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Supercell programを使い第一原理計算用のcifファイルを作成し第一原理計算用の.inファイルを作成する

Last updated at Posted at 2024-03-20

Supercell program (https://orex.github.io/supercell/) を用いて元素置換をした場合のciifファイルを作成し、cif2cellから第一原理計算用の.inファイルを作成する方法の備忘録

必要な環境
・Ubuntu
・VESTA
・cif2cell
・supercell

Supercell programのドキュメントに記載の通りに、supercell programをsupercell-startのディレクトリ中に、以下のコマンドでダウンロード、解凍。

$ mkdir supercell-start && cd supercell-start
$ wget https://orex.github.io/supercell/external/exe/supercell-linux.tar.gz -O - | tar -xzvf -

今回は例として次のPbTe.cif(https://next-gen.materialsproject.org/materials/mp-19717) を使用。Pbサイトの一部をSnに置換した系を考える。PbTe.cifを任意のディレクトリに保存し、VESTAで開く。VESTA中のEdit→Editdata→Structure parameterを開く。写真のようにPbサイトにSnを加える。Occupancyはsupercellのプログラムから可変なので適当に50%としておく。
image.png

次にUnit CellからRemove symmetryで対称性を失わせる。次にKeep Structure parameters unchangedを選択し、Applyする。
image.png
ユニットセル中のPb/Sn原子数(=4)を覚えておく。File→Export Dataでcifファイルとして保存。今回はPbSnTe.cifとした。

ubuntuでciffileのあるディレクトリ中に入り下記を実行する。 -iでcifファイルを指定する。 -sでcellをどの程度拡張するか。 -p以下で置換元素の割合を指定する。(ユニットセル拡張前のPb/Sn原子数は4で、2x2x2に拡張したので原子数は4x8=32個となる。32このうちPb1が29個(p=29),Sn1が3個(p=3)と指定した。) -oでexportするデータ名を指定。

supercell -i PbSnTe.cif -s 2x2x2 -m -p Pb1:p=29 -p Sn1:p=3 -o Pb29Sn3Te32.cif
Random SEED: 3176339887
CIF file info:
  INFO: Using symmetries from space group.

Manual properties
Label   |fixed  |charge |popul  |
Pb1     |N/A    |N/A    |29     |
Sn1     |N/A    |N/A    |3      |

Initial system:
  Chemical Formula: Pb2 Sn2 Te4

Supercell system (2x2x2):
  Size a=13.0836, b=13.0836, c=13.0836

Current charge balance option is "try"
Total charge oxidation state (cif):  0
Total charge cell:   0
Charge balancing:   yes
----------------------------------------------------------------
| Atom Label    |       charge          | mult  | occup x mult
|               | Ox. state     | Used  | (cif) |
----------------------------------------------------------------
|  Pb1          |  0            |  0    |  4    |  2
|  Sn1          |  0            |  0    |  4    |  2
|  Te0          |  0            |  0    |  4    |  4
----------------------------------------------------------------

Chemical formula of the supercell: Pb29 Sn3 Te32
Total charge of supercell: 0

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

 Group 1 (32 atomic positions in supercell):
  * Site #1: Pb1 (occ. 0.5) -> distributed over 29 positions out of 32 (actual occ.: 0.906).
  * Site #2: Sn1 (occ. 0.5) -> distributed over 3 positions out of 32 (actual occ.: 0.094).
  Number of combinations for the group is 4960

 Group 2 (32 atomic positions in supercell):
  * Site #1: Te0 (occ. 1) -> FIXED with occupancy 1.000.

Minimal distance between atoms of two distinct groups: 3.2709 A.

-------------------------------------------------
The total number of combinations is 4960
-------------------------------------------------
1536 symmetry operation found for supercell.
Total enumeration time: 0:00:0.051864
Combinations after merge: 14

複数.cifファイルが生成される。その1つをvestaではなくメモ帳などで確認する。3行目data_のあとがなくエラーの原因となるためdata_ → data_Pb29Sn3Te32と記入し保存する。

変更前

# CIF file generated by supercell program. See https://orex.github.io/supercell
# E_e = 0.0000000000 eV
data_
_chemical_name_common ''
_cell_length_a 13.0836
_cell_length_b 13.0836
_cell_length_c 13.0836
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_space_group_IT_number 1
_space_group_name_H-M_alt 'P 1'
_space_group_name_Hall 'P 1'
loop_
    _space_group_symop_operation_xyz
    x,y,z
loop_
    _atom_site_label

・・・・・・・・

変更後

# CIF file generated by supercell program. See https://orex.github.io/supercell
# E_e = 0.0000000000 eV
data_Pb29Sn3Te32
_chemical_name_common ''
_cell_length_a 13.0836
_cell_length_b 13.0836
_cell_length_c 13.0836
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_space_group_IT_number 1
_space_group_name_H-M_alt 'P 1'
_space_group_name_Hall 'P 1'
loop_
    _space_group_symop_operation_xyz
    x,y,z
loop_
    _atom_site_label

・・・・・・・・

Ubuntuにもどりcif2cellを実行。cif2cellは(https://qiita.com/fch/items/c3e037a106d400190218) を参照されたい。

$ cif2cell --force -p pwscf --setup-all --print-symmetry-operations --pwscf-atomic-units --pwscf-pseudostring=.pbe-spn-kjpaw_psl.1.0.0.UPF -f Pb29Sn3Te32.cif_i0004_w96.cif

下記の通りに.inファイルが作成される。

#************************************************************************************
#*                  Generated by cif2cell 1.2.10 2024-03-20 21:00                   *
#*  T. Bjorkman, Comp. Phys. Commun. 182, 1183-1186 (2011). Please cite generously. *
#*                                                                                  *
#*                                         ()                                       *
#*             Failed to get author information, No journal information             *
#************************************************************************************

&SYSTEM
  ibrav = 0
  celldm(1) =   24.72442
  nat = 64
  ntyp = 3
/
CELL_PARAMETERS {alat}
  1.000000000000000   0.000000000000000   0.000000000000000 
  0.000000000000000   1.000000000000000   0.000000000000000 
  0.000000000000000   0.000000000000000   1.000000000000000 
ATOMIC_SPECIES
  Pb  207.20000  Pb.pbe-spn-kjpaw_psl.1.0.0.UPF
  Te  127.60000  Te.pbe-spn-kjpaw_psl.1.0.0.UPF
  Sn  118.71000  Sn.pbe-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
Pb   0.000000000000000   0.000000000000000   0.250000000000000 
Pb   0.250000000000000   0.000000000000000   0.000000000000000 
Pb   0.000000000000000   0.250000000000000   0.000000000000000 
Pb   0.250000000000000   0.250000000000000   0.250000000000000 
Pb   0.000000000000000   0.000000000000000   0.750000000000000 
Pb   0.250000000000000   0.000000000000000   0.500000000000000 
Pb   0.000000000000000   0.250000000000000   0.500000000000000 
Pb   0.250000000000000   0.250000000000000   0.750000000000000 
Pb   0.000000000000000   0.500000000000000   0.250000000000000 
Pb   0.250000000000000   0.500000000000000   0.000000000000000 
Pb   0.000000000000000   0.750000000000000   0.000000000000000 
Pb   0.250000000000000   0.750000000000000   0.250000000000000 
Pb   0.000000000000000   0.500000000000000   0.750000000000000 
Pb   0.250000000000000   0.500000000000000   0.500000000000000 
Pb   0.000000000000000   0.750000000000000   0.500000000000000 
Pb   0.250000000000000   0.750000000000000   0.750000000000000 
Pb   0.500000000000000   0.000000000000000   0.250000000000000 
Pb   0.750000000000000   0.000000000000000   0.000000000000000 
Pb   0.500000000000000   0.250000000000000   0.000000000000000 
Pb   0.750000000000000   0.250000000000000   0.250000000000000 
Pb   0.500000000000000   0.000000000000000   0.750000000000000 
Pb   0.750000000000000   0.000000000000000   0.500000000000000 
Pb   0.500000000000000   0.250000000000000   0.500000000000000 
Pb   0.500000000000000   0.500000000000000   0.250000000000000 
Pb   0.750000000000000   0.500000000000000   0.000000000000000 
Pb   0.500000000000000   0.750000000000000   0.000000000000000 
Pb   0.500000000000000   0.500000000000000   0.750000000000000 
Pb   0.750000000000000   0.500000000000000   0.500000000000000 
Pb   0.500000000000000   0.750000000000000   0.500000000000000 
Te   0.000000000000000   0.000000000000000   0.000000000000000 
Te   0.000000000000000   0.250000000000000   0.250000000000000 
Te   0.250000000000000   0.000000000000000   0.250000000000000 
Te   0.250000000000000   0.250000000000000   0.000000000000000 
Te   0.000000000000000   0.000000000000000   0.500000000000000 
Te   0.000000000000000   0.250000000000000   0.750000000000000 
Te   0.250000000000000   0.000000000000000   0.750000000000000 
Te   0.250000000000000   0.250000000000000   0.500000000000000 
Te   0.000000000000000   0.500000000000000   0.000000000000000 
Te   0.000000000000000   0.750000000000000   0.250000000000000 
Te   0.250000000000000   0.500000000000000   0.250000000000000 
Te   0.250000000000000   0.750000000000000   0.000000000000000 
Te   0.000000000000000   0.500000000000000   0.500000000000000 
Te   0.000000000000000   0.750000000000000   0.750000000000000 
Te   0.250000000000000   0.500000000000000   0.750000000000000 
Te   0.250000000000000   0.750000000000000   0.500000000000000 
Te   0.500000000000000   0.000000000000000   0.000000000000000 
Te   0.500000000000000   0.250000000000000   0.250000000000000 
Te   0.750000000000000   0.000000000000000   0.250000000000000 
Te   0.750000000000000   0.250000000000000   0.000000000000000 
Te   0.500000000000000   0.000000000000000   0.500000000000000 
Te   0.500000000000000   0.250000000000000   0.750000000000000 
Te   0.750000000000000   0.000000000000000   0.750000000000000 
Te   0.750000000000000   0.250000000000000   0.500000000000000 
Te   0.500000000000000   0.500000000000000   0.000000000000000 
Te   0.500000000000000   0.750000000000000   0.250000000000000 
Te   0.750000000000000   0.500000000000000   0.250000000000000 
Te   0.750000000000000   0.750000000000000   0.000000000000000 
Te   0.500000000000000   0.500000000000000   0.500000000000000 
Te   0.500000000000000   0.750000000000000   0.750000000000000 
Te   0.750000000000000   0.500000000000000   0.750000000000000 
Te   0.750000000000000   0.750000000000000   0.500000000000000 
Sn   0.750000000000000   0.250000000000000   0.750000000000000 
Sn   0.750000000000000   0.750000000000000   0.250000000000000 
Sn   0.750000000000000   0.750000000000000   0.750000000000000 

# k-space resolution ~0.2/A.
K_POINTS automatic
2 2 2  0 0 0
1
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