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* *
* Aflow STEFANO CURTAROLO - Duke University 2003-2021 *
* High-Throughput ab-initio Materials Discovery *
* *
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LATEST VERSION OF THE FILE: materials.duke.edu/AFLOW/README_AFLOW_CCE.TXT
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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
Please cite this article 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 Prints the results of the full CCE anaysis, i.e. cation coordination
numbers, oxidation numbers, and CCE corrections and formation enthalpies,
for the given 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