orex/supercell

The program allows you to create regular structure supercell from cif file with partial occupancy and/or substitutions.

supercell's Issues

Coulomb energy calculation

Dear developers,
I have tried to run supercell with Coulomb energy calculation option (-q) for a perovskite material KTa_{1-x}Nb_xO_3. As a result I obtained all calculated supercells with the same energy.
Here is the command I run:

supercell -i KTN23_6122.cif -m -q -s 2x2x2

The cif file is attached here. I have changed the extension to TXT because this forum does not allow .cif file. Please change it to .cif when you run it.

KTN23_6122.txt

Could you please have a look why the Coulomb energy are the same? I tried with a larger supercell (3x3x3) and still have the same energy every where.
Thank you very much.
Tra

installation problem

Hi,

I followed quick installation instruction for supercell. But i always meet a problem which I show in attached picture.

I am sure that I succeeded in installation of Open babel in my computer. making test also shows 100% pass. and then I use the command that: git clone --recursive https://github.com/orex/supercell.git && cd supercell && \ mkdir build && cd build && cmake ../ && make && sudo make install

I am very confusing with this Error. I work on Ubuntu OS with administrator permission.

could you help me solve this problem?

I am looking forward to your reply.

thanks,

Build fails with the recent Open Babel 2.4.1

root@debian-16gb ~/supercell/build # make
[  9%] Building CXX object src/sc_cli/CMakeFiles/supercell.dir/__/core/d2o_main_class.cpp.o
/root/supercell/src/core/d2o_main_class.cpp:16:32: fatal error: openbabel/elements.h: No such file or directory
 #include <openbabel/elements.h>
                                ^
compilation terminated.

Isn't this related to the following?

All operations on the structure of the compound ... are done with a customized version of the OpenBabel  [39] library, which was modified by KO to handle partial occupancy in CIF file reading and writing operations. This version of OpenBabel is available from the official Website [40], and the corresponding changes will be merged to the official OpenBabel repository  [41]

Combining selection (-n) options possible?

Hello,

I'd like to use SuperCell to generate random Si/Al distributions in zeolite structures, similar to the Rb-PST reference in the manual.
I have noticed that selecting for the lowest energy structures does an excellent job in selecting the structures that abide by Loewenstein's criterion. However, even when treating the different symmetry groups of T-sites separately like suggested in the tutorial, in some cases the total number of configuration still exceeds what my computer (and supercell itself) can handle due to large unit cells involved.
Is it possible to, for instance, request only the first 10^8 structures generated ( -n f100000000 ) and on top, out of those 10^8 only write the 50 structures with the lowest energy from electrostatic calculation ( -n l50 )?

Thanks a lot,

karel

the coulomb_energy for all stucture is zero.

Fm_il00.cif 0.000 eV
Fm_il01.cif 0.000 eV
Fm_il02.cif 0.000 eV
Fm_il03.cif 0.000 eV
Fm_il04.cif 0.000 eV
Fm_il05.cif 0.000 eV
...........
The command line: ./supercell -i NaYF4-P63m.cif -s 1x1x2 -q -n l20 -o Fm
the oxidation state of elements as I show below:
“_atom_type_symbol
_atom_type_oxidation_number
F1- -1
Na1+ 1
Y3+ 3”

Ox charge is nan

Hi,
when I tried to run the supercell.exe on In2O3 2310009.cif (as shown below), ./supercell -d -i 2310009.cif, it outputs

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)	|		 
----------------------------------------------------------------
|  In1		|  nan		|  0	|  8	|  8
|  In2		|  nan		|  0	|  24	|  24
|  O1		|  nan		|  0	|  48	|  48
----------------------------------------------------------------

Chemical formula of the supercell: In32 O48
Total charge of supercell: 0

If I manually set the charge
./supercell -d -p "In1:c=+3" -p "In2:c=+3" -p "O1:c=-2" -i 2310009.cif
I still get nan in the ox.state table.

----------------------------------------------------------------
| Atom Label	| 	charge  	| mult	| occup x mult
| 		| Ox. state	| Used	| (cif)	|		 
----------------------------------------------------------------
|  In1		|  nan		|  3	|  8	|  8
|  In2		|  nan		|  3	|  24	|  24
|  O1		|  nan		|  -2	|  48	|  48
----------------------------------------------------------------

I've managed to run the examples in the tutorials without any problems, the Ox.state column would show the correct values.

I don't see a problem in the cif. file below. How do I set the Ox charge properly?

#------------------------------------------------------------------------------
#$Date: 2016-02-21 11:56:54 +0200 (Sun, 21 Feb 2016) $
#$Revision: 176809 $
#$URL: svn://www.crystallography.net/cod/cif/2/31/00/2310009.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/. The original data for this entry
# were provided by IUCr Journals, http://journals.iucr.org/.
#
# The file may be used within the scientific community so long as
# proper attribution is given to the journal article from which the
# data were obtained.
#
data_2310009
loop_
_publ_author_name
'Marezio, M.'
_publ_section_title
;
 Refinement of the crystal structure of In2O3 at two wavelengths
;
_journal_issue                   6
_journal_name_full               'Acta Crystallographica'
_journal_page_first              723
_journal_page_last               728
_journal_volume                  66
_journal_year                    1966
_chemical_formula_structural     'In2 O3'
_chemical_formula_sum            'In2 O3'
_chemical_name_systematic        'Indium Oxide'
_space_group_IT_number           206
_symmetry_Int_Tables_number      206
_symmetry_space_group_name_Hall  '-I 2b 2c 3'
_symmetry_space_group_name_H-M   'I a -3'
_cell_angle_alpha                90.
_cell_angle_beta                 90.
_cell_angle_gamma                90.
_cell_formula_units_Z            16
_cell_length_a                   10.117(1)
_cell_length_b                   10.117(1)
_cell_length_c                   10.117(1)
_cell_volume                     1035.51(18)
_cod_data_source_file            In2O3_Ia-3_DC235.cif
_cod_data_source_block           chateigner_1508504
_cod_original_cell_volume        1035.51
_cod_database_code               2310009
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 '-z, x, y+1/2'
2 'z, x+1/2, -y'
3 'z+1/2, -x, y'
4 '-z, -x, -y'
5 'y+1/2, -z, x'
6 '-y, z, x+1/2'
7 'y, z+1/2, -x'
8 '-y, -z, -x'
9 'x, y+1/2, -z'
10 'x+1/2, -y, z'
11 '-x, y, z+1/2'
12 '-x, -y, -z'
13 'z, -x, -y+1/2'
14 '-z, -x+1/2, y'
15 '-z+1/2, x, -y'
16 'z, x, y'
17 '-y+1/2, z, -x'
18 'y, -z, -x+1/2'
19 '-y, -z+1/2, x'
20 'y, z, x'
21 '-x, -y+1/2, z'
22 '-x+1/2, y, -z'
23 'x, -y, -z+1/2'
24 'x, y, z'
25 '-z+1/2, x+1/2, y'
26 'z+1/2, x, -y+1/2'
27 'z, -x+1/2, y+1/2'
28 '-z+1/2, -x+1/2, -y+1/2'
29 'y, -z+1/2, x+1/2'
30 '-y+1/2, z+1/2, x'
31 'y+1/2, z, -x+1/2'
32 '-y+1/2, -z+1/2, -x+1/2'
33 'x+1/2, y, -z+1/2'
34 'x, -y+1/2, z+1/2'
35 '-x+1/2, y+1/2, z'
36 '-x+1/2, -y+1/2, -z+1/2'
37 'z+1/2, -x+1/2, -y'
38 '-z+1/2, -x, y+1/2'
39 '-z, x+1/2, -y+1/2'
40 'z+1/2, x+1/2, y+1/2'
41 '-y, z+1/2, -x+1/2'
42 'y+1/2, -z+1/2, -x'
43 '-y+1/2, -z, x+1/2'
44 'y+1/2, z+1/2, x+1/2'
45 '-x+1/2, -y, z+1/2'
46 '-x, y+1/2, -z+1/2'
47 'x+1/2, -y+1/2, -z'
48 'x+1/2, y+1/2, z+1/2'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_attached_hydrogens
_atom_site_B_iso_or_equiv
In1 In3+ 8 b 0.25 0.25 0.25 1. 0 0.46
In2 In3+ 24 d 0.4663(1) 0 0.25 1. 0 0.41
O1 O2- 48 e 0.3912(12) 0.1558(11) 0.3796(13) 1. 0 0.45
loop_
_atom_type_symbol
_atom_type_oxidation_number
In3+ +3
O2- -2

Precompiled supercell program in Ubuntu 14.04.

Partial occupancy groups get fixed by themselves

Hi,

I'm trying to generate some disordered cells, but with all the .cif files I use the occupancy gets fixed.
I tried to do some tests with different percentages and it seems it chooses 1 for the atom with the highest percentage, even if it's 51. This is one of the .cif files, with just one partial occupied site:

_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 5.60256400
_cell_length_b 5.60256400
_cell_length_c 5.60256400
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural Fe3Si
_chemical_formula_sum 'Fe12 Si4'
_cell_volume 175.85733158
cell_formula_units_Z 4
loop
_symmetry_equiv_pos_site_id
symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe0 1 0.25000000 0.25000000 0.75000000 0.5
Si Si0 1 0.25000000 0.25000000 0.75000000 0.5
Fe Fe1 1 0.00000000 0.00000000 0.00000000 1
Fe Fe2 1 0.25000000 0.75000000 0.75000000 1
Fe Fe3 1 0.25000000 0.75000000 0.25000000 1
Fe Fe4 1 0.00000000 0.50000000 0.50000000 1
Fe Fe5 1 0.25000000 0.25000000 0.25000000 1
Fe Fe6 1 0.75000000 0.25000000 0.25000000 1
Fe Fe7 1 0.50000000 0.00000000 0.50000000 1
Fe Fe8 1 0.75000000 0.75000000 0.25000000 1
Fe Fe9 1 0.75000000 0.75000000 0.75000000 1
Fe Fe10 1 0.50000000 0.50000000 0.00000000 1
Fe Fe11 1 0.75000000 0.25000000 0.75000000 1
Si Si12 1 0.50000000 0.00000000 0.00000000 1
Si Si13 1 0.50000000 0.50000000 0.50000000 1
Si Si14 1 0.00000000 0.00000000 0.50000000 1
Si Si15 1 0.00000000 0.50000000 0.00000000 1

and here is the output I got after executing supercell -d -i <input>.cif -m:

The other groups are fixed, as they should be.
What am I doing wrong?

Special quasirandom structure: example PbSnTe gives errors

Dear Supercell developers.

I installed Supercell and Gulp on linux and tested both softwares separately and they seem to work. I added both gulp and supercell to Path in the /.bashrc.
However every time i run the df_cfg.bash from the quasirandom structure example with PbSnTe i get the following error:

sed: can't read /home/stanroozen/GULP/PbSnTe/cell_1x1x2/.cif: No such file or directory
STOP GULP terminated with an error
STOP GULP terminated with an error
STOP GULP terminated with an error
STOP GULP terminated with an error
sed: can't read /home/stanroozen/GULP/PbSnTe/cell_1x2x2/.cif: No such file or directory
STOP GULP terminated with an error
STOP GULP terminated with an error
STOP GULP terminated with an error
STOP GULP terminated with an error

The first for loop in the df_cfg.bash file makes a new folder with the supercell structures. However, when i run the complete script the cif files get overwritten by a folder called * which has a folder called gulp that has gulp input files.

I was wondering if you had any idea what is going on?

Greetings,
Stan Roozen

df_cfg_bash.txt

The Coulomb energy is zero

Hello!
llzoyb_out/llzo_il00000000_w4.cif 0.000 eV
llzoyb_out/llzo_il00000001_w4.cif 0.000 eV
llzoyb_out/llzo_il00000002_w4.cif 0.000 eV
llzoyb_out/llzo_il00000003_w4.cif 0.000 eV
llzoyb_out/llzo_il00000004_w4.cif 0.000 eV

Here is the log file

Minimal distance between atoms of two distinct groups: 0.652594 A.

The total number of combinations is 52097760(~5.2e+07)

4 symmetry operation found for supercell.
Symmetries operation assigned to groups.
Start Coulomb matrix (106x106) calculation.
Coulomb matrix calculation finished.
Output files was deleted successfully
Finished 68.2%. Stored 9413720 configurations. Left 14442880
Total enumeration time: 0:00:1.46505
Combinations after merge: 13024440

CIF
_chemical_name_common 'Heptalithium trilanthanum dizirconium '
_cell_length_a 11.261361
_cell_length_b 11.261361
_cell_length_c 11.261361
_cell_angle_alpha 109.471222
_cell_angle_beta 109.471222
_cell_angle_gamma 109.471222
_cell_volume 1099.387373
_space_group_name_H-M_alt 'P 1'
_space_group_IT_number 1

loop_
_space_group_symop_operation_xyz
'x, y, z'

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_U_iso_or_equiv
_atom_site_type_symbol
Li1 0.5640 0.625000 0.375000 0.250000 Uiso 0.026000 Li
Li1 0.5640 0.375000 0.625000 0.750000 Uiso 0.026000 Li
Li1 0.5640 0.875000 0.125000 0.750000 Uiso 0.026000 Li
Li1 0.5640 0.125000 0.875000 0.250000 Uiso 0.026000 Li
Li1 0.5640 0.250000 0.625000 0.375000 Uiso 0.026000 Li
Li1 0.5640 0.750000 0.375000 0.625000 Uiso 0.026000 Li
Li1 0.5640 0.750000 0.875000 0.125000 Uiso 0.026000 Li
Li1 0.5640 0.250000 0.125000 0.875000 Uiso 0.026

issue with large number combination

I am using your "Supercell" code to remove the partial occupancy of the attached oxynitride structure. The lattice parameter in .cif is large. So I am considering only 1x1x1 supercell. There are three groups. Group 2 and group 3 is Zr1 and Zr2 site, respectively. Group 1 is O1/N1 with partial occupancies. The problem is that it is showing "Number of combinations for the group is 2254848913647", which is a really big number to treat. Can you please help how to proceed with the "Supercell" code to remove the partial occupancies of O/N?
EntryWithCollCode50197.cif.zip

ERROR: Group has no unique connection.

There is a error when deal with file below which is generated by findit.
Cu2Se-41141.cif.zip

Occupancy of 0.000 treated as 1.000

Dear Kirill,

I just stumbled upon a minor issue when introducing an occupancy factor of zero for in the cif file. (I know I could simply delete these atoms instead of setting it to zero. But it is easier for me this way in order to keep a better overview and for potential use of the cif file at some later point in case I want to change the occupancies again to non-zero values.) Instead of the zero occupation factor the supercell code uses 1.000 which screws up the composition and total charge of the supercell.

Example output if occupancy of all atoms A1 are set to 0.000 in the cif file:
Group 5 (120 atomic positions in supercell):
Site #1: A1 (occ. 1) -> FIXED with occupancy 1.000.

Quick and dirty solution; set it to a very small value and the supercell code will automatically fix the occupancy to zero:
Group 5 (120 atomic positions in supercell):
Site #1: A1 (occ. 1e-06) -> FIXED with occupancy 0.000.

However, it would be nice if an occupancy of 0.00 would be treated as such in order to avoid confusion for future users.

Best regards,
Marcel

A problem in calculating the coulomb energy

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               -
-                  ([email protected])    -
-                 * Sylvian Cadars                  -
-                  ([email protected])     -
-                 * Thibault Charpentier            -
-                  ([email protected])    -
-----------------------------------------------------
-  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

bug: changing the angles in cif file results in wrong number of atomic sites

When running the supercell program I expired that it might give wrong results depending on the angles of the Crystal structure.

Here is an example:

An example structure contains 24 sites with 0.8633 occupancy. That should result in 21 occupied sites and a total number of combinations of 2024.
Using the cif file below that exactly is the output of the supercell program. No Problem.

Now the the alpha angle in the cif file below is changed from 71.55 to 71.56 without touching anything else. The new supercell output says there would only be 21 sites and supercell wants to occupy 18 of it (which would be the right occupancy but applied to the wrong number of atomic sites). Changing the angle seems to have kicked out some atoms.

--------------Cif file------------------

CIF file generated by openbabel 2.4.1, see http://openbabel.sf.net
data_I
_chemical_name_common 'Supercell generated structure'
_cell_length_a 7.93821
_cell_length_b 11.22630
_cell_length_c 17.75040
_cell_angle_alpha 71.55
_cell_angle_beta 90
_cell_angle_gamma 90
_space_group_name_H-M_alt 'P 1'
_space_group_name_Hall 'P 1'

loop_
_symmetry_equiv_pos_as_xyz
x,y,z

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Al1 Al -0.000000 0.500000 1.000000 0.8633
Al1 Al -0.000000 0.666667 0.666667 0.8633
Al1 Al -0.000000 0.833333 0.333333 0.8633
Al1 Al -0.000000 0.166667 0.666667 0.8633
Al1 Al -0.000000 0.333333 0.333333 0.8633
Al1 Al -0.000000 0.000000 1.000000 0.8633
Al1 Al 0.250000 0.083333 0.833333 0.8633
Al1 Al 0.250000 0.250000 0.500000 0.8633
Al1 Al 0.250000 0.416667 0.166667 0.8633
Al1 Al 0.250000 0.583333 0.833333 0.8633
Al1 Al 0.250000 0.750000 0.500000 0.8633
Al1 Al 0.250000 0.916667 0.166667 0.8633
Al1 Al 0.500000 0.166667 0.166667 0.8633
Al1 Al 0.500000 0.333333 0.833333 0.8633
Al1 Al 0.500000 0.500000 0.500000 0.8633
Al1 Al 0.500000 0.666667 0.166667 0.8633
Al1 Al 0.500000 0.833333 0.833333 0.8633
Al1 Al 0.500000 0.000000 0.500000 0.8633
Al1 Al 0.750000 0.083333 0.333333 0.8633
Al1 Al 0.750000 0.250000 1.000000 0.8633
Al1 Al 0.750000 0.416667 0.666667 0.8633
Al1 Al 0.750000 0.583333 0.333333 0.8633
Al1 Al 0.750000 0.750000 1.000000 0.8633
Al1 Al 0.750000 0.916667 0.666667 0.8633

loop_
_atom_type_symbol
_atom_type_oxidation_number
Al1 3

most of the example failed

Hi,
I try to run the examples with the script, but:

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct null not valid

Please help me,
what kind of information do you need?

Best Regards!
Thanks for the tool.

symmetry operations _space_group_symop_operation_xyz

Dear Orex,

Thanks for this amazing code to get the structures with partial occupancies.

I have to generate the cation distribution in a supercell which is transformed from the primitive unit cell (space group 91). I have to use conventional unit cell of space group which is transformed according to the operation given below.

_space_group_transform_Pp_abc 'a-b,a+b,c;0,0,0'

Due to this transformation, the symmetry operations are also changed. As I found that supercell code does not uses the symmetry operations which are given in cif file (correct me if I am wrong). Please let me know how to solve this problem.

Here is my cif file.
#======================================================================

CRYSTAL DATA

#----------------------------------------------------------------------
data_VESTA_phase_1

_chemical_name_common 'CoFe2O4'
_cell_length_a 8.485281
_cell_length_b 8.485281
_cell_length_c 8.325200
_cell_angle_alpha 90.000000
_cell_angle_beta 90.000000
_cell_angle_gamma 90.000000
_cell_volume 599.414352
_space_group_name_H-M_alt 'P 41 2 2'

_space_group_IT_number 91
_space_group_transform_Pp_abc 'a-b,a+b,c;0,0,0'

loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x, -y, z+1/2'
'-y, x, z+1/4'
'y, -x, z+3/4'
'-y, -x, -z'
'y, x, -z+1/2'
'-x, y, -z+3/4'
'x, -y, -z+1/4'
'x+1/2, y+1/2, z'
'-x+1/2, -y+1/2, z+1/2'
'-y+1/2, x+1/2, z+1/4'
'y+1/2, -x+1/2, z+3/4'
'-y+1/2, -x+1/2, -z'
'y+1/2, x+1/2, -z+1/2'
'-x+1/2, y+1/2, -z+3/4'
'x+1/2, -y+1/2, -z+1/4'

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
Co1 1.0 0.875000 0.625000 0.000000 Biso 1.000000 Co
Fe1 1.0 0.625000 0.375000 0.000000 Biso 1.000000 Fe
Fe5 1.0 0.250000 0.500000 0.125000 Biso 1.000000 Fe
O1 1.0 0.375000 0.375000 0.000000 Biso 1.000000 O
O9 1.0 0.125000 0.625000 0.000000 Biso 1.000000 O

Equivalent postion tolerance

How does the tolerance option work becuase I think it's not what I initially thought it did. For my system, I have a cif file that has no symmetry operations. But that's only because the coordinates of the atoms have many decimal points. If you rounded to the third decimal place, that would start to be symmetry again. I work with AIMD, so atoms move around. So a few hundredths of an angstrom difference is the same from a chemistry point of view. Is there an option within supercell that can force equivalent positions based on a tolerance? Thanks for the help

Consider relicensing to MIT/BSD

MIT/BSD is more permissive.

ERROR: Number of total combinations is too high to work with.

Dear all experts,
I have encountered an error with "ERROR: Number of total combinations is too high to work with." so I am here to ask that how to solve the said error.
I know that I am trying with large super-cell because my atomic contribution is 0.034 so to keep existence of atom, I have to go with selection of 5x5x3.
If you need information of system or file, please let me know.

Thank you

Please tag releases

I am interested in building supercell from the source. However, I cannot find a way to obtain the source pertaining to supercell v2.0 as git HEAD may already contain commits on top of v2.0. In Git, usually Git tags are used to mark releases as they point to a specific commit (immutable source, in theory). It would be very nice if tags were added for stable releases of supercell, at least for v2.0.

Fixing occupancies

Structure.txt
output.txt

In order to reduce the time required to convert this structure into a 3x3x3 ordered supercell, I tried using the recommended commands in the tutorial however, the occupancies are not remaining fixed but always changed to 0 and 1.

Input: supercell -i Structure.cif -p "*:fixed"
Output: Attached

A problem in calculating the coulomb energy

Thanks for Professor Okhotniikov's kind help.

My original letter is as follows:

Dear professor,
I'm writing to ask for your help with the problem in using the Supercell program. These days I want to get the model with the lowest energy for the crystal (Sn24P19.3I8), however, there's some errors when I calculated the coulomb energy.
When I type:
supercell -i snip.cif -q -p "Sn*:c=+2" -p "I*:c=-1" -p "P*:c=-2.07" -m -n l10 -o mod1/snip
An error was reported as below:

Current charge balance option is "try"
Total charge oxidation state (cif): nan
Total charge cell: 0.06142
Charge balancing: yes

| Atom Label | charge | mult | occup x mult
| | Ox. state | Used | (cif) |

| I1 | nan | -1 | 2 | 2
| I2 | nan | -1 | 6 | 6
| P1 | nan | -2.07 | 16 | 16
| P2 | nan | -2.07 | 6 | 3.294
| Sn1 | nan | 2 | 24 | 13.176
| Sn2 | nan | 2 | 24 | 10.824

Create atoms population error:
Change supercell size
Switch off charge balancing
Check manual population settings

If I change the charge of P* from 2.07 to 2, the errors will be :

ERROR: Electrostatic energy cannot be calculated without charge balancing.
Also I changed the supercell with 1x2x1, the above error still exist.

I’ve found that the examples in your tutorial only refer to some models with the integral charge. Is it means that we can only calculate the coulomb energy of systems with integral and balanced charge? If so, I would love to hear your kind suggestion with these problems.
The model (snip.cif) and the corresponding reference are in the attachments. Thanks for your kind attention and look forward your reply.
Best regards,
Jiang Lu

Professor's apply:

Dear Jiang Lu,

Thank you for the question. The supercell program is working correct.

1. Electrostatic energy of any cells can be only calculated in electrically neutral systems. This is not a limitation of the implemented algorithms, but a "natural" limitation. Energy of charged cell will be infinite.
2. Supercell can work with partial charges, but not in your case. A correction of phosphorus amount to satisfy integer occupation requires an integer charge. P=+2. In you case the correction is quite small I think you can do this as me myself and many users of my program did. You can increase cell size to make the correction smaller.
3. This I cannot reproduce
   If I change the charge of P* from 2.07 to 2, the errors will be :
   ERROR: Electrostatic energy cannot be calculated without charge balancing.
   Also I changed the supercell with 1x2x1, the above error still exist.
   The code /supercell -q -i snip.cif -c yes -p "Sn*:c=+2" -p "I*:c=-1" -p "P*:c=-2" -m -n l10 -o mod1/snip is working as expected without error. Probably, you forget to force charge calculation "-c yes"?

Don't hesitate to contact me in case of any question, but I really appreciate if you will create an issue on github site (starting from your initial letter). It will take for you no more than a couple of minutes to create an account, if needed.
https://github.com/orex/supercell/issues/

Using the approach, not only me but other people can see your problem and help you.

Sincerely yours,
Kirill Okhotniikov.

novikov2012.pdf
snip.txt

Can't open the program

I have installed the supercell program on windows, but it will crash unexpectedly when I open the EXE file. After installation on Linux, it will display "input file cannot be opened." Could you help me solve this problem?

"Total oxidation state (cif): nan" & "Error:Group has no unique connection"

Good day Supercell developers and users,
I am trying to use the .cif of a hydrotalcite, a clay with partial occupancy of Al and Mg in the same site.
However, when I run it with supercell, I get two different issues.

• Total charge oxidation state (cif):nan

• Error: Group has no unique connection

The first one is that the charge is not recognized. Even in the Oxidation table, I get the nan output. I can correct the Used charges in the table by manually assigning the values with:

./supercell -q -p "Mg*:c=+2" -p "Al*:c=+3" -p "O*:c=-2" -p "C*:c=+4" -p "H*:c=+1"

However, the nan does not change in the charge oxidation state and the total charge of the cell is not neutral. Regarding the second issue, I have seen it happens when the sites are too close. I tried to fix it by changing the tolerance value. The problem is that from the 0.75 Å of the preset value, the error was fixed until the tolerance was 11.49 Å which seems too large. Moreover, supercells groups all the sites in a single group and fixes the occupancy to zero for all of them. In consequence, it says there is only one combination possible.

./supercell -q -p "Mg*:c=+2" -p "Al*:c=+3" -p "O*:c=-2" -p "C*:c=+4" -p "H*:c=+1" -i /home/ubuntu/Documents/CIF/ICSD86655.cif -t 11.49  -o /home/ubuntu/Documents
-----------------------------------------------------
-               Supercell program                   -
-----------------------------------------------------
-      Authors:   * Kirill Okhotnikov               -
-                  ([email protected])    -
-                 * Sylvian Cadars                  -
-                  ([email protected])     -
-                 * Thibault Charpentier            -
-                  ([email protected])    -
-----------------------------------------------------
-  please cite:                                     -
-    K. Okhotnikov, T. Charpentier and S. Cadars    -
-    J. Cheminform. 8 (2016) 17 – 33.               -
-----------------------------------------------------

Manual properties
Label	|fixed	|charge	|popul	|
Al1	|N/A	|3	|N/A	|
C1	|N/A	|4	|N/A	|
H1	|N/A	|1	|N/A	|
H2	|N/A	|1	|N/A	|
Mg1	|N/A	|2	|N/A	|
O1	|N/A	|-2	|N/A	|
O2	|N/A	|-2	|N/A	|

Initial system:
  Chemical Formula: Al0.99 C0.498 H9 Mg2.01 O9.006

Supercell system (1x1x1):
  Size a=3.04535, b=3.04535, c=22.701

Current charge balance option is "try"
Total charge oxidation state (cif):  nan
Total charge cell:   -0.0299997
Charge balancing:   yes
----------------------------------------------------------------
| Atom Label	| 	charge  	| mult	| occup x mult
| 		| Ox. state	| Used	| (cif)	|		 
----------------------------------------------------------------
|  Al1		|  nan		|  3	|  3	|  0.99
|  C1		|  nan		|  4	|  6	|  0.498
|  H1		|  nan		|  1	|  6	|  6
|  H2		|  nan		|  1	|  6	|  3
|  Mg1		|  nan		|  2	|  3	|  2.01
|  O1		|  nan		|  -2	|  6	|  6
|  O2		|  nan		|  -2	|  18	|  3.006
----------------------------------------------------------------

Chemical formula of the supercell: Al0 C0 H0 Mg0 O0
Total charge of supercell: 0

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

 Group 1 (1 atomic positions in supercell):
  * Site #1: Mg1 (occ. 2.01) -> FIXED with occupancy 0.000.
  * Site #2: Al1 (occ. 0.99) -> FIXED with occupancy 0.000.
  * Site #3: O1 (occ. 6) -> FIXED with occupancy 0.000.
  * Site #4: O2 (occ. 3.006) -> FIXED with occupancy 0.000.
  * Site #5: C1 (occ. 0.498) -> FIXED with occupancy 0.000.
  * Site #6: H1 (occ. 6) -> FIXED with occupancy 0.000.
  * Site #7: H2 (occ. 3) -> FIXED with occupancy 0.000.
  Crystallographic sites with different positions found for this group.
  Maximum distance within the group: 11.4791 A.

Minimal distance between atoms of two distinct groups: -1 A.

-------------------------------------------------
The total number of combinations is 1
-------------------------------------------------

I have tried with bigger cells (3x3x1) but the Error: Group has no unique connection appears again.
I would really appreciate if you could help me to fix both problems so that I can generate the geometry of a supercell with adequate fixed occupancy. I require it for running Molecular Dynamics simulations.

Thank you for any help you can provide,

Phebe

PS: The cif files is the following:

#(C) 2017 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  All rights reserved.
data_86655-ICSD
_database_code_ICSD 86655
_audit_creation_date 2000-07-15
_chemical_name_systematic
'Magnesium aluminium hydroxide carbonate hydrate (0.67/0.33/2/0.17/0.48)'
_chemical_formula_structural '(Mg0.67 Al0.33 (O H)2) (C O3)0.165 (H2 O)0.48'
_chemical_formula_sum 'C0.165 H2.96 Al0.33 Mg0.67 O2.975'
_chemical_name_structure_type Hydrotalcite
_exptl_crystal_density_diffrn 2.12
_publ_section_title

;
New synthetic routes to hydrotalcite-like compounds characterisation and
properties of the obtained materials
;
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'European Journal of Inorganic Chemistry  (online)' 1998 1998 1439 1446
EJICFO
loop_
_publ_author_name
'Costantino, U.'
'Marmottini, F.'
'Nocchetti, M.'
'Vivani, R.'
_cell_length_a 3.04535(9)
_cell_length_b 3.04535(9)
_cell_length_c 22.7010(13)
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 120.
_cell_volume 182.33
_cell_formula_units_Z 3
_symmetry_space_group_name_H-M 'R -3 m H'
_symmetry_Int_Tables_number 166
_refine_ls_R_factor_all 0.056
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x-y, -y, -z'
2 '-x, -x+y, -z'
3 'y, x, -z'
4 'x-y, x, -z'
5 'y, -x+y, -z'
6 '-x, -y, -z'
7 '-x+y, y, z'
8 'x, x-y, z'
9 '-y, -x, z'
10 '-x+y, -x, z'
11 '-y, x-y, z'
12 'x, y, z'
13 'x-y+2/3, -y+1/3, -z+1/3'
14 '-x+2/3, -x+y+1/3, -z+1/3'
15 'y+2/3, x+1/3, -z+1/3'
16 'x-y+2/3, x+1/3, -z+1/3'
17 'y+2/3, -x+y+1/3, -z+1/3'
18 '-x+2/3, -y+1/3, -z+1/3'
19 '-x+y+2/3, y+1/3, z+1/3'
20 'x+2/3, x-y+1/3, z+1/3'
21 '-y+2/3, -x+1/3, z+1/3'
22 '-x+y+2/3, -x+1/3, z+1/3'
23 '-y+2/3, x-y+1/3, z+1/3'
24 'x+2/3, y+1/3, z+1/3'
25 'x-y+1/3, -y+2/3, -z+2/3'
26 '-x+1/3, -x+y+2/3, -z+2/3'
27 'y+1/3, x+2/3, -z+2/3'
28 'x-y+1/3, x+2/3, -z+2/3'
29 'y+1/3, -x+y+2/3, -z+2/3'
30 '-x+1/3, -y+2/3, -z+2/3'
31 '-x+y+1/3, y+2/3, z+2/3'
32 'x+1/3, x-y+2/3, z+2/3'
33 '-y+1/3, -x+2/3, z+2/3'
34 '-x+y+1/3, -x+2/3, z+2/3'
35 '-y+1/3, x-y+2/3, z+2/3'
36 'x+1/3, y+2/3, z+2/3'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Mg2+ 2
Al3+ 3
O2- -2
C4+ 4
H1+ 1
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
Mg1 Mg2+ 3 a 0 0 0 0.0137(6) 0.67 0
Al1 Al3+ 3 a 0 0 0 0.0137(6) 0.33 0
O1 O2- 6 c 0 0 0.37631(10) 0.0266(9) 1. 0
O2 O2- 18 h 0.1075(10) 0.8925(10) 0.50034(48) 0.0198(22) 0.167 0
C1 C4+ 6 c 0.3333 0.6667 0.5003(5) 0.053(11) 0.083 0
H1 H1+ 6 c 0 0 0.4220(17) 0.082(13) 1. 0
H2 H1+ 6 c 0.3333 0.6667 0.5006(5) 0.082(13) 0.5 0
#End of TTdata_86655-ICSD

ERROR output in example Ca2Al2SiO7

I run supercell using file(https://github.com/orex/supercell/blob/master/data/examples/Ca2Al2SiO7/Ca2Al2SiO7.cif) with command:

supercell -d -i Ca2Al2SiO7.cif -m

However, I got error output,

ERROR: Label AlT2 belong to 2 or more groups.

Comparison to icet code

Dear Kirill @orex,

How does the supercell code compare to the icet code? Could they replace each other?

Many thanks for your time!

Antisite defect calculation.

Hi I had been trying to create structures with antisite defects in a simple Bi2Te3 system but to no avail. The -p property is not giving more than 1 structure, despite mentioning the A and B site occupancies of Bi atoms. Would it be possible to provide an example for such a system? I am attaching the .cif file I am using for the system. (Had to convert to a .txt extension for uploading)
Bi2Te3_prim_pristine_1.cif.txt

Error: Input file cannot be opened

Dear developers,
I've just discovered your potentially great program Supercell that could help me to build disordered supercell crystal. I have installed it without any issue. But when I test it by running the examples you provided along side with the software, I always have this error: "Input file cannot be opened".
For more information:

• My OS is Debian 7. Actually I'm working on a cluster computer of my Institute. I only have permission in my own place and I don't have root permission.
• Before installing Supercell, I've installed Eigen3 and OpenBabel.
• All of the 3 packages (eigen3, openbabel and supercell) are cloned from server (mercurial for Eigen3, git for openbabel and supercell).
• To build and install the packages, I have specified the destination directory as my personal folder (/users/myname/bin)
• When building supercell, an error appeared stating that the eigen3/Eigen/Core or Dense cannot be included. So I modified the line number 14 in src/sc_cli/main.cpp and parse_d2o_input.h :
  #include </users/myname/bin/include/eigen3/Eigen/Core>
  And the building and installation worked.

- Here is the out put of "ldd /users/thnguyen/bin/bin/supercell":

linux-vdso.so.1 =>  (0x00007ffcc1593000)
libopenbabel.so.4 => /users/thnguyen/bin/usr/local/lib/libopenbabel.so.4 (0x00007f951558b000)
libboost_regex.so.1.49.0 => /usr/lib/libboost_regex.so.1.49.0 (0x00007f9515a8d000)
libboost_program_options.so.1.49.0 => /usr/lib/libboost_program_options.so.1.49.0 (0x00007f9515a26000)
libboost_filesystem.so.1.49.0 => /usr/lib/libboost_filesystem.so.1.49.0 (0x00007f9515a05000)
libboost_system.so.1.49.0 => /usr/lib/libboost_system.so.1.49.0 (0x00007f9515a01000)
libboost_random.so.1.49.0 => /usr/lib/libboost_random.so.1.49.0 (0x00007f95159fd000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9515387000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f9515170000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f9514e69000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9514be7000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f95149d1000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9514646000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f951442a000)
libicuuc.so.48 => /usr/lib/x86_64-linux-gnu/libicuuc.so.48 (0x00007f95140bb000)
libicui18n.so.48 => /usr/lib/x86_64-linux-gnu/libicui18n.so.48 (0x00007f9513cf0000)
libicudata.so.48 => /usr/lib/x86_64-linux-gnu/libicudata.so.48 (0x00007f9512980000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f9512778000)
/lib64/ld-linux-x86-64.so.2 (0x00007f95159cb000)

Could you please help me out to fix this?
All the best,
Tra Nguyen

Problem to initiate the supercell calculation for a Garnet structure

Hi Kirill and others

I have used supercell program over the past year and find it every helpful for my reseach. I already tried more than 20 different structures for calculation and all of them were successful. But recently, I have a problem to initiate the supercell calculation for a garnet structure, with a space group of Fm-3mLi5La3Nb2O12.cif . The garnet cif was first downloaded from ICSD database. Subsequently, I modified slightly for the the oxidation states of atoms in the cif file as follow

loop_
_atom_type_symbol
_atom_type_oxidation_number
La1 +3
Nb1 +5
O1 -2
Li1 +1
Li2 +1
Li3 +1

I didn't modify anything for the atomic positions of the atoms.

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_occupancy
La1 La3+ 24 c 0.125 0 0.25 0.006(1) 1
Nb1 Nb5+ 16 a 0 0 0 0.002(1) 1
O1 O2- 96 h 0.2844(5) 0.1044(6) 0.1996(6) 0.007(3) 1
Li1 Li1+ 24 d 0.25 0.875 0 0.01 0.836
Li2 Li1+ 48 g 0.125 0.6798 0.5702 0.01 0.11
Li3 Li1+ 96 h 0.095 0.6818 0.5778 0.01 0.152

When I tried to initiate the supercell calculation, I typed "supercell -i Li5La3Nb2O12.cif -d -q -m -n l10 -s 2x2x2"

I got the output message as follow:

Random SEED: 2466491342
CIF file info:
INFO: Using symmtries from space group.

Initial system:
Chemical Formula: La24 Li39.936 Nb16 O96

Supercell system (2x2x2):
Size a = 25.5898, b 25.5898, c = 25.5898

Current charge balance option is "try"
Total charge oxidation state (cif): -0.064
Total charge cell: -0.064
Charge balancing: yes

ERROR: Group has no unique connection.
Create occupation groups error.

Below is a printscreen of the window.

I am not sure what was wrong in the calculation. Would you provide me some advice to solve it? Thank you very much!

best,
Jack

Supercell cmake error

Dear Supercell developers,

I am now trying to install Supercell on my Mac. But I meet the following issue when "cmake ../". I know this error arise from Eigen3(the failure of locating Eigen3). But I do not know how to solve this problem even after googling for a long time. I am not familiar with CMake. Could you give me some instructions on this issue? Thanks for your help.
---------------------------------Error log listed below---------------------------

CMake Error at src/CMakeLists.txt:9 (find_package):
By not providing "FindEigen3.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Eigen3", but
CMake did not find one.

Could not find a package configuration file provided by "Eigen3" with any
of the following names:

Eigen3Config.cmake
eigen3-config.cmake

Add the installation prefix of "Eigen3" to CMAKE_PREFIX_PATH or set
"Eigen3_DIR" to a directory containing one of the above files. If "Eigen3"
provides a separate development package or SDK, be sure it has been
installed.

-- Configuring incomplete, errors occurred!
See also "/Users/wzb/repos/supercell/build/CMakeFiles/CMakeOutput.log".

Error with non-integer oxidation state

Dear developers,
I'm trying to model a structure with chemical formula of Cu58S32, however it seems that I can not use a non-integer oxidation state (Cu +1.1, S -2). The error was

Create atoms population error:
Change supercell size
Switch off charge balancing
Check manual population settings

Then I tried the oxidation state of (Cu +1, S -2) and switch off charge balancing. The new problem is

ERROR: Electrostatic energy cannot be calculated without charge balancing.

If I switch on charge balancing, the formula will be adjusted to Cu64S32.
How can I deal with this structure?

Thank you!
Cu58S32.txt

The program get stuck when dealing with surface model

I create a surface model, and tried to use supercell to make disorder replacement, but the prgrom got stuck after I execute
supercell -i CdS-110.cif -v 2 -p "*T2:fixed" -p "*T3:fixed" -p "*T4:fixed" -p "*T5:fixed" -p "*T6:fixed" -n r1 -o step1

Here are the log file and cif file I use:
surface.zip

The output file is empty

Dear Orex,

I would like to express my gratitude for Supercell, which is a great software. I have been using it recently to generate structures and the user experience has been fantastic.

However, I have recently encountered some problems that I cannot resolve, and therefore, I am hoping that you could provide assistance. The problem is as follows:

In my input file, there are four Al atoms in partly occupied sites. Directly generating the structure would result in a large number of results. Therefore, I have used the following commands step by step:

./supercell -i gamma.cif -p ":fixed" -o gamma_abg
./supercell -i gamma_abg.cif -p "Al1:fixed" -p "Al3*:fixed" -p "Al4*:fixed" -m -q -g -v 2 -n l1 -o fixed134_step1/fixed134
./supercell -i fixed134.cif -p "Al3*:fixed" -p "Al4*:fixed" -m -q -g -v 2 -n l1 -o fixed34_step2/fixed34

Everything went smoothly until here, and I obtained the cif file for Al1 and Al2 randomly distributed, and Al3 and Al4 fixed. However, when I proceeded to the next step:

./supercell -i fixed34.cif -p "Al4*:fixed" -m -q -g -v 2 -n l1 -o fixed4_step3/fixed4

There were txt files and cif files in the folder, but they were empty files, with no content. I have tried to expand the virtual machine's disk space, but the result was still the same. Did I do anything wrong? I would greatly appreciate your answer and help.

Thank you once again for providing such a great software.

Sincerely,
Duanmu.

Example-PbSnTe-SQS stops without any error

I am a new supercell user. When I run the example PbSnTe-SQS with df.cfg.bash script the program runs but after few seconds it got stuck without any errors.
The program requires gulp. I have it installed it and the other examples (like ice-Ih) which also requires gulp runs perfectly.

OS:Ubuntu 20.04 LTS
Gulp: 5.2
Supercell version: Latest (installed with the following commands)
git clone --recursive https://github.com/orex/supercell.git && cd supercell && mkdir build && cd build && cmake ../ && make && sudo make install)

The path shows the gulp executable.

Choice of atoms when maintaining charge

Hello

I am currently doping a disordered structure and then using the program to order it into a supercell. I would like to understand what is logic that the program chooses when it tries to maintain the charge neutral.

In other words, if my dopant has a charge of 3+ and is substituting a element with a different charge say 4+, the program will try to remove some elements in order to compensate for the charge. How does it make the choice?

Thank you!

How to start with supercell

Dear Supercell developers,

I would like to ask a simple but confusing question for me. The problem is, when I try to start the supercell program like the tutorial and find:

bash : supercell : command not find ..

I think it's because I didn't add it to the environment. But I don't know what I need to add to the environment.

Thank you very much, and your answer is very important to me.

Sorry, maybe i has download the source code. I well try the compiled binaries.

unexpected output when there are only two atoms in the unit cell

I create a cif file that only contains two atoms:

Zn15-T1      0.5   0   0   0.5
Cd15-T1     0.5   0  0   0.5

I expect supercell would output 2 configurations, which contain one type of atom in the unit cell, respectively, but there is only one output configuration, here is the output:

Chemical formula of the supercell: Cd1 Zn0
Total charge of supercell: 0

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

 Group 1 (1 atomic positions in supercell):
   Site #1: Zn15-T1 (occ. 0.5) -> FIXED with occupancy 0.000.
   Site #2: Cd15-T1 (occ. 0.5) -> FIXED with occupancy 1.000.

Minimal distance between atoms of two distinct groups: -1 A.

-------------------------------------------------
The total number of combinations is 1

Here are the detailed log and cif files I use.
cif.zip

output.txt

The supercell is not generating the coulomb_energy.txt file.

Hello Supercell experts,
I am new to this program and wanted to calculate the examples of this program mentioned in the manual. but the problem is i am not able to generate the coulomb_energy.txt file, while all the procedure is according to the manual. I want to know if this is a bug or i am doing something wrong.

Bug with Te-metal structure

Dear Orex ;o)

I am experiencing 2 distinct problems with the following structure (generated with VESTA) based on Te Metal (P 31 2 1 space group) and mixing with another element (no matter the amount of mixing between the two or the nature of the second element).

test-02.cif

#======================================================================
# CRYSTAL DATA
#----------------------------------------------------------------------
data_VESTA_phase_1

_chemical_name_common                  ''
_cell_length_a                         4.456000
_cell_length_b                         4.456000
_cell_length_c                         5.921000
_cell_angle_alpha                      90.000000
_cell_angle_beta                       90.000000
_cell_angle_gamma                      120.000000
_cell_volume                           101.815999
_space_group_name_H-M_alt              'P 31 2 1'
_space_group_IT_number                 152

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

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_U_iso_or_equiv
   _atom_site_type_symbol
   Te1         0.5    -0.263600     0.000000     0.333333    Biso  ? Te
   Se1         0.5    -0.263600     0.000000     0.333333    Biso  ? Se

In older versions of supercell (a few months old), when I try a dryrun with the -m option :

supercell -d -i test-02.cif -s 3x2x1 -m

the program keeps writing :

ERROR: wrong combination symmetry.
ERROR: wrong combination symmetry.
ERROR: wrong combination symmetry.
...

I downloaded that lastest (linux) pre-compiled version and has a different problem :

supercell -i test-02.cif -s 3x3x1 -d -m

-------------------------------------------------
The total number of combinations is 20058300(~2.0e+07)
-------------------------------------------------
1674 symmetry operation found for supercell.
Total enumeration time: 0:00:0.128357
Combinations after merge: 0
ERROR: Combination left 20058300 != 0
Write files error.

Any idea what is wrong with the structure and/or the program ?
Thank you very much.
All the best.
Sylvian.

Fe Supercell issues

have recently started using the supercell software, however I’m having trouble with the symmetry outputs.

I’ve attached an example of the output I’m getting. In this example I have 16 Fe atoms (2x2x2 bcc unit cell) and have given 4 of them an occupancy of 0.5, which gives the initial system a formula of Fe14. However, the supercell formula is coming up as Fe12, which in this case is incorrect as this should be Fe14 (4 atoms at 0.5 = 2 and 12 at 1 occupancy = 12+2 = 14)
It also comes up with 1 as the number of combinations, which again doesn’t make sense.
I was hoping to get some pointers as to where im going wrong

i am using a Linux operating system and supercell version: 23rd May 2019
Attached is my input file (input_Fe_222.txt) and output file i get to my screen (output_Fe_222.txt)
The command i use to launch supercell is ./supercell -i Fe_222.cif -m -q -g -o=supercell

input_Fe_222.txt
supercell_coulomb_energy.txt
output Fe_222.txt
supercell_i0_w1.txt

Many Thanks
Debbie

An error about the occupancy

Dear Kirill,
Here is a occupancy difference between my original model and the gained models. In my original model, the occupancy of P1a is 0.167, after the supercell process, the occupancy is 0. What's more, the occupancy of P4a is 0.278, which changed to 0.333 after the supercell process.
The sn3p4-adv.cif is in attachment, which is gained from sn3p4.cif with specific P atoms grouped and all the atoms fixed.

supercell -i sn3p4.cif -p "*:fixed" -o sn3p4-adv.cif

Then all the 8 P atoms in a sphere were grouped as a-f for sn3p4-adv.cif

Next, type

supercell -d -i sn3p4-adv.cif

There is an error, although it is not reported in the process.

Group 1 (1 atomic positions in supercell):

• Site #1: P1a (occ. 0.167) -> FIXED with occupancy 0.000.
  Group 19 (3 atomic positions in supercell):
• Site #1: P4a (occ. 0.278) -> distributed over 1 positions out of 3 (actual occ.: 0.333).

Hoping for your early reply.
Best wishes,
Jane

sn3p4.zip

Nan Oxidation State + High Displacement Disordering

Hello Developers,

I am a new user to Supercell, and have worked through a number of the examples successfully. I am writing about issues that are similar to comment 18, for which I was also able to run successfully after making the edits suggested in that thread. I am dealing with similar issues as the user PheLiBoP, where I am obtaining two key error messages when running ./supercell: 1) “Nan” Charge Oxidation States in the atom enumeration tables and 2) “ERROR: Group has no unique connection”. Additionally, another error, 3) “Create occupation groups error” appeared. If I could have help on any of these three errors, that would be wonderful.

1. For error 1, the Nan charge, I have decided to identify the charges through specifying them when calling the supercell executable rather than in the .cif (-p "Mo1:c=+6" -p "Mo2:c=+2" -p "N*:c=-3" -p "O*:c=-2" -p "H*:c=+1"). However, the Nan error can be reproduced by adding the following lines to the cif below the _atom_site_fract_symmform, which follows with what was recommended in comment 18. However, this makes it so “Used” in the table goes to 0, so therefore I believe specifying the oxidation states in the command line explicitly is more successful for this case.

loop_
_atom_type_oxidation_number
N1 -3
N2 -3
O1 -2
H1  1
H2  1
Mo1 6
Mo2 2

2. For error 2, I tried to identify ways that I could simplify the .cif where there is fractional occupancy for the hydrogen, as I believe this could be where the error lies for “ERROR: Group has no unique connection”. Similarly to comment 18 for oxygen, this structure produces a situation where there are many possible places for hydrogen to occur. Therefore, I think given what the developers discussed for comment 18, hydrogen could be considered to be displacement disordered? There are two unique sites each with a 24 multiplicity, meaning that each unit cell we’re looking for has about 1 of each unique hydrogen, or two H’s.

The two unique positions can be seen when visualizing the .cif, again similar to what the developer did for comment 18. H1 lies closer to the Mo2 atom, between the transition metal-nitrogen bonds. On the other hand, H2 lies very close to the fractional O/N site, nearly halo-ing the anion. This can be seen in the pictures below, labelled, though due to the number of atomic sites, it could be helpful for the developers and any reading this post to visualize the system yourself.

Hydrogen 1


Hydrogen 2

Unlike comment 18, I don’t see an easy way to reduce the complexity of where the hydrogens can exist within the cif, without making a decision about where they would be in the cell. If I am not missing something, is there a way to handle the “ERROR: Group has no unique connection” without choosing a spot for each hydrogen in the .cif?

3. Unfortunately, I was not able to find instances of the error “Create occupation groups error” in other examples or comments on the GitHub, though I could have missed them. Therefore, I’m not quite sure exactly what it indicates. However, I want to point it out in case this helps the developers address the issue or other users in the future see this error.

As a background, these cells were created by a collaborator from diffraction patterns after a synthesis, and thus are a bit complicated. The goal is to develop a supercell for which we can do a DFT relaxation, followed by looking at other characteristics with DFT (i.e. electronic band structures and NMR). Below I have included my .cif and my output. The full command I used to obtain the output was (./supercell -d -i Mo-O-N-H.cif -m -p "Mo1:c=+6" -p "Mo2:c=+2" -p "N*:c=-3" -p "O*:c=-2" -p "H*:c=+1”). Thank you!

OUTPUT

./supercell -d -i Mo-O-N-H-700C-3.cif -m -p "Mo1:c=+6" -p "Mo2:c=+2" -p "N*:c=-3" -p "O*:c=-2" -p "H*:c=+1"

-----------------------------------------------------
-               Supercell program                   -
-----------------------------------------------------
-      Authors:   * Kirill Okhotnikov               -
-                  ([email protected])    -
-                 * Sylvian Cadars                  -
-                  ([email protected])     -
-                 * Thibault Charpentier            -
-                  ([email protected])    -
-----------------------------------------------------
-  please cite:                                     -
-    K. Okhotnikov, T. Charpentier and S. Cadars    -
-    J. Cheminform. 8 (2016) 17 – 33.               -
-----------------------------------------------------

Manual properties
Label	|fixed	|charge	|popul	|
H1	|N/A	|1	|N/A	|
H2	|N/A	|1	|N/A	|
Mo1	|N/A	|6	|N/A	|
Mo2	|N/A	|2	|N/A	|
N1	|N/A	|-3	|N/A	|
N2	|N/A	|-3	|N/A	|
O1	|N/A	|-2	|N/A	|

Initial system:
  Chemical Formula: H2.2656 Mo2.6176 N2.488 O1.512

Supercell system (1x1x1):
  Size a=4.183, b=4.183, c=4.183

Current charge balance option is "try"
Total charge oxidation state (cif):  nan
Total charge cell:   -0.0912
Charge balancing:   yes
----------------------------------------------------------------
| Atom Label	| 	charge  	| mult	| occup x mult
| 		| Ox. state	| Used	| (cif)	|		 
----------------------------------------------------------------
|  H1		|  nan		|  1	|  24	|  1.1208
|  H2		|  nan		|  1	|  24	|  1.1448
|  Mo1		|  nan		|  6	|  1	|  0.724
|  Mo2		|  nan		|  2	|  3	|  1.8936
|  N1		|  nan		|  -3	|  1	|  1
|  N2		|  nan		|  -3	|  3	|  1.488
|  O1		|  nan		|  -2	|  3	|  1.512
----------------------------------------------------------------

ERROR: Group has no unique connection. 
ERROR: Group has no unique connection. 
ERROR: Group has no unique connection. 
Create occupation groups error.

CIF

# CIF file created by FINDSYM, version 7.1

data_findsym-output
_audit_creation_method FINDSYM

_cell_length_a    4.1829990000
_cell_length_b    4.1829990000
_cell_length_c    4.1829990000
_cell_angle_alpha 90.0000000000
_cell_angle_beta  90.0000000000
_cell_angle_gamma 90.0000000000
_cell_volume      73.1919439945

_symmetry_space_group_name_H-M "P 4/m -3 2/m"
_symmetry_Int_Tables_number 221
_space_group.reference_setting '221:-P 4 2 3'
_space_group.transform_Pp_abc a,b,c;0,0,0

loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 x,-y,-z
3 -x,y,-z
4 -x,-y,z
5 y,z,x
6 y,-z,-x
7 -y,z,-x
8 -y,-z,x
9 z,x,y
10 z,-x,-y
11 -z,x,-y
12 -z,-x,y
13 -y,-x,-z
14 -y,x,z
15 y,-x,z
16 y,x,-z
17 -x,-z,-y
18 -x,z,y
19 x,-z,y
20 x,z,-y
21 -z,-y,-x
22 -z,y,x
23 z,-y,x
24 z,y,-x
25 -x,-y,-z
26 -x,y,z
27 x,-y,z
28 x,y,-z
29 -y,-z,-x
30 -y,z,x
31 y,-z,x
32 y,z,-x
33 -z,-x,-y
34 -z,x,y
35 z,-x,y
36 z,x,-y
37 y,x,z
38 y,-x,-z
39 -y,x,-z
40 -y,-x,z
41 x,z,y
42 x,-z,-y
43 -x,z,-y
44 -x,-z,y
45 z,y,x
46 z,-y,-x
47 -z,y,-x
48 -z,-y,x

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_fract_symmform
Mo1   Mo   1 a 0.00000 0.00000 0.00000 0.72400 0,0,0
Mo2   Mo   3 c 0.00000 0.50000 0.50000 0.63120 0,0,0
N1  N    1 b 0.50000 0.50000 0.50000 1.00000 0,0,0
N2  N    3 d 0.50000 0.00000 0.00000 0.49600 0,0,0
O1  O    3 d 0.50000 0.00000 0.00000 0.50400 0,0,0
H1    H   24 m 0.38270 0.38270 0.25400 0.04670 Dx,Dx,Dz
H2    H   24 m 0.07310 0.07310 0.56900 0.04770 Dx,Dx,Dz

# end of cif

Question about Coulomb Energy Calculation

First, thank you for the effort! For me the supercell code is really helpful, it does exactly what it should.
However, I came along a question concerning the Coulomb Energy Calculation.

In my case, I have a big structure that contains:
i) Several atomic sites with different occupancy factors for the same atomic species A. These sites are either occupied or empty.
ii) Some other sites that are shared by two species B and C. The sites are always occupied with one or the other.

All of that cannot be done in a single run due to an overflow of possibilities. I went step by step and generated some structures by first occupying only a part of the species while fixing the rest. Finally, I arrived at some reasonable starting structures for further electronic structure calculations.

For the analysis of the material I want to see whether some structural changes can be correlated to the disorder of the B/C site. I thought I could get some first hints from a purely electrostatic point of view and looked at the Coulomb Energy. Therefore, I wanted to clarify how the Coulomb Energy is calculated if some partially occupied sites are kept fix via the -p "A:fixed" switch.

To be more concrete, let's look at the following three examples:

1.) I attributed an oxidation state of +2 to species A. There are 20 A sites in the cell which are only occupied a probability of 30%. Will the Coulomb calculation then use an average oxidation state of
+2*0.3 = +0.6
for all 20 sites if -p "A:fixed" is used?

2.) For the mixed B/C sites i attributed an oxidation state of -1 to B and -2 to C. If those sites would be occupied with 25% of B and 75% of C, would the Coulomb Energy calculation use
(-1*0.25) + (-2*0.75) = -1.75
for all these sites if I would fix them?

3.) Hypothetical case, similar to the previous point: If there were sites that would be occupied by 50% of a species with oxidation state +2 and with 50% of a species with oxidation state -2, would the Coulomb Energy calculation take a oxidation state of zero if those are fixed during program execution?

I hope you can clarify this issue to me.

Best regards,
Marcel

supercell does not read cif file correctly

supercell -d -i Ca2Al2SiO7.cif -m

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:oop_

*** Open Babel Error in CIFReadValue
Warning: Trying to read a value but found a new CIF tag !

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:+2

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:AlT1 +3

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:AlT2 +3

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:SiT2 +4

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:O1 -2

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:O2 -2

*** Open Babel Warning in Parse
Warning: one line could not be interpreted while reading a CIF file:
-> line contents:O3 -2
Initial system:
Chemical Formula: *4 Al6 O14 Si4

Compilation details:

1. Get supercell: git clone --recursive
   https://github.com/orex/supercell.git
2. Get openbabel: git clone https://github.com/openbabel/openbabel
3. Build openbabel
   a. cd openbabel
   b. mkdir -p 64-bit && cd 64-bit
   c. cmake .. -DCMAKE_INSTALL_PREFIX=/opt/openbabel
   d. gmake -j4
   e. sudo gmake install
4. Build supercell
   a. cd supercell
   b. mkdir -p 64-bit && cd 64-bit
   c. cmake .. -DOpenBabel2_DIR=/opt/openbabel/lib/cmake/openbabel2
   -DCMAKE_INSTALL_PREFIX=/opt/supercell -DCMAKE_BUILD_TYPE=Release
   d. gmake -j4
   e. sudo gmake install

Tools:
CC --version
FreeBSD clang version 3.4.1 (tags/RELEASE_34/dot1-final 208032) 20140512
Target: x86_64-unknown-freebsd10.3
Thread model: posix

Fail to generate supercell model by SUPERCELL

We are trying to generate supercell model of Fe doped alumina-rich spinel (MgO·1.8Al2O3) by using Supercell program, but failed.

• Supercell v2.0
• the Cif was referred to the MgAlFeO4.cif example. the cif was checked by VESTA and attached here (please remove the ".txt"
  MgAl2O4.cif.txt).
• command line:
  supercell.exe -i MgAl2O4.cif -p MgA:p=5 -p AlA:p=3 -p FeA:p=0 -p MgB:p=0 -p AlB:p=14 -p FeB:p=1 -m -o out/spd
• output information comes:
  "Command line: E:\xxx\supercell.exe -i MgAl2O4.cif -p MgA:p=5 -p AlA:p=3 -p FeA:p=0 -p MgB:p=0 -p AlB:p=14 -p FeB:p=1 -m -o out/spd
  Random SEED: 104959513
  Unhandled Exception reached the top of main: MgAl2O4.cif:262:1: Wrong number of values in the loop, application will now exit"

We don't know what does it means. Could you give us some suggestion?

mixing the element by setting -s 1x1x1

Hi

I have a question.

I would like to mix element by keeping the cell size. just mix the initial element with the other element

EX.) SiO2

There are 8 Si and 16 O.

8 Si -> 4 Si and 4 Ge So, i prepared the file cif

if I expand cell (e.g. -s 2x1x1 ) is fine to make cell. but -s 1x1x1 case just give only 1 configuration.

but, There are 8C4= 70 cases

And Although I add charge for each element and consider those charges , it does also give 1 configuration.

Q1. Is it difficult to calculate the intermixing like this case for 1x1x1 in the large unit cell( total number of atoms > 80 , here 32 SI -> 16 Si and 16 Ge)

Thanks

Internal representation of structures and programmatic usage (Python)

Dear Kirill @orex,

so far the only possibility to use supercell is via CIF files. However, integrating into a programmatic pipeline (e.g. for high-throughput) does not necessarily implies CIF, moreover, generating and writing CIFs even in P1 assumes some redundant I/O-overhead.

Could you point me to the internal handling of structures? Something like this: https://github.com/atztogo/spglib/blob/master/example/example.c (see lattice, position etc.)

Or would you recommend to dive in from the Open Babel's side?

My ultimate goal would be to create e.g. a Python module, however currently I'm not able to estimate the required efforts adequately.

Unhandled Exception reached the top of main: single data block expected, got 2, application will now exit

Hello! What is the reason for this error when using the supercell program?
Unhandled Exception reached the top of main: single data block expected, got 2, application will now exit

Taking too long time for 1961256 no of total combinations

I am trying sampling out lowest 50 Coulomb energy structures from a cif file, where total no of the combination is 1961256 (As printed at the end of a dry run). But it is taking too long time and as the time progresses the no of configuration finished, stored are increasing as well as the no of configuration left is also increasing. How is it possible? Is there any error? And how can I estimate the time remaining to finish this calculation?

Also, I have archived the output files but the Coulomb_energy.txt file is huge alone. How can I handle that?

An error in repeating the example of "ice-Ih-adv"

Dear professor,
I've repeated the example of "ice-Ih-adv" , but I found there are a lot of structures in the "ice-Ih-cfgs-final" file. However, in your tutorial, it writes

"The process gives only 9 structures which obey both conditions, and which may be found in the ice-Ih-cfgs-final/ directory. "

 I assume that the "**Checking H-H distance**" process do not works well here. If so, I would love to hear your kind suggestion with these problems. 
 It should be mentioned that I added two lines in your **df_cfg.bash**, which I renamed **t2.bash**.

module load node/11.1.0
export PRG_GULP=/public1/soft/node/11.1.0/bin/gulp

All the materials are in the attachments. Thanks for your kind attention and look forward your reply.
Best regards,
Jiang Lu

ice-Ih-adv.zip