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,wannier90,lobster}
                ...

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, wannier90, lobster

sub-command help

Sub-commands:

validate

Validate Abinit input file.

abinp.py validate [-h] [-v] [--loglevel LOGLEVEL] [--mapi-key MAPI_KEY]
                  [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
                   [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
                [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
             [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
                 [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
            [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
                [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
                 [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
              [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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] [--mapi-key MAPI_KEY]
               [--endpoint ENDPOINT] [-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”

--mapi-key

Pymatgen MAPI_KEY used if mp identifier is used to select structure. Use value in .pmgrc.yaml if not specified.

--endpoint

Pymatgen database.

Default: “https://www.materialsproject.org/rest/v2

-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”

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.