Yavar-Azar / CUBE

cube file analysis

CUBE

Electronic structure codes create cube files to represent 3D scalar data such as charge, potential and LDOS

properties and methods of this class

Discussions

There are several challenges against using cube files as reliable outputs

• First of all the maximum value are strongly dependent on the origin of grid

• The summation of all values is also grid dependent (making denser grid can solve problem somehow)

Properties

cube.xyz mesh: This return a list containing Three 3D arrays (grids) related to the cube file in other word one can extract all these arrays by

X,Y,Z=cube1("test.cube").xyzmesh

This can be used to form a desired function of these mesh points and compare it with other data

for example we can make a function for electrostatic potential as follows:

$\phi(\bf{r})=\sum_\alpha\frac{Z_\alpha}{|r-R_\alpha|}$

This

TECHNICALITIES

• gaussian cubegen

  you need an input file like this

   -1   -6.512752   -6.512752   -6.512752
   -83    0.168040    0.000000    0.000000
   79    0.000000    0.168040    0.000000
   79    0.000000    0.000000    0.168040

to create your own cube file with cubegen by following command

cubegen 1 fdensity=scf Test.FChk result.cube -1 < value.txt

• NWCHEM input to generate inputs

  In the case of nwchem we can change

  start n1  
  geometry  units au noautosym noautoz nocenter
    C  0.0 0.0 0.0
    O  2.1 0.0 0.0
  end  
  basis; * library cc-pvdz;end 
  dft
   iterations 50
   vectors  output co.movecs
   print  kinetic_energy  
   xc xpbe96 cpbe96  
  end  
  dplot  
    TITLE charge  
    vectors co.movecs  
  LimitXYZ units au  
  -5. 5.0 79    
  -5. 5.0 79   
  -5. 5.0 79 
   spin total 
   gaussian  
   output chargedensity2.cube  
  end