This section has descriptions of files and parameters, required for the package.

Working folder¶

When initializing the calculations, the contents of the working folder would resemble the following:

.
├── batch.header (content of batch jobmission script except commands)
├── config.json (Main input file)
├── input.in (Main control file for calculations)
├── mpid-list.in (Files to stored {id} and {name} of compounds before download process)
├── mpid.in (after download process)
├── run-vasp.sh (VASP submission script)
├── run-scf.sh, run-elph.sh, run-q2r.sh, ... etc (QE submission scripts)
├── pp (QE pseudopotentials)
│   ├── B.upf
│   └── Mg.upf
├── Rmp-763-B2Mg1 (VASP input files stored here)
│   └── relax
│       ├── INCAR
│       ├── KPOINTS
│       ├── POSCAR
│       └── POTCAR
├── scf_dir (QE input files stored here)
│   └── scf-mp-763.in
├── Rmp-763-B2Mg1 (unlike VASP, QE folder created only after process = 1)
│   └── relax
│       └── scf.in
└── vasp.in (File to update VASP INCAR file)

batch.header¶

This file is used to generate job submission scripts for different calculations.

#!/bin/bash

## SBATCH commands

#SBATCH ....

#module load ....

These lines constitute standard content for any batch submission script.

config.json¶

This JSON file serves as the main input file of the package. It contains a dictionary with various keys to configure different aspects of the package’s functionality.

JSON: {
    "name": "John",
    "age": 30,
    "is_student": false,
    "favorite_fruits": ["apple", "banana", "orange"],
    "address": null
}

Python: {
    "name": "John",
    "age": 30,
    "is_student": False,
    "favorite_fruits": ["apple", "banana", "orange"],
    "address": None
}

In JSON, boolean values are represented as "true" and "false", while in Python they are represented as True and False.

JSON uses "null" to represent the absence of value, whereas Python uses None.

Lists are represented with square brackets [] in both JSON and Python, and they contain comma-separated values.

{
  "job_script": {
  "batch":"batch.header",
  "which_calc": "qe",
  "parallel_command": "mpirun",
  "nproc": "1",
  "command_list":["scf","elph"],
  "command_combine":false,
  "calc_visible_with":"id"
  },
  "mpi_key": {
    "API_KEY": {
      "key": "use_your_API_KEY"
    }
  },
  "download": {
    "mode": "chemsys",
    "element": {
      "metal": false,
      "FE": false,
      "thermo_stable": false,
      "exclude": ["Lu"],
      "ntype": [1, 2],
      "elm": ["B"],
      "prop": ["material_id", "formula_pretty", "structure", "formation_energy_per_atom", "band_gap", "energy_above_hull", "total_magnetization", "ordering", "total_magnetization_normalized_formula_units", "num_magnetic_sites", "theoretical", "nsites"],
      "ordering": "NM",
      "nsites": 10,
      "spacegroup": null
    },
    "inp": {
      "start": 1,
      "end": 20,
      "nkpt": 200,
      "evenkpt": false,
      "plot": "phband",
      "calc": "VASP",
      "use_cif2cell": false,
      "kpath_pbc": null
    },
    "chemsys": {
      "entries": ["Cr", "Pd", "P"],
      "size_constraint": 60,
      "ntype_constraint": 4,
      "must_include": ["Cr","Pd","P"],
      "FE": false,
      "thermo_stable": 0.08,
      "metal": false,
      "magnetic": true,
      "spacegroup": null
    },
    "oqmd": {
      "limit": 400,
      "entries": ["Mg", "B"],
      "size_constraint": 60,
      "ntype_constraint": 4,
      "must_include": [],
      "metal": false,
      "magnetic": true,
      "spacegroup": null,
      "thermo_stable": true,
      "FE": true,
      "prop": ["composition", "spacegroup", "volume", "band_gap", "stability"]
      },
    "aflow": {
        "elm": ["B"],
        "nelm": 5,
        "nsites": 10,
        "metal": true,
        "FE": true,
        "spacegroup": null,
        "limit": 5000,
        "filter": false,
        "prop": ["spacegroup_relax", "Pearson_symbol_relax"]
        ]
    }
  },
  "conv_test": {
     "param": "ecut",
     "ecut": [400, 500, 600],
     "kpoint": [[6, 6, 6], [12, 12, 12], [18, 18, 18]]
    },
  "magmom": {
    "magmom": {
      "Cr": 5,
      "Pd": 0,
      "P": 0
    },
    "type":"",
    "saxis":[[0,0,1],[1,0,0],[1,1,0],[1,1,1]],
    "order": ["ferromagnetic", "antiferromagnetic", "ferrimagnetic_by_motif"]
  },
  "pseudo": {
    "pot": {
      "H":"H",
      "He":"He",
      "Li":"Li_sv",
      "Be":"Be",
      "B":"B",
      "C":"C",
      "N":"N",
      "O":"O",
      "F":"F",
      "Ne":"Ne",
      "Na":"Na_pv",
      "Mg":"Mg",
      "Al":"Al",
      "Si":"Si",
      "P":"P",
      "S":"S",
      "Cl":"Cl",
      "Ar":"Ar",
      "K":"K_sv",
      "Ca":"Ca_sv",
      "Sc":"Sc_sv",
      "Ti":"Ti_sv",
      "V":"V_sv",
      "Cr":"Cr_pv",
      "Mn":"Mn_pv",
      "Fe":"Fe",
      "Co":"Co",
      "Ni":"Ni",
      "Cu":"Cu",
      "Zn":"Zn",
      "Ga":"Ga_d",
      "Ge":"Ge_d",
      "As":"As",
      "Se":"Se",
      "Br":"Br",
      "Kr":"Kr",
      "Rb":"Rb_sv",
      "Sr":"Sr_sv",
      "Y":"Y_sv",
      "Zr":"Zr_sv",
      "Nb":"Nb_sv",
      "Mo":"Mo_sv",
      "Tc":"Tc_pv",
      "Ru":"Ru_pv",
      "Rh":"Rh_pv",
      "Pd":"Pd",
      "Ag":"Ag",
      "Cd":"Cd",
      "In":"In_d",
      "Sn":"Sn_d",
      "Sb":"Sb",
      "Te":"Te",
      "I":"I",
      "Xe":"Xe",
      "Cs":"Cs_sv",
      "Ba":"Ba_sv",
      "La":"La",
      "Ce":"Ce",
      "Pr":"Pr_3",
      "Nd":"Nd_3",
      "Pm":"Pm_3",
      "Sm":"Sm_3",
      "Eu":"Eu_2",
      "Gd":"Gd_3",
      "Tb":"Tb_3",
      "Dy":"Dy_3",
      "Ho":"Ho_3",
      "Er":"Er_3",
      "Tm":"Tm_3",
      "Yb":"Yb_2",
      "Lu":"Lu_3",
      "Hf":"Hf_pv",
      "Ta":"Ta_pv",
      "W":"W_sv",
      "Re":"Re",
      "Os":"Os",
      "Ir":"Ir",
      "Pt":"Pt",
      "Au":"Au",
      "Hg":"Hg",
      "Tl":"Tl_d",
      "Pb":"Pb_d",
      "Bi":"Bi_d",
      "Po":"Po_d",
      "At":"At",
      "Rn":"Rn",
      "Fr":"Fr_sv",
      "Ra":"Ra_sv",
      "Ac":"Ac",
      "Th":"Th",
      "Pa":"Pa",
      "U":"U",
      "Np":"Np",
      "Pu":"Pu",
      "Am":"Am",
      "Cm":"Cm"
     },
    "PSEUDO": {
      "H": 60,
      "Li": 40,
      "Be": 40,
      "N": 60,
      "F": 45,
      "Na": 40,
      "Mg": 30,
      "Al": 30,
      "Si": 30,
      "P": 30,
      "S": 35,
      "Cl": 40,
      "K": 60,
      "Ca": 30,
      "Sc": 40,
      "Ti": 35,
      "V": 35,
      "Cr": 40,
      "Mn": 65,
      "Fe": 90,
      "Co": 45,
      "Ni": 45,
      "Cu": 55,
      "Zn": 40,
      "Ga": 70,
      "Ge": 40,
      "As": 35,
      "Br": 30,
      "Rb": 30,
      "Sr": 30,
      "Y": 35,
      "Zr": 30,
      "Nb": 40,
      "Mo": 35,
      "Tc": 30,
      "Ru": 35,
      "Rh": 35,
      "Pd": 45,
      "Ag": 50,
      "Cd": 60,
      "In": 50,
      "Sn": 60,
      "Sb": 40,
      "Te": 30,
      "I": 35,
      "Cs": 30,
      "Ba": 30,
      "La": 40,
      "Hf": 50,
      "Ta": 45,
      "W": 30,
      "Re": 30,
      "Os": 40,
      "Ir": 55,
      "Pt": 35,
      "Hg": 50,
      "Tl": 50,
      "Pb": 40,
      "Bi": 45,
      "Po": 30,
      "At": 30,
      "Rn": 30,
      "Fr": 30,
      "Ra": 30,
      "Ac": 30,
      "Th": 30,
      "Pa": 30,
      "U": 30,
      "Np": 30,
      "Pu": 30,
      "Am": 30,
      "Cm": 30,
      "B": 35,
      "C": 45
    }
  },
  "substitute": {
    "mode": 2,
    "elm": "Cr",
    "sub": {
      "Cr": 0,
      "Al": 1
    },
    "new_sub": {
      "Cr": "Fe",
      "Pd": "Pd",
      "I": "I"
    }
  },
  "pwscf_in": {
    "magnetic": false,
    "control": {
      "calculation": "vc-relax",
      "nstep": 300,
      "restart_mode": "from_scratch",
      "pseudo_dir": "../../pp/",
      "outdir": "./",
      "tprnfor": true,
      "tstress": true,
      "etot_conv_thr": 1e-05,
      "forc_conv_thr": 0.0001
    },
    "system": {
      "smearing": "gauss",
      "occupations": "smearing",
      "degauss": 0.02
    },
    "electrons": {
      "diagonalization": "david",
      "mixing_mode": "plain",
      "mixing_beta": 0.7,
      "conv_thr": 1e-16,
      "electron_maxstep": 300
    }
  },
  "strain": [-0.01, -0.005, 0.005, 0.01],
  "wanniertools_input": {
    "tb_file": {
      "Hrfile": "'ex_hr.dat'",
      "Package": "'QE'"
    },
    "control": {
      "BulkBand_calc": "T",
      "BulkFS_calc": "F",
      "BulkGap_cube_calc": "F",
      "BulkGap_plane_calc": "F",
      "FindNodes_calc": "F",
      "SlabBand_calc": "F",
      "WireBand_calc": "F",
      "Dos_calc": "F",
      "JDos_calc": "F",
      "SlabSS_calc": "F",
      "SlabArc_calc": "F",
      "SlabQPI_calc": "F",
      "SlabSpintexture_calc": "F",
      "wanniercenter_calc": "F",
      "Z2_3D_calc": "F",
      "Chern_3D_calc": "F",
      "WeylChirality_calc": "F",
      "BerryPhase_calc": "F",
      "BerryCurvature_calc": "F",
      "AHC_calc": "F"
    },
    "parameters": {
      "E_arc": "0.0",
      "Eta_Arc": "0.001",
      "OmegaMin": "0.0",
      "OmegaMax": "0.0",
      "OmegaNum": "100",
      "Nk1": "10",
      "Nk2": "10",
      "Nk3": "10",
      "NP": "2",
      "Gap_threshold": "0.1"
    },
    "system": {
      "NSlab": "10",
      "NSlab1": "1",
      "NSlab2": "1",
      "NumOccupied": "1",
      "SOC": "1",
      "E_FERMI": "0.0",
      "Bx": "0.0",
      "By": "0.0",
      "Bz": "0.0",
      "surf_onsite": "0.0"
    },
    "surface": {
      "surface": [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
      "KPATH_SLAB": {},
      "KPLANE_SLAB": {},
      "EFFECTIVE_MASS": "0.0",
      "SELECTED_ATOMS": {}
    }
  },
 "kptden": 0.025,
 "chull_cutoff": 0.04,
 "kpt_opt": true,
 "elph_mode": "serial",
 "plot": {
    "xlim": null,
    "ylim" : [-5, 5],
    "atomproj": null,
    "bandproj": {
      "proj_type": "element-orbital",
      "proj": {"Zr": "dxz", "Pd": "dxz"},
      "colormap": "Reds"
    }
}

job_script: Information about creating job submission scripts. here
mpi_key: Materials Project API key. If not provided, data extraction from the Materials Project is not possible. However, extraction from the OQMD and AFLOW databases is still accessible without any key. here
download: Information required for downloading and preparing inputs. here
conv_test: Parameters for performing convergence tests.
magmom: Specifies magnetic moment configurations. This key is essential for magnetic calculations. here
pseudo: Pseudopotential file, with two subkeys: pot for VASP and PSEUDO for QE. here
substitute: Parameters for preparing input files with substitution. here
pwscf_in: Input parameters for Quantum Espresso (QE). here
strain: Strain inputs, useful for elastic properties calculations.
wanniertools_input: Input parameters for WannierTools. here
kptden: Kpoint density.
chull_cutoff: It controls the display of thermodynamically unstable systems in convexhull plot. It can be logical or value in eV/atom. Default is false, doesn’t show systems with energy above hull (EBH) larger than zero. If true, it shows all the systems in consideration. If it has the value 0.04, it shows the systems with EBH less than 0.04 eV/atom.
kpt_opt: Flag for generating KPOINTS_OPT file to perform band structure in VASP
elph_mode: Parameter for performing DFPT calculations in various modes in QE.
- serial: Serial mode (Default)
- parallel_q: Parallel over q-points
- parallel_irr: Parallel over q-points and irreducible representations
  - only_init: Use this key first to obtain irreducible representations.
plot: Plot variables, especially, x-limit (list of 2 numbers) and y-limit.

job_script¶

"job_script": {
  "batch": "batch.header",
  "which_calc": "qe",
  "parallel_command": "mpirun",
  "nproc": "1",
  "command_list": ["scf", "elph"],
  "command_combine":false,
  "calc_visible_with":"id"}

batch: Usual batch script
which_calc: Type of calculations. Available options: 'QE' or 'qe', 'VASP' or 'vasp', 'wannier', 'epw', etc.
parallel_command: Parralization command. Available options: mpirun, srun, …
nproc: Numper of processer to use.
command_list: List of command to execute.
- QE commands:
  - Work with "which_calc":"qe" or "QE"
  - scf: scf calculations, pw.x < scf.in > scf.out
  - band: band calculations, pw.x < scf-band.in > nscf-band.out
  - bandp: band processing, bands.x < band.in > band.out
  - dos: Density of States (DOS) calculations, pw.x < scf-dos.in > scf-dos.out
  - dosp: DOS postprocessing, dos.x < dos.in > dos.out
  - elph: DFPT electron-phonon coupling (EPC) calculations, ph.x < elph.in > elph.out
  - q2r: Converting force constant in reciprocal to real space, q2r.x < q2r.in > q2r.out
  - matdyn: Calculating phonon frequencies in generic q points, matdyn.x < matdyn.in > matdyn.out
  - matdyn-dos: Calculating phonon DOS, matdyn.x < matdyn-dos.in > matdyn-dos.out
  - lambda: Calculating EPC strength constant, lambda. lambda.x < lambda.in > lambda.out
  - pdos: Calculating partial DOS, projwfc.x < pdos.in > pdos.out
- VASP commands:
  - Work with "which_calc":"vasp" or "VASP"
  - vasp: Performing VASP calculations, vasp_std. Modify the code in generate_submission.py as needed, and then proceed to reinstall the package if you require commands other than vasp_std.
  - wannier: Performing WANNIER90 calculations with VASP. This add wannier90.x wannier90 in batch.header file.

ifermi: Utilizing ifermi package to compute Fermi surface related properties, 'ifermi'. Please locate the ifermi.json file in the utility/input_files directory and move it to the current working directory.
Note: Please checkout original documentation of the ifermi package. Use true or false for keys that don’t have values. When set to true, the key will be included as a flag in the command.
{
    "info": {
        "--filename": "vasprun.xml",
        "--mu": 0.0,
        "--wigner": false,
        "--interpolation-factor": 8.0,
        "--property": "velocity",
        "--projection-axis": "0 0 1",
        "--decimate-factor": 0.8,
        "--smooth": false,
        "--norm": false,
        "--precision": 4
    },
    "plot": {
        "--filename": "vasprun.xml",
        "--mu": 0.0,
        "--wigner": false,
        "--interpolation-factor": 8.0,
        "--property": "velocity",
        "--projection-axis": "0 0 1",
        "--decimate-factor": 0.8,
        "--smooth": false,
        "--output": "output.png",
        "--symprec": 0.001,
        "--azimuth": 45.0,
        "--elevation": 35.0,
        "--type": "plotly",
        "--color-property": false,
        "--property-colormap": "viridis",
        "--vector-property": false,
        "--vector-colormap": "plasma",
        "--vector-spacing": 0.2,
        "--cmin": 0.0,
        "--cmax": 1.0,
        "--vnorm": 1.0,
        "--scale-linewidth": false,
        "--hide-surface": false,
        "--plot-index": 1,
        "--hide-labels": false,
        "--hide-cell": false,
        "--spin": "up",
        "--slice": "0.5 0.5 0.5 0.0",
        "--scale": 4
    }
}
WANNIER commands:

Work with "which_calc":"wannier" or "WANNIER"

scf: QE scf command, pw.x < scf.in > scf.out

nscf: QE nonscf command, pw.x < scf.in > nscf.out

wannier_prepare: Preparing for wannier calculations, wannier90.x -pp ex

pw2wannier90: Generating input files for WANNIER90 from QE output, pw2wannier90.x -in pw2wan.in > pw2wan.out

wannier_band: Performing wannierization, wannier90.x ex

EPW commands:

Work with "which_calc":"epw" or "EPW"

scf: QE scf command, pw.x < scf.in > scf.out

ph: QE phonon calculations, ph.x < elph.in > elph.out

proj: QE nonscf calculations to run with projwfc.x, pw.x < nscf-proj.in > nscf-proj.out

epw_nscf: QE nonscf calculations for EPW calculations, pw.x < nscf_epw.in > nscf_epw.out

epw: EPW calculations, epw.x -npools -nproc -i epw.in > epw.out

command_combine: When set to true, commands will be consolidated into one file named run-{last_command}.sh, following the order specified in the command_list. Otherwise, each command will be written to separate files named run-{command}.sh.
calc_visible_with: It determines the naming convention for the job submission scripts after submission. Available options include "id", "name", or "id-name". If not provided, the scripts will be named simply as run-{command}.sh files for QE, and run.sh for VASP calculations.
- id: Materials_id, CALC_VISIBLE_WITH_ID file created.
- name: Compound_name, CALC_VISIBLE_WITH_NAME file created.
- id-name: Materials_id-Compound_name, CALC_VISIBLE_WITH_ID-NAME file created.
- If you prefer not to display the compounds information, please provide an empty string "".

mpi_key¶

Find your materials project key here, under API key section.

https://next-gen.materialsproject.org/api#api-key

download¶

It has a dictionary of the form.

"download": {
    "mode": "element",
    "element": {
      "metal": false,
      "FE": false,
      "thermo_stable": false,
      "exclude": ["Lu"],
      "ntype": [1, 2],
      "elm": ["B"],
      "prop": ["material_id", "formula_pretty", "structure", "formation_energy_per_atom", "band_gap", "energy_above_hull", "total_magnetization", "ordering", "total_magnetization_normalized_formula_units", "num_magnetic_sites", "theoretical", "nsites"],
      "ordering": "NM",
      "nsites": 10,
      "spacegroup": null},
    "inp": {
      "start": 1,
      "end": 2,
      "nkpt": 200,
      "evenkpt": false,
      "plot": "phband",
      "calc": "QE",
      "use_cif2cell": false,
      "kpath_pbc": null},
    "chemsys": {
      "entries": ["Fe", "Pd", "I"],
      "size_constraint": 60,
      "ntype_constraint": 4,
      "must_include": ["Fe", "Pd", "I"],
      "FE": false,
      "thermo_stable": 0.08,
      "metal": false,
      "magnetic": true,
      "spacegroup": null},
    "oqmd": {
      "limit": 400,
      "entries": ["Mg", "B"],
      "size_constraint": 60,
      "ntype_constraint": 4,
      "must_include": [],
      "metal": false,
      "magnetic": true,
      "spacegroup": null,
      "thermo_stable": true,
      "FE": true,
      "prop": ["composition", "spacegroup", "volume", "band_gap", "stability"]
      },
    "aflow": {
      "elm": ["B"],
      "nelm": 5,
      "nsites": 10,
      "metal": true,
      "FE": true,
      "spacegroup": null,
      "limit": 5000,
      "filter": false,
      "prop": ["spacegroup_relax", "Pearson_symbol_relax"]}

(A)mode:
- The keyword 'mode' controls the preparation of input files.
  - There are 2 modes for preparing input files from materials project database. In addition, input preparation utilizing .cif and .vasp structure files are also available:
    - element: Extracts data from the Materials Project (MP) database using element-based search method. It uses the parameters within the element dictionary.
    - chemsys: Extracts data from the MP database using chemsys (e.g., Mg-O) based search method, utilizing parameters from chemsys dictionary.
    - fromcif: Converts generic .cif files into Quantum Espresso (QE) and VASP input files.
    - fromvasp: Converts POSCAR files in .vasp format into VASP input files.
    - Note: Once you have finished generating the input, set the flag to empty string "" if you wish only to update the INCAR file according to vasp.in.
(B)element:
- metal: - true selects zero bandgap systems.
- FE: - true selects compounds with negative formation energy.
- thermo_stable: - true selects compounds on the convex hull.
- exclude: - List of elements to exclude from the search.
- ntype: - Number of different types of elements in compounds.
- elm: - The element to search in compounds. Can use up to 2 elements. For example, ['B', 'C'] to search boron and/or carbon-containing compounds.
- prop: - List of properties to extract.
- ordering: - Magnetic ordering to search. "NM" for nonmagnetic, "FM" for ferro, and "AFM" for antiferromagnetic, and so on.
- nsites: - Total number of ions in the compound.
- spacegroup: - Spacegroup symbol to choose. If null, then the code doesn’t select based on spacegroup.
(B)inp:
- start: Determines the starting index within various tracking files identified by the “mpid”.
- end: Determines the ending index (exclusive) within various tracking files identified by the “mpid”. Tracking file may be mpid-list.in, used as in input.in.
- nkpt: Specifies the total number of k-points in the Brillouin zone sample along the high symmetry path, crucial for electronic and phonon bandstructure calculations, particularly when VASP line mode is not utilized.
- evenkpt: Indicates whether an even k-mesh should be used, particularly relevant for electron-phonon coupling calculations where selecting k-mesh integer multiples of q is beneficial.
- plot: Defines the type of plot to be generated. Options include:
  - eband: Bandstructure excluding line-mode kpath, applicable to QE/VASP.
  - vasp-line: Bandstructure for VASP line mode k-path.
  - phband: Phonon band for QE.
  - pdos: Density of states and partial DOS, applicable to QE/VASP.
  - gammaband: Electron-phonon coupling strength projected phonon band for QE-DFPT.
  - wann_band: Bandstructure from wannier calculation.
  - phonproj: Atom-projected phonon for QE-DFPT. Provide value for atomproj cutoff for plotting atomic projections on phonon dispersion.
  - bandproj: Atom or orbital projected band structure. (Turn on only after processing/plotting band structure with eband/vasp-line)
- calc: Type of DFT calculations. Options are QE/VASP.
- use_cif2cell: If True, cif2cell package will be utilized to read .cif files. Install cif2cell to use this function.
- kpath_pbc: Determine periodic boundary condition for kpath with default [1, 1, 1] for 3D. Generating kpath for 2D systems with vacuum along z-direction requires [1, 1, 0]
(C)chemsys: - The “chemsys” keyword mirrors the construction of the Materials Project database and is utilized to search for compounds.
- entries: -It employs the “mp_api.client.MPRester.get_entries_in_chemsys” function to explore atoms, binary, ternary, and other combinations based on the “entries” keyword. - This functionality is valuable in studying thermodynamic stability using convex hull phase diagrams. - Besides “entries”, other keys within chemsys include:
- size_constraint: - 60: Maximum size allowed. Search includes structures with less than 60 ions per cell.
- ntype_constraint: - 4: Limit of different species allowed. Search includes structures with less than 4 different species.
- must_include: - ["Fe", "Pd", "I"]: All of these elements are included in the search. If only ["Fe", "Pd"], then “I” only elements are not searched.
- FE: - false: If true, compounds with negative formation energies are searched. Otherwise, include all.
- thermo_stable: - If true, compounds with energy above hull less than 0.001 eV/atom is searched. - If 0.08, compounds with energy above hull less than 0.08 eV/atom is searched. - If It holds the false value, no filter is applied.
- metal: - false: If true, compounds with zero bandgap are searched. Otherwise, include all.
- magnetic: - true: If true, all magnetic orderings are searched.
- spacegroup: - null: Spacegroup symbol to search. Otherwise, include all.
(D)oqmd:
- Extract data from OQMD database, utilizing parameters from oqmd dictionary.
- It needs qmpy-rester API package.
- limit: 400 - Specifies the initial limit for the search. If the search doesn’t succeed, the number is decreased by a factor of 0.2 of this limit and the search is performed again
- entries: [“Mg”, “B”] - List of elements to include in the search
- size_constraint: 60 - Maximum size allowed for compounds
- ntype_constraint: 4 - Limit of different species allowed
- must_include: [] - List of elements must be included in the search. Here, Here, its role differs from the must_include parameter in Materials Project’s chemsys mode. For instance, in the configuration "element_set": "(Fe-Mn),O" (here), the entries consist of ["Fe", "Mn"], while the must_include parameter contains ["O"].
- metal: false - If true, searches for compounds with zero bandgap
- magnetic: true - If true, searches for compounds with magnetic properties
- spacegroup: null - Spacegroup symbol to search; if null, the code doesn’t select based on spacegroup
- thermo_stable: true - If true, selects compounds on the convex hull indicating thermodynamic stability
- FE: true - If true, selects compounds with negative formation energy
- prop: [“composition”, “spacegroup”, “volume”, “band_gap”, “stability”] - List of properties to extract for each compound
(E)aflow:
- Extract data from AFLOW Database, utilizing parameters from aflow dictionary.
- The AFLUX search API
- elm: [“B”] - Element to search for in compounds
- nelm: 5 - Number of different types of elements in compounds
- nsites: 10 - Total number of ions in the compound
- metal: true - If true, selects compounds with metallic properties
- FE: true - If true, selects compounds with negative formation energy
- spacegroup: null - Spacegroup symbol to search; if null, the code doesn’t select based on spacegroup
- limit: 5000 - Specifies the limit for the search
- filter: If set to True, applies filters such as metal, FE, nsites, spacegroup. Many entries in the database may not have these data, which can limit the search space. To broaden the search and include more structures, set filter to False. Example: 'filter': false.
- prop: Specify properties to retrieve. By default, set to ["spacegroup_relax", "Pearson_symbol_relax"] with filter set to False to search for additional structures. Other available properties include: ["Bravais_lattice_orig", "Bravais_lattice_relax", "composition", "density", "dft_type", "eentropy_cell", "enthalpy_cell", "enthalpy_atom", "enthalpy_formation_cell", "enthalpy_formation_atom", "entropic_temperature", "kpoints", "volume_cell", "volume_atom"]. Example: "prop": ["spacegroup_relax", "Pearson_symbol_relax"] with "filter": false.
- Note: Setting filter to True or using more than 2 properties in prop, or both, can significantly narrow down the search space. Many entries may not have these specified data, which can limit the results.

conv_test¶

"conv_test": {
   "param": "ecut",
   "ecut": [400, 500, 600],
   "kpoint": [[6, 6, 6], [12, 12, 12], [18, 18, 18]]
  },

conv_test: This provides the parameters for the convergence tests.

-param: Parameter to perform convergence tests. Available options are ecut and kpoint.

-ecut: List of kinetic energy cutoff (eV for VASP and Ry for QE).

-kpoint: List of kpoint mesh.

-Note: For ecut convergence, smallest kmesh is utilized and vice-versa.

magmom¶

"magmom": {
    "magmom": {
      "Sr": 5,
      "Al": 0,
      "I": 0},
    "type":"anisotropy",
    "saxis":[[0,0,1],[1,0,0],[1,1,0],[1,1,1]],
    "order": ["ferromagnetic", "antiferromagnetic", "ferrimagnetic_by_motif"]}

magmom:
- magmom: This holds a dictionary with elements as keys and initial magnetic moment in \(\mu_B\) as values (available only for VASP).
- type: This parameter is required when the magnetic enumeration (mainprogram magenum) process is run. Available options are:
  - ordering: This creates structures with different magnetic ordering using the order list. It uses MagneticStructureEnumerator class.
  - anisotropy: This option changes the SAXIS keyword to calculate magnetic anisotropic calculations with values given by the saxis list.
  - Note: Don’t include LSORBIT tag in vasp.in, if you are not doing spin-orbit calculations. If you are not utilizing the magenum process, remember to configure the type setting to either null or an empty string (“”).

pseudo¶

"pseudo": {
    "pot": {
      "H":"H",
      "He":"He",
      "Li":"Li_sv",
      "Be":"Be"},
    "PSEUDO": {
      "H": 60,
      "Li": 40,
      "Be": 40,
      "N": 60,
      "F": 45}}

pseudo: Pseudopotential information
- pot: Recommended pseudopotential for VASP. To use VASP POTCARs, please consult vasp developers https://www.vasp.at/.
  - Suppose we have POTCARS as POT_GGA_PAW_PBE/Mg/POTCAR
  - pmg config -p ~/path_along_directory_POT_GGA_PAW_PBE PBE52
  - After that add path to .pmgrc.yaml
  - pmg config –add PMG_VASP_PSP_DIR PBE52
  - Check your ~/.pmgrc.yaml for the path to pseudopotential, if you can find the POTCARs in “.gz” extension.
- PSEUDO:
  - elements and energy cutoff (in Ry) as dictionary key-value pairs.
  - Checkout QE pseudopotentials and energy cutoff at SSSP.
  - Put your pseudopotentials in pp folder in the working directory in “element.upf” format.

substitute¶

"substitute": {
    "mode": 2,
    "elm": "Cr",
    "sub": {"Cr": 0,"Al": 1},
    "new_sub": {"Cr": "Fe","Pd": "Pd","I": "I"}}

Parents compound needed for substitution.

keyword mode: “Mode” of the substitution. Two options are available:
- Mode 1: Changes the substitution on the “elm” keyword with compositions defined by the “sub” dictionary. If multiple substitutions need to be performed, simply use a list of dictionaries for different compositions. This performs substitution according to https://bsym.readthedocs.io/en/latest/api/interface/pymatgen.html?highlight=unique%20structures#.
- Mode 2: Simply replaces the elements using the “new_sub” dictionary. Here, each key is replaced by its corresponding value pair.
- elm: Element to be replaced. Here “Cr” is being replaced by “Al”, defined by “sub” dictionary.

pwscf_in¶

"pwscf_in": {
    "magnetic": false,
    "control": {
      "calculation": "vc-relax",
      "nstep": 300,
      "restart_mode": "from_scratch",
      "pseudo_dir": "../../pp/",
      "outdir": "./",
      "tprnfor": true,
      "tstress": true,
      "etot_conv_thr": 1e-05,
      "forc_conv_thr": 0.0001},
    "system": {
      "smearing": "gauss",
      "occupations": "smearing",
      "degauss": 0.02},
    "electrons": {
      "diagonalization": "david",
      "mixing_mode": "plain",
      "mixing_beta": 0.7,
      "conv_thr": 1e-16,
      "electron_maxstep": 300}}

magnetic: if true, it will assigns starting_magnetization in Ferromagnetic ordering.
control: control (QE)
system: system (QE)
electrons: electrons (QE)

strain¶

"strain": [-0.01, -0.005, 0.005, 0.01]

List of strain (both tensile (+ve) and compressive (-ve)) for deforming relaxed crystal structure to compute elastic properties.

wanniertools_input¶

"wanniertools_input": {
    "tb_file": {
      "Hrfile": "'ex_hr.dat'",
      "Package": "'QE'"},
    "control": {
      "BulkBand_calc": "T",
      "BulkFS_calc": "F",
      "BulkGap_cube_calc": "F",
      "BulkGap_plane_calc": "F",
      "FindNodes_calc": "F",
      "SlabBand_calc": "F",
      "WireBand_calc": "F",
      "Dos_calc": "F",
      "JDos_calc": "F",
      "SlabSS_calc": "F",
      "SlabArc_calc": "F",
      "SlabQPI_calc": "F",
      "SlabSpintexture_calc": "F",
      "wanniercenter_calc": "F",
      "Z2_3D_calc": "F",
      "Chern_3D_calc": "F",
      "WeylChirality_calc": "F",
      "BerryPhase_calc": "F",
      "BerryCurvature_calc": "F",
      "AHC_calc": "F"},
    "parameters": {
      "E_arc": "0.0",
      "Eta_Arc": "0.001",
      "OmegaMin": "0.0",
      "OmegaMax": "0.0",
      "OmegaNum": "100",
      "Nk1": "10",
      "Nk2": "10",
      "Nk3": "10",
      "NP": "2",
      "Gap_threshold": "0.1"},
    "system": {
      "NSlab": "10",
      "NSlab1": "1",
      "NSlab2": "1",
      "NumOccupied": "1",
      "SOC": "1",
      "E_FERMI": "0.0",
      "Bx": "0.0",
      "By": "0.0",
      "Bz": "0.0",
      "surf_onsite": "0.0"},
    "surface": {
      "surface": [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
      "KPATH_SLAB": {},
      "KPLANE_SLAB": {},
      "EFFECTIVE_MASS": "0.0",
      "SELECTED_ATOMS": {}}}

This keyword provides input parameters for WannierTools calculations. While it has the capability to function with codes other than QE, only QE is currently implemented in our codebase. The definition of these input parameters can be found in the WannierTools Documentation.

plot¶

It has following keys and values.

xlim/ylim: List showing range of the plot along x- or y- direction.
atomproj: Cutoff for plotting atomic projection on phonon dispersion.
bandproj: Dictionary requires for projected band structure.
- plot_type: Available options are:
- element: String or list of strings representing species. for eg.: “Mg” or [“Mg”, “B”]
- orbital: String or list of strings representing orbitals. for eg.: “px”, “dxy” for VASP and “2px”, “2dxy” for QE.
- element-orbital: Dictionary of elements and orbitals combinations. Variaous options are
- QE:
{“Mg”: “3s”, “B”: “2p”}, {“Mg”: “3s”, “B”: [“2px”, “2py”, “2pz”]}, {“Mg”: “3s”, “B”: “2px”}, etc.
- VASP:
{“Mg”: “s”, “B”: “p”}, {“Mg”: “s”, “B”: [“px”, “py”, “pz”]}, {“Mg”: “s”, “B”: “px”}, etc.
- colormap: Color map to use for projection. Its better use sequential colormaps such as “Reds”, “Greens”, etc. Look matplotlib colormap for more options.

wannier90.json¶

{
  "config_settings": {
    "use_ws_distance": ".true.",
    "dis_num_iter": 200,
    "write_hr": ".true.",
    "iprint": 2,
    "spinors": ".false."
  },
  "plot_settings": {
    "fermi_surface_plot": ".true.",
    "bands_plot": ".true.",
    "wannier_plot": ".true.",
    "wannier_plot_supercell": 3
  }
}

config_settings: Configuration settings for WANNIER90 calculations. This dictionary contains most parameters required for WANNIER90 calculations, excluding plotting.
plot_settings: Parameters for plotting are presented in this dictionary.

epw.json¶

{
  "prefix": "MgB2",
  "outdir": "./",
  "dvscf_dir": "~/path_to_phonon/save",
  "ep_coupling": true,
  "elph": true,
  "epwwrite": true,
  "epwread": false,
  "etf_mem": 1,
  "wannierize": true,
  "nbndsub": 1,
  "bands_skipped": "exclude_bands = 1:1",
  "wdata": ["fermi_surface_plot = .true.", "dis_num_iter = 2000"],
  "max_memlt": "XXX",
  "auto_projections": true,
  "scdm_entanglement": "erfc",
  "scdm_proj": true,
  "scdm_mu": 0.123,
  "scdm_sigma": 0.456,
  "num_iter": 500,
  "dis_froz_min": "XXX",
  "dis_froz_max": "XXX",
  "dis_win_min": "XXX",
  "dis_win_max": "XXX",
  "iverbosity": 2,
  "fsthick": 0.2,
  "degaussw": 0.05,
  "ephwrite": true,
  "eliashberg": true,
  "laniso": true,
  "limag": true,
  "lpade": true,
  "lacon": false,
  "nsiter": 300,
  "conv_thr_iaxis": 1.0e-4,
  "wscut": 1.0,
  "muc": 0.16,
  "nstemp": 10,
  "temps": [10, 55],
  "specfun_el": false,
  "scattering": false,
  "scattering_0rta": false,
  "scattering_serta": false,
  "lscreen": false,
  "scr_typ": 0,
  "phonselfen": false,
  "a2f": false,
  "nest_fn": false,
  "lpolar": false,
  "longrange": false,
  "elecselfen": false
}

This keyword provides input parameters for EPW calculations. The definition of these input parameters can be found in the EPW Documentation.