Hello ATAT users/developers,
I am a PhD student in geology and i am trying to generate a SQS for the mineral tourmaline. Tourmaline is a borosilicate mineral that crystallizes in the trigonal R3m space group. the attached .cif file shows the structure in the conventional hexagonal unit cell which has 3 formula units. The primitive trigonal unit cell only has one formula unit. I understand that ATAT is able to make a SQS structure by monte carlo methods.
I am a complete novice to ATAT. I started this afternoon to try to make a SQS structure however everytime no matter how big i make the unit cell i get the error message:
Impossible to match point correlations due to incompatible supercell size.
- I would like to know what are some ‘rule of thumb’ for the size of the supercell compared to the amount of sites where disordering can take place? I started with only considering pairwise correlations within 3 angstrom (which is the shortest distance between the neighboring disordered cation sites to keep it simple).
As you can see my structure has a lot of atoms in the structure and only at 6 sites there is order-disorder. As I would like to make DFT calculations i would like the supercell to be as small as possible.
-
Is it possible to make a SQS structure at all of a system of my size?
-
Lastly I was wondering if the rndstr.in file is correct or if i have to modify it?
I see that i cannot upload attachements (every time I do i get logged out of the site?) so i just copy and paste the cif and rndstr.in files here.
cif file:
data_Drav
_audit_creation_date 2020-02-10
_audit_creation_method ‘Materials Studio’
_symmetry_space_group_name_H-M ‘R3M’
_symmetry_Int_Tables_number 160
symmetry_cell_setting trigonal
loop
_symmetry_equiv_pos_as_xyz
x,y,z
-y,x-y,z
-x+y,-x,z
-y,-x,z
-x+y,y,z
x,x-y,z
x+2/3,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
-y+2/3,-x+1/3,z+1/3
-x+y+2/3,y+1/3,z+1/3
x+2/3,x-y+1/3,z+1/3
x+1/3,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
-y+1/3,-x+2/3,z+2/3
-x+y+1/3,y+2/3,z+2/3
x+1/3,x-y+2/3,z+2/3
_cell_length_a 15.9450
_cell_length_b 15.9450
_cell_length_c 7.2100
_cell_angle_alpha 90.0000
_cell_angle_beta 90.0000
cell_angle_gamma 120.0000
loop
atom_type_oxidation_number
AlZ +3
MgZ +2
SiT +4
O1 -2
O2 -2
O3 -2
O4 -2
O5 -2
O6 -2
O7 -2
O8 -2
CaX +2
MgY +2
B +3
H1 +1
H3 +1
loop
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
AlZ Al 0.29802 0.26159 0.61070 0.00545 Uiso 0.8333
MgZ Mg 0.29802 0.26159 0.61070 0.00545 Uiso 0.1666
SiT Si 0.19175 0.18990 -0.00135 0.00520 Uiso 1.00
O6 O 0.19581 0.18592 0.77662 0.00840 Uiso 1.00
O7 O 0.28489 0.28483 0.07811 0.00850 Uiso 1.00
O8 O 0.20927 0.27006 0.44018 0.00962 Uiso 1.00
CaX Ca 0.00000 0.00000 0.23250 0.02040 Uiso 1.00
O1 O 0.00000 0.00000 0.74000 0.01350 Uiso 1.00
H1 H 0.00000 0.00000 0.90000 0.04000 Uiso 1.00
MgY MgY 0.12426 0.06213 0.63250 0.00810 Uiso 1.00
O3 O 0.26510 0.13255 0.50989 0.01250 Uiso 1.00
H3 H 0.25600 0.12800 0.40000 0.04500 Uiso 1.00
O5 O 0.18433 0.09216 0.09025 0.01010 Uiso 1.00
B B 0.10987 0.21974 0.45360 0.00650 Uiso 1.00
O2 O 0.06106 0.12212 0.48347 0.01023 Uiso 1.00
O4 O 0.09310 0.18620 0.06931 0.01017 Uiso 1.00
rndstr.in:
15.945 15.944999999999999 7.21 90 90 119.99999999999999
1 0 0
0 1 0
0 0 1
0.29802 0.26159 0.6107 Al=0.8334,Mg=0.1666
0.73841 0.03643 0.6107 Al=0.8334,Mg=0.1666
0.96357 0.70198 0.6107 Al=0.8334,Mg=0.1666
0.73841 0.70198 0.6107 Al=0.8334,Mg=0.1666
0.96357 0.26159 0.6107 Al=0.8334,Mg=0.1666
0.29802 0.03643 0.6107 Al=0.8334,Mg=0.1666
0.9646867 0.5949233 0.9440333 Al=0.8334,Mg=0.1666
0.4050767 0.3697633 0.9440333 Al=0.8334,Mg=0.1666
0.6302367 0.0353133 0.9440333 Al=0.8334,Mg=0.1666
0.4050767 0.0353133 0.9440333 Al=0.8334,Mg=0.1666
0.6302367 0.5949233 0.9440333 Al=0.8334,Mg=0.1666
0.9646867 0.3697633 0.9440333 Al=0.8334,Mg=0.1666
0.6313533 0.9282567 0.2773667 Al=0.8334,Mg=0.1666
0.0717433 0.7030967 0.2773667 Al=0.8334,Mg=0.1666
0.2969033 0.3686467 0.2773667 Al=0.8334,Mg=0.1666
0.0717433 0.3686467 0.2773667 Al=0.8334,Mg=0.1666
0.2969033 0.9282567 0.2773667 Al=0.8334,Mg=0.1666
0.6313533 0.7030967 0.2773667 Al=0.8334,Mg=0.1666
0.19175 0.1899 0.99865 Si
0.8101 0.00185 0.99865 Si
0.99815 0.80825 0.99865 Si
0.8101 0.80825 0.99865 Si
0.99815 0.1899 0.99865 Si
0.19175 0.00185 0.99865 Si
0.8584167 0.5232333 0.3319833 Si
0.4767667 0.3351833 0.3319833 Si
0.6648167 0.1415833 0.3319833 Si
0.4767667 0.1415833 0.3319833 Si
0.6648167 0.5232333 0.3319833 Si
0.8584167 0.3351833 0.3319833 Si
0.5250833 0.8565667 0.6653167 Si
0.1434333 0.6685167 0.6653167 Si
0.3314833 0.4749167 0.6653167 Si
0.1434333 0.4749167 0.6653167 Si
0.3314833 0.8565667 0.6653167 Si
0.5250833 0.6685167 0.6653167 Si
0.19581 0.18592 0.77662 O
0.81408 0.00989 0.77662 O
0.99011 0.80419 0.77662 O
0.81408 0.80419 0.77662 O
0.99011 0.18592 0.77662 O
0.19581 0.00989 0.77662 O
0.8624767 0.5192533 0.1099533 O
0.4807467 0.3432233 0.1099533 O
0.6567767 0.1375233 0.1099533 O
0.4807467 0.1375233 0.1099533 O
0.6567767 0.5192533 0.1099533 O
0.8624767 0.3432233 0.1099533 O
0.5291433 0.8525867 0.4432867 O
0.1474133 0.6765567 0.4432867 O
0.3234433 0.4708567 0.4432867 O
0.1474133 0.4708567 0.4432867 O
0.3234433 0.8525867 0.4432867 O
0.5291433 0.6765567 0.4432867 O
0.28489 0.28483 0.07811 O
0.71517 0.00006 0.07811 O
0.99994 0.71511 0.07811 O
0.71517 0.71511 0.07811 O
0.99994 0.28483 0.07811 O
0.28489 0.00006 0.07811 O
0.9515567 0.6181633 0.4114433 O
0.3818367 0.3333933 0.4114433 O
0.6666067 0.0484433 0.4114433 O
0.3818367 0.0484433 0.4114433 O
0.6666067 0.6181633 0.4114433 O
0.9515567 0.3333933 0.4114433 O
0.6182233 0.9514967 0.7447767 O
0.0485033 0.6667267 0.7447767 O
0.3332733 0.3817767 0.7447767 O
0.0485033 0.3817767 0.7447767 O
0.3332733 0.9514967 0.7447767 O
0.6182233 0.6667267 0.7447767 O
0.20927 0.27006 0.44018 O
0.72994 0.93921 0.44018 O
0.06079 0.79073 0.44018 O
0.72994 0.79073 0.44018 O
0.06079 0.27006 0.44018 O
0.20927 0.93921 0.44018 O
0.8759367 0.6033933 0.7735133 O
0.3966067 0.2725433 0.7735133 O
0.7274567 0.1240633 0.7735133 O
0.3966067 0.1240633 0.7735133 O
0.7274567 0.6033933 0.7735133 O
0.8759367 0.2725433 0.7735133 O
0.5426033 0.9367267 0.1068467 O
0.0632733 0.6058767 0.1068467 O
0.3941233 0.4573967 0.1068467 O
0.0632733 0.4573967 0.1068467 O
0.3941233 0.9367267 0.1068467 O
0.5426033 0.6058767 0.1068467 O
0 0 0.2325 Ca
0.6666667 0.3333333 0.5658333 Ca
0.3333333 0.6666667 0.8991667 Ca
0 0 0.74 O
0.6666667 0.3333333 0.0733333 O
0.3333333 0.6666667 0.4066667 O
0 0 0.9 H
0.6666667 0.3333333 0.2333333 H
0.3333333 0.6666667 0.5666667 H
0.12426 0.06213 0.6325 Mg
0.93787 0.06213 0.6325 Mg
0.93787 0.87574 0.6325 Mg
0.7909267 0.3954633 0.9658333 Mg
0.6045367 0.3954633 0.9658333 Mg
0.6045367 0.2090733 0.9658333 Mg
0.4575933 0.7287967 0.2991667 Mg
0.2712033 0.7287967 0.2991667 Mg
0.2712033 0.5424067 0.2991667 Mg
0.2651 0.13255 0.50989 O
0.86745 0.13255 0.50989 O
0.86745 0.7349 0.50989 O
0.9317667 0.4658833 0.8432233 O
0.5341167 0.4658833 0.8432233 O
0.5341167 0.0682333 0.8432233 O
0.5984333 0.7992167 0.1765567 O
0.2007833 0.7992167 0.1765567 O
0.2007833 0.4015667 0.1765567 O
0.256 0.128 0.4 H
0.872 0.128 0.4 H
0.872 0.744 0.4 H
0.9226667 0.4613333 0.7333333 H
0.5386667 0.4613333 0.7333333 H
0.5386667 0.0773333 0.7333333 H
0.5893333 0.7946667 0.0666667 H
0.2053333 0.7946667 0.0666667 H
0.2053333 0.4106667 0.0666667 H
0.18433 0.09216 0.09025 O
0.90784 0.09217 0.09025 O
0.90783 0.81567 0.09025 O
0.8509967 0.4254933 0.4235833 O
0.5745067 0.4255033 0.4235833 O
0.5744967 0.1490033 0.4235833 O
0.5176633 0.7588267 0.7569167 O
0.2411733 0.7588367 0.7569167 O
0.2411633 0.4823367 0.7569167 O
0.10987 0.21974 0.4536 B
0.78026 0.89013 0.4536 B
0.10987 0.89013 0.4536 B
0.7765367 0.5530733 0.7869333 B
0.4469267 0.2234633 0.7869333 B
0.7765367 0.2234633 0.7869333 B
0.4432033 0.8864067 0.1202667 B
0.1135933 0.5567967 0.1202667 B
0.4432033 0.5567967 0.1202667 B
0.06106 0.12212 0.48347 O
0.87788 0.93894 0.48347 O
0.06106 0.93894 0.48347 O
0.7277267 0.4554533 0.8168033 O
0.5445467 0.2722733 0.8168033 O
0.7277267 0.2722733 0.8168033 O
0.3943933 0.7887867 0.1501367 O
0.2112133 0.6056067 0.1501367 O
0.3943933 0.6056067 0.1501367 O
0.0931 0.1862 0.06931 O
0.8138 0.9069 0.06931 O
0.0931 0.9069 0.06931 O
0.7597667 0.5195333 0.4026433 O
0.4804667 0.2402333 0.4026433 O
0.7597667 0.2402333 0.4026433 O
0.4264333 0.8528667 0.7359767 O
0.1471333 0.5735667 0.7359767 O
0.4264333 0.5735667 0.7359767 O
