cubman

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 update: 23 September 2011