Copyright 2010, Torbjorn Bjorkman

• This is test version

• Use 2to3 and expand tools

• Modified uctools.py (for gcd and L)

• "*.bak" are old version (python2)

• cif2cell support cif file

• You can get VESTA old version from this URL: http://jp-minerals.org/vesta/archives/

• expert user recommend to change "symmetry" part on cif file. new version cif remove "symmetry" and add "alt."

• Currently, "_space_group_name_Hall" is not written in the VESTA cif file. You need to add "_space_group_name_Hall" for "reduce" to work. It is described in "Materials Project" and "https://cci.lbl.gov/sginfo/hall_symbols.html".

• Tested for Python 3.10
• Other python 3.x version is developed on another repo.
• Let's cite Computer Physics Communications, Volume 182, Issue 5, p. 1183-1186..

I have added support for LAMMPS .data files with orthogonal and triclinic boxes. To convert a CIF-file to LAMMPS data file, simply run (in this directory)

./cif2cell /path/to/file.cif --no-reduce -p lammps -o cif_file.data

It would be a good idea to use Ovito (GUI) code as well. However, please note that the order of elements in Ovito is easily changed.

A tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The code will generate the crystal structure for the primitive cell or the conventional cell.

The distribution includes:

• This README file.
• The file LICENSE with the GPLv3 license.
• The python files cif2cell, uctools.py and spacegroupdata.py
• Installation files, setup.py and MANIFEST.
• A manual.
• The directory cifs/ containing a set of example CIF files as well as the crystal structures of the full periodic table from COD, the Crystallography Open Database http://www.crystallography.net and also a few from ICSD (with permission).
• The file PyCifRW-X.X.tar.gz, containing the PyCifRW package needed for parsing CIF files.
• VESTA is also available on CUI.: e.g., On PowerShell

'C:\Program Files\VESTA-win64\VESTA.exe' -nogui -i POSCAR -o POSCAR.cif

Prerequisites: The program requires Python 3.10 or higher and the PyCIFRW python package (which will be installed automatically if not present, see below for manual installation instructions). Note however that the output may be slightly different (but formally equivalent) with Python 3.10 than with later versions.

To install the program in your systems standard location, simply type:

(sudo) python setup.py install

To choose a different location, add --prefix=where/you/want/it to the above line. For help and more options type

python setup.py --help

The installation will also create a directory $PREFIX/lib/cif2cell that contains the manual and sample cif files.

The setup will install the manual, cif2cell.pdf, into the $PREFIX/lib/cif2cell/docs directory.

Run cif2cell -h to get a listing of the different options. Example:

cif2cell Ni20Mn3P6.cif -p vasp --vasp-cartesian-positions

will generate a POSCAR file for VASP with the positions in cartesian format.

cif2cell is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

cif2cell is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with cif2cell. If not, see http://www.gnu.org/licenses/.

Happy computing!

Torbjorn Bjorkman COMP, Aaalto University School ofScience and Technology, Department of Applied Physics, Espoo, Finland [email protected]

[1] https://github.com/torbjornbjorkman/cif2cell
[2] https://github.com/andeplane/cif2cell-lammps
[3] https://github.com/kmu/cif2cell

cif2cell support cif file (from VESTA version 3.1.0 - 3.1.7 in 2013-2014. you can get VESTA old version from this URL: http://jp-minerals.org/vesta/archives/)
Or, expert user recommend to change "_symmetry_" part on cif file. new version cif remove "_symmetry_" and add "alt."

1. sudo apt update
2. sudo apt -y install python3 python3-setuptools python3-dev
3. git clone https://github.com/by-student-2017/cif2cell-informal_py3.git
4. cd cif2cell-informal_py3
5. tar zxvf PyCifRW-4.4.5.tar.gz
6. cd PyCifRW-4.4.5
7. sudo python3 setup.py install
8. cd ..
9. sudo python3 setup.py install

!apt update
!apt install -y git python python-setuptools python-dev gcc
%cd /content
!git clone https://github.com/by-student-2017/cif2cell-informal_py3.git
%cd cif2cell-informal_py3
!tar zxvf PyCifRW-4.4.5.tar.gz
%cd PyCifRW-4.4.5
!python3 setup.py install
%cd /content/cif2cell-informal
!python3 setup.py install

• cif2cell -h

• VASP

  cif2cell -p vasp --vasp-format=5 --vasp-encutfac=1.0 --vasp-pseudo-libdr="/home/username/vasp.5.4.1/potpaw_PBE" --vasp-cartesian-lattice-vectors --setup-all -f *.cif

• Abinit

  cif2cell -p abinit --abinit-pseudo-JTH-libdr='/home/username/JTH' --setup-all -f *.cif

• PWscf

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/username/PSLibrary' --setup-all -f *.cif

• Elk

  cif2cell -p elk --setup-all -f *.cif

• Akai-KKR ("cpa2002v009c.tar.gz" around 2015)

  cif2cell -p akaikkr --setup-all -f *.cif

• OpenMX

  cif2cell -p openmx --openmx-pseudo-libdr=/home/username/openmx3.8/DFT_DATA13/PAO --setup-all -f *.cif

• Lammps

  cif2cell -p lammps --no-reduce --setup-all --lammps-pottype=ReaxFF --lammps-dt=0.25 --lammps-runtype=ann --lammps-temperature=300 --lammps-pressure=1.0 --lammps-Nsteps=4000 --lammps-rdf=yes --lammps-show-temp=yes --lammps-pot-lib="./" -f *.cif

• MOPAC

  cif2cell -p mopac --setup-all --mopac-type=PM6 --mopac-charge=0 --mopac-run-type="opt+cis" -f *.cif

• DFTB+

  cif2cell -p dftb --no-reduce --setup-all --dftb-htype=GFN1-xTB --dftb-runtype=md --dftb-dt=0.25 --dftb-temperature=300 --dftb-pressure=1.0 --dftb-Nsteps=4000 --lammps-pot-lib="./" -f *.cif

• FDMNES

  cif2cell -p fdmnes --no-reduce -f *.cif

• PWscf

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/username/PSLibrary' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.48 --pwscf-brav --pwscf-spin=no --run-calc --pwscf-run-type=scf -f *.cif

  export PWscf_PAWLIB=$HOME/PSLibrary

  Number of k point * lattice constant = 10 - 13 Angstrom for SCF calculation. This range is from --k-resolution=23.1415/13=0.48 to --k-resolution=23.1415/10=0.62. The default setting is --k-resolution=0.2. This setting is enough to calculate DOS. Hence, nk(DOS) = nk(SCF)*2. nk = number of k point. This code set automatically [--k-resolution value / 2] for DOS calculation.

• PWscf (TDDFT)

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/username/PSLibrary' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.48 --pwscf-run-type=tddft --pwscf-spin=no --run-calc -f *.cif

  If you would calculate it with gamma point only for B3LYP or HSE, set large value to --k-resolution, e.g. --k-resolution=10 for molecule.

• PWscf (EELS)

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/username/PSLibrary' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.48 --pwscf-run-type=eels --pwscf-spin=no --run-calc -f *.cif

  If you would calculate it with gamma point only for B3LYP or HSE, set large value to --k-resolution, e.g. --k-resolution=10 for molecule.

• PWscf (PWcond)

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/username/PSLibrary' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.48 --pwscf-run-type=lead --run-calc -f *.cif

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/username/PSLibrary' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.48 --pwscf-run-type=scat --run-calc -f *.cif

• PWscf (NEB)

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/username/PSLibrary' --setup-all --k-resolution=0.48 --pwscf-bin-dir=$HOME/q-e-qe-*/bin --pwscf-run-type=neb-start --pwscf-neb-ems=bc2 --pwscf-neb-mu=0.0 --pwscf-neb-bias-voltage=0.5 -f start-structure.cif

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/' --setup-al --pwscf-run-type=neb-end --pwscf-neb-ems=bc2 --pwscf-neb-mu=0.0 --pwscf-neb-bias-voltage=0.5 --run-calc -f end-structure.cif

• PWscf (relax for interface)

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/student/psl' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.40 --pwscf-run-type=opt --pwscf-fix-all-pos -f *.cif

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/student/psl' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.40 --pwscf-run-type=relax --pwscf-fix-atomic-species="Pd" -f *.cif

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/student/psl' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.40 --pwscf-run-type=opt --pwscf-fix-all-pos --pwscf-move-atomic-species="Pd" -f *.cif

  cif2cell -p pwscf --pwscf-pseudo-PSLibrary-libdr='/home/student/psl' --pwscf-bin-dir=$HOME/q-e-qe-6.3/bin --setup-all --k-resolution=0.40 --pwscf-run-type=opt --pwscf-fix-all-pos --pwscf-move-atomic-species="Pd" --pwscf-space-group -f *.cif

• Abinit (Phonon)

  cif2cell -p abinit --abinit-pseudo-JTH-libdr='/home/student/jth' --setup-all --abinit-run-type=phonon --k-resolution=0.4 --abinit-q-resolution=0.8 -f *.cif

• Akai-KKR (brvtyp mode) ("cpa2002v009c.tar.gz" around 2015)

  cif2cell -p akaikkr --setup-all --akaikkr-brvtyp --akaikkr-collect-atoms --akaikkr-run-level=2 -f *.cif

• FDMNES (TDDFT, L23 edge, Photon energy, Green function, Eimag 0.2, LDA, DOS, Molecular)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-run-type=tddft --fdmnes-edge=L23 --fdmnes-photon-energy --fdmnes-green --fdmnes-eimag=0.2 --fdmnes-dos --fdmnes-dft-type=LDA --fdmnes-molecular --run-calc -f *.cif

• FDMNES (XES, Photon energy, 1.0 core hole, Green function, Eimg 0.2, Crystal structure, auto run)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-run-type=xes --fdmnes-photon-energy --fdmnes-core-hole=1.0 --fdmnes-green --fdmnes-eimag=0.2 --run-calc -f *.cif

• FDMNES (XANES, FDM, Crystal structure, 0.5 core hole, DOS for all atom, Crystal structure, auto run)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-photon-energy --fdmnes-core-hole=0.5 --fdmnes-dos-all --run-calc -f *.cif

• FDMNES (Photon energy, 1.0 core hole, Green function, Eimag 0.2, DOS for all atom, LDA, auto run, DAFS, Crystal structure)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-photon-energy --fdmnes-core-hole=1.0 --fdmnes-green --fdmnes-eimag=0.2 --fdmnes-dos-all --fdmnes-dft-type=LDA --run-calc --fdmnes-run-type=dafs -f *.cif

• FDMNES (Photon energy, 1.0 core hole, Green function, Eimag 0.2, DOS for all atom, LDA, auto run, RXS, Crystal structure)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-photon-energy --fdmnes-core-hole=1.0 --fdmnes-green --fdmnes-eimag=0.2 --fdmnes-dos-all --fdmnes-dft-type=LDA --run-calc --fdmnes-run-type=rxs -f *.cif

• FDMNES (Photon energy, 1.0 core hole, Green function, Eimag 0.2, DOS_comp, LDA, auto run, Optic, Crystal structure)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-photon-energy --fdmnes-core-hole=1.0 --fdmnes-green --fdmnes-eimag=0.2 --fdmnes-dos-comp --fdmnes-dft-type=LDA --run-calc --fdmnes-run-type=opitc -f *.cif

• FDMNES (Photon energy, 1.0 core hole, Green function, Eimag 0.2, DOS_comp, LDA, auto run, Circular, Crystal structure)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-photon-energy --fdmnes-core-hole=1.0 --fdmnes-green --fdmnes-eimag=0.2 --fdmnes-dos-comp --fdmnes-dft-type=LDA --run-calc --fdmnes-run-type=circular -f *.cif

• FDMNES (Photon energy, 1.0 core hole, Green function, Eimag 0.2, DOS for all atom, LDA, auto run, Dichroism, Crystal structure)

  cif2cell -p fdmnes --no-reduce --setup-all --fdmnes-dir=$HOME/fdmnes --fdmnes-photon-energy --fdmnes-core-hole=1.0 --fdmnes-green --fdmnes-eimag=0.2 --fdmnes-dos-all --fdmnes-dft-type=LDA --run-calc --fdmnes-run-type=dichroism -f *.cif

• VASP

  cif2cell -p vasp --vasp-format=5 --vasp-encutfac=1.0 --vasp-cartesian-lattice-vectors --setup-all -f *.cif

  export VASP_PAWLIB = $HOME/vasp.5.4.1/potpaw_PBE

• Abinit

  cif2cell -p abinit --setup-all -f *.cif

  export ABINIT_PAWLIB = $HOME/JTH

• PWscf

  cif2cell -p pwscf --setup-all -f *.cif

  export PWscf_PAWLIB = $HOME/PSLibrary

• This project (modified version) is/was partially supported by the following :
  • meguREnergy Co., Ltd.
  • ATSUMITEC Co., Ltd.

• 1.2.47+PyCifRW-4.4.5: Python 3.10 version (test version) could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.39+PyCifRW-4.4: add FDMNES option. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.38+PyCifRW-4.4: modified k-point settings for PWscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.37+PyCifRW-4.4: modified phonon option and k mesh (dos) for Abinit. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.36+PyCifRW-4.4: add --abinit-run-type option for Phonon (trial version). could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.35+PyCifRW-4.4: add --abinit-k-point-even=yes and --elk-k-point-even=yes option (default: yes) for Abinit and Elk. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.34+PyCifRW-4.4: modified DFT+U option. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.33+PyCifRW-4.4: add --pwscf-k-point-even=yes option (default: yes) for PWscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.32+PyCifRW-4.4: add NEB option for PWscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.31+PyCifRW-4.4: add tddft and eels option for PWscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.30+PyCifRW-4.4: add pwcond-lead and pwcond-scat option for PWscf (PWcond calulation). could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.29+PyCifRW-4.4: add cif2cell-lammps code could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.28+PyCifRW-4.4: modified input_dft part for PWscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.27+PyCifRW-4.4: add LDA+U option for PWscf, Abinit, Elk, OpenMX and VASP. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.26+PyCifRW-4.4: refine k-point setting for band dispersion on PWscf. (under construction) could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.25+PyCifRW-4.4: add --run-calc option. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.24+PyCifRW-4.4: add ibrav option for PWscf. get number of cup (cif2cell.py) could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.23+PyCifRW-4.4: show calculation command. make automatically dos.in file for PWscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.22+PyCifRW-4.4: show calculation command. make automatically bands.in and bands.plot file for PWscf. Please, input ef value from picene.scf.out file (fermi energy). [the Fermi energy is X.XXXXX ev] on *.scf.out. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.21+PyCifRW-4.4: add run-type option for pwscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.20+PyCifRW-4.4: bug fix. reading pslibrary (H atom) for pwscf. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.19+PyCifRW-4.4: replace PycifRW-3.3 to PyCifRW-4.4. could use new verion cif (e.g. new version vesta in 2018-2019)

• 1.2.19: automatically set energy cutoff from pseudo-potential to Abinit and PWscf input files.

• 1.2.18: bug fix making k-point setting. Add vasp option (run type setting) (test version). Set total energy convergence to 1 meV/atom for Elk, Abinit, PWscf, OpenMX and VASP. (change part: ESPInterfaces.py)

• 1.2.17: support OpenMX (test version), bug fix Abinit part. (test version) (change part: cif2cell, ESPInterfaces.py, utils.py, elementdata.py)

• 1.2.16: potential file option for Elk, Abinit(ONCVPSP, GBRV, JTH), PWscf(GBRV, PSLibrary(0.3.1 and 1.0.0)) (test version) (change part: cif2cell, ESPInterfaces.py)

• 1.2.15: potential file option for Elk, Abinit(ONCVPSP, GBRV, JTH), PWscf(GBRV, PSLibrary-0.3.1) (test version). (change part: cif2cell, ESPInterfaces.py)

• 1.2.14: modified input file for abinit and elk. Add run option (scf, dos, band, etc.) (test version).
  (change part: cif2cell, ESPInterfaces.py)

• 1.2.13: support Akai-KKR option (test version). (change part: cif2cell, ESPInterfaces.py)

• 1.2.12: support Akai-KKR (test version). (change part: cif2cell, ESPInterfaces.py)

• 1.2.11: mofified incarfile on cif2cell and modified VASP(INCAR) and PWscf inputf file on ESPInterfaces.py. (change part: cif2cell, ESPInterfaces.py)