******************************************************************************** * * * Aflow STEFANO CURTAROLO - Duke University 2003-2021 * * High-Throughput ab-initio Materials Discovery * * * ******************************************************************************** LATEST VERSION OF THE FILE: materials.duke.edu/AFLOW/README_AFLOW_CCE.TXT ******************************************************************************** Written by Rico Friedrich, Corey Oses, and Marco Esters, 2018-2021 USER INSTRUCTIONS: (i) GENERAL INFORMATION: Implementation to obtain corrected DFT formation enthalpies based on the coordination corrected enthalpies (CCE) methodology described in: Friedrich et al., Coordination corrected ab initio formation enthalpies, npj Comput. Mater. 5, 59 (2019); https://doi.org/10.1038/s41524-019-0192-1 and Friedrich et al., Automated coordination corrected enthalpies with AFLOW-CCE, Phys. Rev. Mater. 5, 043803 (2021) https://doi.org/10.1103/PhysRevMaterials.5.043803 Please cite these articles when using this method and/or this implementation. The corrections depend on the number of cation-anion bonds and on the cation oxidation state. The current implementation requires a structure file as input and will return the CCE corrections for the DFT formation enthalpies for PBE, LDA and SCAN if the oxidation numbers can be determined. The oxidation numbers can be provided by the user or can be automatically determined from the structure using Allen electronegativities. In addition, the user can provide precalculated DFT formation enthalpies for PBE, LDA and SCAN and the implementation will directly calculate and return the CCE formation enthalpies at both 298.15 and 0 K. If DFT formation enthalpies are provided as additional input, the functionals corresponding to those enthalpies are required. They need to be given in the same sequence as the precalculated DFT formation enthalpies they correspond to. However, when you specify only one formation enthalpy, no functional is required as it is assumed to be PBE (default). Details for the options available are explained in the following. (ii) AVAILABLE OPTIONS: --cce Prints user instructions. --cce=STRUCTURE_FILE_PATH Provide the path to the structure file. It can be in any structure format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF. For VASP, a VASP5 POSCAR is required or if a VASP4 POSCAR is used, the species must be written on the right side next to the coordinates for each atom just as for the EXAMPLE INPUT STRUCTURE FOR ROCKSALT MgO below. --enthalpies_formation_dft=|--dfte= Provide a comma separated list of precalculated DFT formation enthalpies, they are assumed to be: (i) negative for compounds lower in enthalpy than the elements, (ii) in eV/cell. Currently, corrections are available for PBE, LDA and SCAN. --functionals=|--func=|--functional= Provide a comma separated list of functionals for which corrections should be returned. If used together with --enthalpies_formation_dft, the functionals must be in the same sequence as the DFT formation enthalpies they correspond to. Available functionals are: (i) PBE, (ii) LDA or (iii) SCAN. Default: PBE (if only one DFT formation enthalpy is provided). --oxidation_numbers=|--ox_nums=|--oxidation_number= Provide as a comma separated list the oxidation numbers. It is assumed that: (i) one is provided for each atom of the structure and (ii) they are in the same sequence as the corresponding atoms in the provided structure file. --get_cce_correction|--get_cce_cor|--poscar2cce < STRUCTURE_FILE_PATH Determines the CCE corrections for the structure in STRUCTURE_FILE_PATH. It can be in any structure format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF. For VASP, a VASP5 POSCAR is required or if a VASP4 POSCAR is used, the species must be written on the right side next to the coordinates for each atom just as for the EXAMPLE INPUT STRUCTURE FOR ROCKSALT MgO below. --get_oxidation_numbers|--get_ox_nums|--poscar2ox_nums < STRUCTURE_FILE_PATH Determines the oxidation numbers for the structure in STRUCTURE_FILE_PATH. It can be in any structure format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF. For VASP, a VASP5 POSCAR is required or if a VASP4 POSCAR is used, the species must be written on the right side next to the coordinates for each atom just as for the EXAMPLE INPUT STRUCTURE FOR ROCKSALT MgO below. --get_cation_coordination_numbers|--get_cation_coord_nums|--poscar2cation_coord_nums < STRUCTURE_FILE_PATH Determines the number of anion neighbors for each cation for the structure in STRUCTURE_FILE_PATH. It can be in any structure format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF. For VASP, a VASP5 POSCAR is required or if a VASP4 POSCAR is used, the species must be written on the right side next to the coordinates for each atom just as for the EXAMPLE INPUT STRUCTURE FOR ROCKSALT MgO below. --print= Obtain output in standard format (--print=out), json (--print=json), or as a python script (--print=python). Default: out. (iii) EXAMPLE INPUT STRUCTURE FOR ROCKSALT MgO: Mg1O1 [FCC,FCC,cF8] (STD_PRIM doi:10.1 [FCC,FCC,cF8] (STD_PRIM doi:10.1016/j.commatsci.2010.05.010) 1.224745 0.00000000000000 1.73568248770103 1.73568248770103 1.73568248770103 0.00000000000000 1.73568248770103 1.73568248770103 1.73568248770103 0.00000000000000 Mg O 1 1 Direct(2) [A1B1] 0.00000000000000 0.00000000000000 0.00000000000000 Mg 0.50000000000000 0.50000000000000 0.50000000000000 O (iv) EXAMPLE COMMANDS: Assuming that AFLOW is in your PATH and you saved the above example structure file for MgO in the current directory as POSCAR, the following commands can be executed: aflow --cce=POSCAR --enthalpies_formation_dft=-5.434,-6.220,-6.249 --functionals=PBE,LDA,SCAN This will give you the CCE corrections and CCE formation enthalpies for PBE, LDA, and SCAN for MgO. aflow --cce=POSCAR --enthalpies_formation_dft=-6.220 --functionals=LDA This gives you only the CCE corrections and CCE formation enthalpies for LDA. aflow --cce=POSCAR --enthalpies_formation_dft=-5.434 This gives you the CCE corrections and CCE formation enthalpies for PBE with a warning that PBE is assumed as functional. aflow --cce=POSCAR This gives you the CCE corrections for PBE, LDA, and SCAN and a rough guess of the formation enthalpy based on experimental formation enthalpies per bond. aflow --cce=POSCAR --oxidation_numbers=2,-2 Oxidation numbers for each atom can also be provided as input. (v) AVAILABLE CORRECTIONS: Currently, corrections are available for: OXIDES Ag +1 from Ag2O Al +3 from Al2O3 As +5 from As2O5 B +3 from B2O3 Ba +2 from BaO Be +2 from BeO Bi +3 from Bi2O3 Ca +2 from CaO Cd +2 from CdO Co +2 from CoO Cr +3 from Cr2O3 Cr +6 from CrO3 Cs +1 from Cs2O Cu +1 from Cu2O Cu +2 from CuO Fe +2 from FeO Fe +3 from Fe2O3 Ga +3 from Ga2O3 Ge +4 from GeO2 Hf +4 from HfO2 Hg +2 from HgO In +3 from In2O3 Ir +4 from IrO2 K +1 from K2O Li +1 from Li2O Mg +2 from MgO Mn +2 from MnO Mn +4 from MnO2 Mo +4 from MoO2 Mo +6 from MoO3 Na +1 from Na2O Nb +2 from NbO Ni +2 from NiO Os +4 from OsO2 Os +8 from OsO4 Pb +2 from PbO Pb +4 from PbO2 Pd +2 from PdO Rb +1 from Rb2O Re +4 from ReO2 Re +6 from ReO3 Rh +3 from Rh2O3 Ru +4 from RuO2 Sb +3 from Sb2O3 Sb +5 from Sb2O5 Sc +3 from Sc2O3 Se +4 from SeO2 Si +4 from SiO2(al-quartz) Sn +2 from SnO Sn +4 from SnO2 Sr +2 from SrO Te +4 from TeO2 Ti +2 from TiO Ti +3 from Ti2O3 Ti +4 from TiO2(rutile) Tl +1 from Tl2O Tl +3 from Tl2O3 V +2 from VO V +3 from V2O3 V +4 from VO2 V +5 from V2O5 W +4 from WO2 W +6 from WO3 Y +3 from Y2O3 Zn +2 from ZnO Zr +4 from ZrO2 for per- and superoxides O2 -2 from Li2O2 O2 -1 from KO2 NITRIDES Al +3 from AlN B +3 from BN Ca +2 from Ca3N2 Li +1 from Li3N Zn +2 from Zn3N2 Be +2 from Be3N2 Cr +3 from CrN Ga +3 from GaN Hf +3 from HfN In +3 from InN La +3 from LaN Mg +2 from Mg3N2 Nb +3 from NbN Sc +3 from ScN Si +4 from Si3N4 Ta +3 from TaN Ti +3 from TiN V +3 from VN Y +3 from YN Zr +3 from ZrN