- Description
- Options
- Examples
Description
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.
sprod
Take the scalar product of vectors in two cubes, producing a new cube of scalars.
vprod
Take the vector product of 3-vectors in two cubes, producing a new cube of 3-vectors.
magnitude
Compute the magnitude of vectors in a cube, producing a new cube of scalars.
normalize
Normalize the vectors in a cube, producing a new cube of vectors.
select
Select among the values per point and produce a new cube.
toxyz
Convert a cube into a simple list: X,Y,Z,Value,Value, … format.
All operation subcommands can be abbreviated to the shortest unique form.
Example
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 ~ldq∑rdq~, 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: 23 July 2019. [G16 Rev.C.01]
