubman Action [Add, Copy, Difference, Properties, SUbtract, SCale, SQuare]? p Input file? b.cube Is it formatted [no,yes,old]? y 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 Statistics about cube contents 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 $ cubman Action [Add, Copy, Difference, Properties, SUbtract, SCale, SQuare]? 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: Composite 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 Statistics for first 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 Statistics for second cube CBMax= 3.39683 CBMin= .00000 SumOP= .63453 SumON=-.62358 SumO= .01094 Statistics for output 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.
Last updated on: 10 May 2009