A problem in calculating the coulomb energy

[Jackeyha]

Dear professor: Recently I try to use your porgram Supercell to deal with my research system, and I sucessfully created thousands of structures, but when I use the parameter "-q" to compute energy , all the energy I get are 0 ev, if there is anything wrong with my operation? Here are my operation and output result. command: ./supercell -i lagp-1.2.cif -m -q

output result:

-----------------------------------------------------
-               Supercell program                   -
-----------------------------------------------------
-      Authors:   * Kirill Okhotnikov               -
-                  (kirill.okhotnikov@gmail.com)    -
-                 * Sylvian Cadars                  -
-                  (sylvian.cadars@cnrs-imn.fr)     -
-                 * Thibault Charpentier            -
-                  (Thibault.Charpentier@cea.fr)    -
-----------------------------------------------------
-  please cite:                                     -
-    K. Okhotnikov, T. Charpentier and S. Cadars    -
-    J. Cheminform. 8 (2016) 17 ?33.               -
-----------------------------------------------------

Initial system:
  Chemical Formula: Al1.452 Ge10.548 Li7.44 O72 P18

Supercell system (1x1x1):
  Size a=8.2619, b=8.2619, c=20.5656

Current charge balance option is "try"
Total charge oxidation state (cif):  nan
Total charge cell:   0
Charge balancing:   yes
----------------------------------------------------------------
| Atom Label |  charge    | mult     | occup x mult
|     | Ox. state   | Used | (cif)   |    
----------------------------------------------------------------
|  Al1  |  nan  |  0 |  12 |  1.452
|  Ge1  |  nan  |  0 |  12 |  10.548
|  Li1  |  nan  |  0 |  6 |  4.56
|  Li2  |  nan  |  0 |  36 |  2.88
|  O1  |  nan  |  0 |  36 |  36
|  O2  |  nan  |  0 |  36 |  36
|  P1  |  nan  |  0 |  18 |  18
----------------------------------------------------------------

Chemical formula of the supercell: Al1 Ge11 Li8 O72 P18
Total charge of supercell: 0

----------------------------------------------------
 Identification of groups of crystallographic sites 
----------------------------------------------------

 Group 1 (12 atomic positions in supercell):
  * Site #1: Ge1 (occ. 0.879) -> distributed over 11 positions out of 12 (actual occ.: 0.917).
  * Site #2: Al1 (occ. 0.121) -> distributed over 1 positions out of 12 (actual occ.: 0.083).
  Number of combinations for the group is 12

 Group 2 (6 atomic positions in supercell):
  * Site #1: Li1 (occ. 0.76) -> distributed over 5 positions out of 6 (actual occ.: 0.833).
  Number of combinations for the group is 6

 Group 3 (36 atomic positions in supercell):
  * Site #1: Li2 (occ. 0.08) -> distributed over 3 positions out of 36 (actual occ.: 0.083).
  Number of combinations for the group is 7140

 Group 4 (36 atomic positions in supercell):
  * Site #1: O1 (occ. 1) -> FIXED with occupancy 1.000.

 Group 5 (36 atomic positions in supercell):
  * Site #1: O2 (occ. 1) -> FIXED with occupancy 1.000.

 Group 6 (18 atomic positions in supercell):
  * Site #1: P1 (occ. 1) -> FIXED with occupancy 1.000.

Minimal distance between atoms of two distinct groups: 1.26148 A.

-------------------------------------------------
The total number of combinations is 514080(~5.1e+05)
-------------------------------------------------
36 symmetry operation found for supercell.
Combinations after merge: 14328

supercell_coulomb_energy.txt : supercell_i000000_w12.cif 0.000 eV supercell_i000001_w36.cif 0.000 eV supercell_i000002_w36.cif 0.000 eV supercell_i000003_w36.cif 0.000 eV supercell_i000004_w36.cif 0.000 eV supercell_i000005_w36.cif 0.000 eV supercell_i000006_w36.cif 0.000 eV supercell_i000007_w12.cif 0.000 eV supercell_i000008_w36.cif 0.000 eV supercell_i000009_w36.cif 0.000 eV ... all are 0.000 ev

input file lagp-1.2.cif:

======================================================================

CRYSTAL DATA

----------------------------------------------------------------------

data_VESTA_phase_1

_chemical_name_common                  ''
_cell_length_a                         8.2619(1)
_cell_length_b                         8.2619(1)
_cell_length_c                         20.5656(5)
_cell_angle_alpha                      90
_cell_angle_beta                       90
_cell_angle_gamma                      120
_space_group_name_H-M_alt              'R -3 c'
_space_group_IT_number                 167

loop_
_space_group_symop_operation_xyz
   'x, y, z'
   '-x, -y, -z'
   '-y, x-y, z'
   'y, -x+y, -z'
   '-x+y, -x, z'
   'x-y, x, -z'
   'y, x, -z+1/2'
   '-y, -x, z+1/2'
   'x-y, -y, -z+1/2'
   '-x+y, y, z+1/2'
   '-x, -x+y, -z+1/2'
   'x, x-y, z+1/2'
   'x+2/3, y+1/3, z+1/3'
   '-x+2/3, -y+1/3, -z+1/3'
   '-y+2/3, x-y+1/3, z+1/3'
   'y+2/3, -x+y+1/3, -z+1/3'
   '-x+y+2/3, -x+1/3, z+1/3'
   'x-y+2/3, x+1/3, -z+1/3'
   'y+2/3, x+1/3, -z+5/6'
   '-y+2/3, -x+1/3, z+5/6'
   'x-y+2/3, -y+1/3, -z+5/6'
   '-x+y+2/3, y+1/3, z+5/6'
   '-x+2/3, -x+y+1/3, -z+5/6'
   'x+2/3, x-y+1/3, z+5/6'
   'x+1/3, y+2/3, z+2/3'
   '-x+1/3, -y+2/3, -z+2/3'
   '-y+1/3, x-y+2/3, z+2/3'
   'y+1/3, -x+y+2/3, -z+2/3'
   '-x+y+1/3, -x+2/3, z+2/3'
   'x-y+1/3, x+2/3, -z+2/3'
   'y+1/3, x+2/3, -z+1/6'
   '-y+1/3, -x+2/3, z+1/6'
   'x-y+1/3, -y+2/3, -z+1/6'
   '-x+y+1/3, y+2/3, z+1/6'
   '-x+1/3, -x+y+2/3, -z+1/6'
   'x+1/3, x-y+2/3, z+1/6'

loop_
   _atom_site_label
   _atom_site_occupancy
   _atom_site_fract_x
   _atom_site_fract_y
   _atom_site_fract_z
   _atom_site_adp_type
   _atom_site_B_iso_or_equiv
   _atom_site_type_symbol
   P1         1.0     0.2874(2)     0.000000      0.250000     Biso  0.344778 P
   O1         1.0     0.1778(2)     0.9815(2)     0.18886(7)   Biso  1.255414 O
   O2         1.0     0.1858(2)     0.1600(2)     0.08333(8)   Biso  1.190494 O
   Li1        0.7600  0.000000      0.000000      0.000000     Biso  0.500000 Li
   Ge1        0.8790  0.000000      0.000000      0.14135(8)   Biso  0.187742 Ge
   Al1        0.1210  0.000000      0.000000      0.14135(8)   Biso  0.187742 Al
   Li2        0.0800 -0.001(8)      0.270(7)      0.062(2)     Biso  0.500000 Li

[orex]

Hello.

Thank very much for using my program. Your problem is obviously because you did not specify charges neither in CIF input file nor in command line. Charges are mandatory to calculate electrostatic energy.

Please go for site http://orex.github.io/supercell/ and check 1) Supercell tutorial, first section, where CIF file structure is described. 2) Supercell manual, -p charge option.

Don't hesitate to continue the discussion if you have any questions, related to the issue, close the issue with small remark, when the problem will be solved and open new issue in case of any other problem with the program.

Kirill.

[Jackeyha]

Hello. Professor, thank you very much for answering my question. I have calculated the energy of each structure, and then I use VASP to optimize each structures. I found that the energy calculated by VASP and Supercell are very different (vasp: -745 ev; Supercell: -6090 ev), Can you tell me why there is such a big differerce between them ?

[orex]

It makes no sense to compare absolute values of energies, especially from different codes. The main purpose of electrostatic energy calculations is to use the result for structure sampling. The approach is described in details in paper

Cadars, S., Ho Ahn, N., Okhotnikov, K., Shin, J., Vicente, A., Bong Hong, S., & Fernandez, C. (2017). Modeling Short-Range Substitution Order and Disorder in Crystals: Application to the Ga/Si Distribution in a Natrolite Zeolite. Solid State Nuclear Magnetic Resonance. https://doi.org/10.1016/j.ssnmr.2017.04.001

[orex]

Closed due to two weeks of inactivity.