[Pw_forum] cube file from pp.x with orthogonal unit cell

[Garold Murdachaew]

Dear pw_forum members,

I am examining charge densities obtained from pw.x.  I use the pp.x program to 
obtain densities in various formats.  Although I am happy with the xsf format 
as provided by pp.x (I can use xcrysden for displaying the densities), a 
colleague wants to use gaussview for which the gaussian cube file is ideal.  I 
notice that when  I use xsf format, pp.x prints some coordinates with strange 
values (see below).  Are these atoms in the next unit cell?

There is another problem with use of cube files:  pp.x does not allow one to 
change the axes so as to have the density within an orthogonal unit cell (my 
unit cell is hexagonal).  I tried to use an input file of the form:

  &inputpp
  /
  &plot
     nfile = 1
     filepp(1) = 'slab.rho'
     weight(1) = 1.0
     iflag = 3
     output_format = 6
     fileout = 'slab_orthog.cube'
     e1(1)=0.75, e1(2)=0.00, e1(3)=0.00,
     e2(1)=0.00, e2(2)=0.75, e2(3)=0.00,
     e3(1)=0.00, e3(2)=0.00, e3(3)=6.00,
     x0(1)=0.00, x0(2)=0.00, x0(3)=0.00,
     nx=48, ny=48, nz=320
  /

but I gather that e_i cell vectors (and x0, n_i) are not allowed for the cube 
output_format=6.  Since gaussview can only read in  cube files with orthogonal 
axes, do I need to write a converter program to convert xsf (after 
orthogonalization) to cube format?  Is there a better way (perhaps fitting and 
interpolating the density in some way)?

Thank you for your time and assistance.

Best,
Garold Murdachaew

-- 
Garold Murdachaew
Postdoctoral Fellow - Condensed Matter Sector
SISSA-ISAS (International School for Advanced Studies)
New Building Room 208
Via Beirut 2-4, 34014 Trieste, Italy

tel   : +39 040 3787 477
fax   : +39 040 3787 528
email : murda at sissa.it


ps: Here are top parts of each density file for a clean Cu(111) slab, with 
three layers of atoms and 3 atoms per layer:


native pw.x "rho" format, slab.rho:

clean_slab.pw
       48      48     320      48      48     320       9       1
      0  9.50068671  0.00000000  0.00000000  0.00000000  0.00000000 0.00000000
   0.750000000000000       0.433012701890000       0.000000000000000E+000
   0.000000000000000E+000  0.866025403780000       0.000000000000000E+000
   0.000000000000000E+000  0.000000000000000E+000   6.00000000000000
       685.9169146890       10.0000000000       30.0000000000     0
    1   Cu   11.00
    1       0.500000000    0.577350269    0.408248290    1
    2       0.000000000    0.577350269    0.408248290    1
    3       0.250000000    0.144337567    0.408248290    1
    4       0.250000000    0.721687836    0.000000000    1
    5       0.500000000    0.288675135    0.000000000    1
    6       0.000000000    0.288675135    0.000000000    1
    7       0.250000000    0.433012702   -0.408248290    1
    8       0.500000000    0.000000000   -0.408248290    1
    9       0.000000000    0.000000000   -0.408248290    1
   3.388479695E-02  3.429044967E-02  3.532584725E-02  3.674544602E-02 
3.830175591E-02
   3.979813932E-02  4.103542694E-02  4.186003670E-02  4.214093017E-02 
4.186003772E-02
   4.103542896E-02  3.979814230E-02  3.830175977E-02  3.674545064E-02 
3.532585250E-02
.
.
.


xsf format, slab.xsf:

  CRYSTAL
  PRIMVEC
     3.770658668    2.176990797    0.000000000
     0.000000000    4.353981594    0.000000000
     0.000000000    0.000000000   30.165269347
  PRIMCOORD
            9           1
Cu        2.513772446    2.902654395    2.052486605
Cu        0.000000000    2.902654395    2.052486605
Cu        1.256886223    0.725663598    2.052486605
Cu        1.256886223    3.628317993    0.000000000
Cu        2.513772446    1.451327200    0.000000000
Cu        0.000000000    1.451327200    0.000000000
Cu        1.256886223    2.176990798   -2.052486605
Cu        2.513772446    0.000000000   -2.052486605
Cu        0.000000000    0.000000000   -2.052486605
BEGIN_BLOCK_DATAGRID_3D
3D_PWSCF
DATAGRID_3D_UNKNOWN
           49          49         321
   0.000000  0.000000  0.000000
   3.770659  2.176991  0.000000
   0.000000  4.353982  0.000000
   0.000000  0.000000 30.165269
   0.33885E-01  0.34290E-01  0.35326E-01  0.36745E-01  0.38302E-01  0.39798E-01
   0.41035E-01  0.41860E-01  0.42141E-01  0.41860E-01  0.41035E-01  0.39798E-01
   0.38302E-01  0.36745E-01  0.35326E-01  0.34290E-01  0.33885E-01  0.34398E-01
.
.
.


cube format with problem in coordinates, slabe.cube:

  Cubfile created from PWScf calculation
   Total SCF Density
     9    0.000000    0.000000    0.000000
    48    0.148448    0.085707    0.000000
    48    0.000000    0.171413    0.000000
   320    0.000000    0.000000    0.178138
    29   29.000000    4.750343    5.485224    3.878639
    29   29.000000    7.125515    9.599142    3.878639
    29   29.000000    2.375172    9.599142    3.878639
    29   29.000000    2.375172    6.856530   57.004120
    29   29.000000    4.750343    2.742612   57.004120
    29   29.000000    7.125515    6.856530   57.004120
    29   29.000000    2.375172    4.113918   53.125481
    29   29.000000    4.750343    8.227836   53.125481
    29   29.000000    7.125515   12.341754   53.125481
   0.33885E-01  0.33291E-01  0.32321E-01  0.31048E-01  0.29553E-01  0.27983E-01
   0.26472E-01  0.25117E-01  0.24038E-01  0.23277E-01  0.22832E-01  0.22745E-01
   0.23008E-01  0.23607E-01  0.24524E-01  0.25740E-01  0.27185E-01  0.28739E-01
.
.
.