`abinp.py`

This script provides a simplified interface to the AbiPy API for constructing input files. It is a useful tool especially for newcomers who are not familiar with the programmatic interface for building workflows. In this case, indeed, one can use abinp.py to generate automatically input files from file providing the crystalline structure of the system and then customize the generated output.

There are also commands operating on input files directly. These options could be useful to get data directly from Abinit.

usage: abinp.py [-h] [--loglevel LOGLEVEL] [-V] [-v]
                {validate,autoparal,abispg,ibz,phperts,gs,ebands,phonons,g0w0,anaph,vasp,wannier90,lobster,slurm}
                ...

Named Arguments

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-V, --version

show program’s version number and exit

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

subcommands

Valid subcommands, use command –help for help

command

Possible choices: validate, autoparal, abispg, ibz, phperts, gs, ebands, phonons, g0w0, anaph, vasp, wannier90, lobster, slurm

sub-command help

Sub-commands

validate

Validate Abinit input file.

abinp.py validate [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
                  [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
                  [--spin-mode SPIN_MODE] [--smearing SMEARING]
                  filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

autoparal

Compute autoparal configurations.

abinp.py autoparal [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
                   [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
                   [--spin-mode SPIN_MODE] [--smearing SMEARING]
                   [-n MAX_NCPUS]
                   filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

-n, --max-ncpus

Maximum number of CPUs

Default: 50

abispg

Call Abinit with chkprim = 0 to find space group.

abinp.py abispg [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
                [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
                [--spin-mode SPIN_MODE] [--smearing SMEARING]
                filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

ibz

Get k-points in the irreducible weights.

abinp.py ibz [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw] [--jdtset JDTSET]
             [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA] [--spin-mode SPIN_MODE]
             [--smearing SMEARING]
             filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

phperts

Get list of phonon perturbations.

abinp.py phperts [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
                 [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
                 [--spin-mode SPIN_MODE] [--smearing SMEARING]
                 filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

gs

Build Abinit input for ground-state calculation.

abinp.py gs [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw] [--jdtset JDTSET]
            [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA] [--spin-mode SPIN_MODE]
            [--smearing SMEARING]
            filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

ebands

Build Abinit input for band structure calculations.

abinp.py ebands [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
                [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
                [--spin-mode SPIN_MODE] [--smearing SMEARING]
                filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

phonons

Build Abinit input for phonon calculations.

abinp.py phonons [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
                 [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
                 [--spin-mode SPIN_MODE] [--smearing SMEARING]
                 filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

g0w0

Generate input files for G0W0 calculations.

abinp.py g0w0 [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
              [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
              [--spin-mode SPIN_MODE] [--smearing SMEARING]
              filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

anaph

Build Anaddb input file for the computation of phonon bands DOS.

abinp.py anaph [-h] [-v] [--loglevel LOGLEVEL] [-m] [--usepaw]
               [--jdtset JDTSET] [-p PSEUDOS [PSEUDOS ...]] [--kppa KPPA]
               [--spin-mode SPIN_MODE] [--smearing SMEARING]
               filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-m, --mnemonics

Print brief description of input variables in the input file.

Default: False

--usepaw

Use PAW pseudos instead of norm-conserving.

Default: False

--jdtset

jdtset index. Used to select the dataset index when the input file contains more than one dataset.

Default: 1

-p, --pseudos

List of pseudopotentials

--kppa

Number of k-points per reciprocal atom. Use default value (1000) if not specified.

--spin-mode

Spin polarization. Default: unpolarized. Allowed values in: [polarized, unpolarized, afm (anti-ferromagnetic), spinor (non-collinear magnetism) spinor_nomag (non-collinear, no magnetism)].

Default: 'unpolarized'

--smearing

Smearing scheme. Defaults to Fermi-Dirac.

Default: 'fermi_dirac:0.1 eV'

vasp

Build VASP input files from a FILE defining the structure.

abinp.py vasp [-h]
              [--dict-set {DictSet,LobsterSet,MITMDSet,MITNEBSet,MITRelaxSet,MPAbsorptionSet,MPHSEBSSet,MPHSERelaxSet,MPMDSet,MPMetalRelaxSet,MPNMRSet,MPNonSCFSet,MPRelaxSet,MPSOCSet,MPScanRelaxSet,MPScanStaticSet,MPStaticSet,MVLElasticSet,MVLGBSet,MVLGWSet,MVLNPTMDSet,MVLRelax52Set,MVLScanRelaxSet,MVLSlabSet,MatPESStaticSet,VaspInputGenerator,VaspInputSet}]
              filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

Named Arguments

--dict-set

Possible choices: DictSet, LobsterSet, MITMDSet, MITNEBSet, MITRelaxSet, MPAbsorptionSet, MPHSEBSSet, MPHSERelaxSet, MPMDSet, MPMetalRelaxSet, MPNMRSet, MPNonSCFSet, MPRelaxSet, MPSOCSet, MPScanRelaxSet, MPScanStaticSet, MPStaticSet, MVLElasticSet, MVLGBSet, MVLGWSet, MVLNPTMDSet, MVLRelax52Set, MVLScanRelaxSet, MVLSlabSet, MatPESStaticSet, VaspInputGenerator, VaspInputSet

VaspDictSet. Default: MPStaticSet. For further info see pymatgen.io.vasp.sets

Default: 'MPStaticSet'

wannier90

Build wannier90 template input file from Abinit input/output file. possibly with electron bands.

abinp.py wannier90 [-h] filepath

Positional Arguments

filepath: File with the crystalline structure (netcdf, cif, POSCAR, input files …)

lobster

Build and print Lobster input file from directory with files file (for pseudos) and GSR.nc output file (multidatasets are not allowed). Supports also directory with vasprun.xml and POTCAR file.

abinp.py lobster [-h] dirpath

Positional Arguments

dirpath: Directory with input files required by COMMAND.

slurm

Print template for Slurm submmission script

abinp.py slurm [-h]

abinp.py

Named Arguments

subcommands

Sub-commands

validate

Positional Arguments

Named Arguments

autoparal

Positional Arguments

Named Arguments

abispg

Positional Arguments

Named Arguments

ibz

Positional Arguments

Named Arguments

phperts

Positional Arguments

Named Arguments

gs

Positional Arguments

Named Arguments

ebands

Positional Arguments

Named Arguments

phonons

Positional Arguments

Named Arguments

g0w0

Positional Arguments

Named Arguments

anaph

Positional Arguments

Named Arguments

vasp

Positional Arguments

Named Arguments

wannier90

Positional Arguments

lobster

Positional Arguments

slurm

`abinp.py`