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QE, WIEN2K, VASP, LAMMPS examples update. (#122)
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* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* Update README.rst

* 'notebook-update'

* 'notebook-update'

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* minor changes (#56)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* pypi fix (#57)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Sync-master-to-zur (#58)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* Docs update (#65)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

Co-authored-by: Daniel Wheeler <[email protected]>

* bug fix for atoms

* Delete get_desc.py

* atoms bug fix (#66)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

Co-authored-by: Daniel Wheeler <[email protected]>

* Sync (#67)

* Docs update (#65)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

Co-authored-by: Daniel Wheeler <[email protected]>

* Delete get_desc.py

* atoms bug fix (#66)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

Co-authored-by: Daniel Wheeler <[email protected]>

Co-authored-by: Daniel Wheeler <[email protected]>

* ml added

* ml added

* ml added

* ml added

* ml added

* ML expanded (#68)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

* Sync (#67)

* Docs update (#65)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

Co-authored-by: Daniel Wheeler <[email protected]>

* Delete get_desc.py

* atoms bug fix (#66)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

Co-authored-by: Daniel Wheeler <[email protected]>

Co-authored-by: Daniel Wheeler <[email protected]>

* ml added

* ml added

* ml added

* ml added

* ml added

Co-authored-by: Daniel Wheeler <[email protected]>

* Update config.yml

* Update test_pkgs.py

* circleci fix

* CircleciFix (#69)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

* Sync (#67)

* Docs update (#65)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

Co-authored-by: Daniel Wheeler <[email protected]>

* Delete get_desc.py

* atoms bug fix (#66)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

Co-authored-by: Daniel Wheeler <[email protected]>

Co-authored-by: Daniel Wheeler <[email protected]>

* ml added

* ml added

* ml added

* ml added

* ml added

* circleci fix

Co-authored-by: Daniel Wheeler <[email protected]>

* Update test_pkgs.py

* Sync (#70)

* CircleciFix (#69)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

* Sync (#67)

* Docs update (#65)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

Co-authored-by: Daniel Wheeler <[email protected]>

* Delete get_desc.py

* atoms bug fix (#66)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

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* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

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* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

Co-authored-by: Daniel Wheeler <[email protected]>

Co-authored-by: Daniel Wheeler <[email protected]>

* ml added

* ml added

* ml added

* ml added

* ml added

* circleci fix

Co-authored-by: Daniel Wheeler <[email protected]>

* Update test_pkgs.py

Co-authored-by: Daniel Wheeler <[email protected]>

* Sync (#73)

* CircleciFix (#69)

* Update inputs.py

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* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

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* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

* Sync (#67)

* Docs update (#65)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

Co-authored-by: Daniel Wheeler <[email protected]>

* Delete get_desc.py

* atoms bug fix (#66)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* build(nix): update for new dependencies (#61)

Update for new Jarvis dependencies and for latest version of Nixpkgs.

* Atoms swap bug fix

* Update utils.py

* Update README.rst

* Args test

Co-authored-by: Daniel Wheeler <[email protected]>

* Update inputs.py

* Update inputs.py

* Update inputs.py

* Update get_desc.py

* Update surface.py

* Update zur.py

* Update solar.py

* Update spillage.py

* Update neighbors.py

* Update atoms.py

* Update lattice.py

* Update specie.py

* Update utils.py

* Update figshare.py

* Update inputs.py

* Update outputs.py

* Update inputs.py

* Update inputs.py

* Update lammps.py

* Update lammps.py

* Update vasp.py

* Update atoms.py

* Update specie.py

* Update lattice.py

* bug fix for atoms

Co-authored-by: Daniel Wheeler <[email protected]>

Co-authored-by: Daniel Wheeler <[email protected]>

* ml added

* ml added

* ml added

* ml added

* ml added

* circleci fix

Co-authored-by: Daniel Wheeler <[email protected]>

* Update test_pkgs.py

Co-authored-by: Daniel Wheeler <[email protected]>

* Colab notebooks added

* restapi test example

* restapi test example

* Update README.rst

* version number update

* docs update

* composiiton update

* Zur (#74)

* Update inputs.py

* Update atoms.py

* Update composition.py

* Update atoms.py

* Docs (#64)

* Notebooks-added (#55)

* readme (#53)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* Merging from master (#54)

* Added minimal docs (#51)

* supercell

* atoms update

* atoms update

* atoms update

* zur update

* zur update

* zur update

* zur bug fix

* for pypi

* vacancy analsis bug fix

* vacancy analsis bug fix

* vacancy module bug fix

* docstrings added

* docstrings added

* docstrings added

* docs added

* docs update

* docs update

* docs update

* docs update

* docs update

* README update

* Update vacancy.py

* Update README.rst

* notebooks

* notebooks

* 'notebook-added'

* 'notebook-added'

* Update default.nix

* Update setup.py

* Delete custodian.nix

* Delete phonopy.nix

* Delete pymatgen.nix

* Update README.md

* Update README.rst

* Update default.nix

* Update default.nix

* Delete requirements.txt

* 'notebook-update'

* 'notebook-update'

* Update README.rst

* Update setup.py

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update README.rst

* Update notes

* Update README.rst

* Increased Coverage (#59)

* kpoints tests

* ci

* exclude few files in coverage

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* increased pytests

* notes

* Update README.rst

* Update README.rst

* Update setup.py

* Update index.rst

* Update README.rst

* Atom swap bug fix (#63)

* Update inputs.py

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* Update …
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15 changes: 15 additions & 0 deletions LICENSE
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
This software was developed by employees of the National Institute of Standards and Technology (NIST), an agency of the Federal Government and is being made available as a public service. Pursuant to title 17 United States Code Section 105, works of NIST employees are not subject to copyright protection in the United States. This software may be subject to foreign copyright. Permission in the United States and in foreign countries, to the extent that NIST may hold copyright, to use, copy, modify, create derivative works, and distribute this software and its documentation without fee is hereby granted on a non-exclusive basis, provided that this notice and disclaimer of warranty appears in all copies.

THE SOFTWARE IS PROVIDED 'AS IS' WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND FREEDOM FROM INFRINGEMENT, AND ANY WARRANTY THAT THE DOCUMENTATION WILL CONFORM TO THE SOFTWARE, OR ANY WARRANTY THAT THE SOFTWARE WILL BE ERROR FREE. IN NO EVENT SHALL NIST BE LIABLE FOR ANY DAMAGES, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, SPECIAL OR CONSEQUENTIAL DAMAGES, ARISING OUT OF, RESULTING FROM, OR IN ANY WAY CONNECTED WITH THIS SOFTWARE, WHETHER OR NOT BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, WHETHER OR NOT INJURY WAS SUSTAINED BY PERSONS OR PROPERTY OR OTHERWISE, AND WHETHER OR NOT LOSS WAS SUSTAINED FROM, OR AROSE OUT OF THE RESULTS OF, OR USE OF, THE SOFTWARE OR SERVICES PROVIDED HEREUNDER.

# Terms of Use
This software was developed at the [National Institute of Standards and Technology](http://www.nist.gov)
by employees of the Federal Government in the course of their official duties.
Pursuant to [title 17 section 105](https://www.copyright.gov/title17/92chap1.html#105)
of the United States Code this software is not subject to copyright protection
and is in the public domain. NIST assumes no responsibility whatsoever for the
use of this software by other parties, and makes no guarantees, expressed or
implied, about its quality, reliability, or any other characteristic.
We would appreciate acknowledgement if the software is used.

This software can be redistributed and/or modified freely provided that any
derivative works bear some notice that they are derived from it, and any
modified versions bear some notice that they have been modified.

9 changes: 6 additions & 3 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ For more details, checkout our latest article: `JARVIS: An Integrated Infrastru
Some important features
=======================================================================

- **Software workflow tasks**: VASP, Quantum Espresso, BoltzTrap, Wannier90, LAMMPS, Scikit-learn, TensorFlow, LightGBM.
- **Software workflow tasks**: VASP, Quantum Espresso, Wien2k BoltzTrap, Wannier90, LAMMPS, Scikit-learn, TensorFlow, LightGBM.

- **HPC clusters**: PBS and SLURM.

Expand Down Expand Up @@ -113,12 +113,15 @@ Please see `Publications related to JARVIS-Tools <https://github.com/usnistgov/j

External links
-----------------------------------------
https://jarvis-materials-design.github.io/dbdocs/

https://figshare.com/authors/Kamal_Choudhary/4445539


https://pypi.org/project/jarvis-tools


https://pypi.org/project/jarvis-tools

https://jarvis-tools.readthedocs.io/en/latest/

https://www.slideshare.net/KAMALCHOUDHARY4

Expand Down
2 changes: 1 addition & 1 deletion jarvis/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
"""Version number."""
__version__ = "2020.9.22"
__version__ = "2020.9.29"
41 changes: 41 additions & 0 deletions jarvis/core/atoms.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -735,6 +735,37 @@ def pymatgen_converter(self):
coords_are_cartesian=False,
)
except Exception:
print("Requires pymatgen for this functionality.")
pass

def phonopy_converter(self, pbc=True):
"""Get phonopy representation of the atoms object."""
try:
from phonopy.structure.atoms import Atoms as PhonopyAtoms

return PhonopyAtoms(
symbols=self.elements,
positions=self.cart_coords,
pbc=pbc,
cell=self.lattice_mat,
)
except Exception:
print("Requires phonopy for this functionality.")
pass

def ase_converter(self, pbc=True):
"""Get ASE representation of the atoms object."""
try:
from ase import Atoms as AseAtoms

return AseAtoms(
symbols=self.elements,
positions=self.cart_coords,
pbc=pbc,
cell=self.lattice_mat,
)
except Exception:
print("Requires ASE for this functionality.")
pass

def spacegroup(self, symprec=1e-3):
Expand Down Expand Up @@ -1276,6 +1307,16 @@ def pmg_to_atoms(pmg=""):
)


def ase_to_atoms(ase_atoms=""):
"""Convert ase structure to Atoms."""
return Atoms(
lattice_mat=ase_atoms.get_cell(),
elements=ase_atoms.get_chemical_symbols(),
coords=ase_atoms.get_positions(),
pbc=True,
)


"""
if __name__ == "__main__":
box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
Expand Down
41 changes: 39 additions & 2 deletions jarvis/db/restapi.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from jarvis.db.jsonutils import dumpjson
import string
from collections import OrderedDict
import json


class Api(object):
Expand Down Expand Up @@ -63,7 +64,24 @@ def send_keyword_query(
raise Exception("Problem occurred while getting the file.")
raise Exception("Check username,password, ... details")

def upload_xml_file(self, filename="", template_id=""):
def get_global_workspace_id(self):
"""Get workspace ID."""
turl = self.base_url + "/rest/workspace/"
response = requests.get(
turl, verify=False, auth=(self.username, self.password)
)
workspace_list = json.loads(response.text)
for workspace in workspace_list:
if workspace["title"] == "Global Public Workspace":
global_workspace_id = workspace["id"]
return global_workspace_id

def upload_xml_file(
self,
filename="",
workspace_id="5df7b6defb7e53000c4652aa",
template_id="",
):
"""Upload file using path of the file and schema/template id."""
print("status: uploading data file...")
xml_file = open(filename, "rb")
Expand All @@ -77,6 +95,7 @@ def upload_xml_file(self, filename="", template_id=""):
data = {
"title": base,
"template": template_id,
"workspace": workspace_id,
"xml_content": xml_content,
}
response = requests.post(
Expand Down Expand Up @@ -395,25 +414,43 @@ def upload_jarvisdft_xmls(
"""
if __name__ == "__main__":
a = Api()
a = Api(base_url="http://test-jarvis.nist.gov")
tid="5f624bc547d1ac011a224672"
tid='5f6909278c6d9e011c8cc8c9'
a.upload_xml_file(filename='JVASP-1004.xml',template_id=tid)
a = Api()
a = Api(base_url="https://jarvis.nist.gov")
x = a.get_global_workspace_id()
print("x=", x)
a = Api()
a = Api(base_url="https://jarvis.nist.gov")
# a.upload_jarvisff_xmls()
# a.upload_jarvisff_xmls()
# a.upload_jarvisdft_xmls()
# tid="5f626925ece4b00035e5277f"
# a.upload_xml_file(filename='JVASP-1067.xml',template_id=tid)
# a.upload_xml_file(filename='JVASP-664.xml',template_id=tid)
# a.upload_xml_file(filename='JVASP-1002.xml',template_id=tid)
# a.delete_all_records()
# filepath="/rk2/knc6/DB/RAW_FILES/JARVIS-DFT-DFPT/JVASP-10088.zip",
# filepath="/rk2/knc6/JARVIS-DFT/Elements-bulkk/
# mp-149_bulk_PBEBO/MAIN-RELAX-bulk@mp-149/CHGCAR"
# x = a.upload_blob(filepath)
print("id", x)
#a.upload_xml_file(filename='JVASP-1067.xml',template_id=tid)
#a.upload_xml_file(filename='JVASP-664.xml',template_id=tid)
#a.upload_xml_file(filename='JVASP-1002.xml',template_id=tid)
# a.delete_all_records()
#filepath="/rk2/knc6/DB/RAW_FILES/JARVIS-DFT-DFPT/JVASP-10088.zip",
#filepath="/rk2/knc6/JARVIS-DFT/Elements-bulkk/
#mp-149_bulk_PBEBO/MAIN-RELAX-bulk@mp-149/CHGCAR"
Expand Down
1 change: 1 addition & 0 deletions jarvis/examples/lammps/Al_test/ELASTIC.json
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@@ -0,0 +1 @@
[{"jobname": "ELASTIC", "initial_pos": {"lattice_mat": [[4.06741, 0.0, 0.0], [0.0, 4.06741, 0.0], [0.0, 0.0, 4.06741]], "coords": [[0.0, 0.0, 0.0], [0.0, 2.033705, 2.033705], [2.033705, 0.0, 2.033705], [2.033705, 2.033705, 0.0]], "elements": ["Al", "Al", "Al", "Al"], "abc": [4.06741, 4.06741, 4.06741], "angles": [90.0, 90.0, 90.0], "cartesian": true, "props": ["", "", "", ""]}, "pair_style": "eam/alloy", "pair_coeff": "/users/knc6/Software/LAMMPS/lammps-master/potentials/Al_zhou.eam.alloy", "final_energy": -14.319995, "en": -3.58, "press": -0.0, "final_str": {"lattice_mat": [[4.081654900784626, 0.0, 0.0], [0.0, 4.081654900784625, 0.0], [0.0, 0.0, 4.081654900784626]], "coords": [[-0.007122450392313417, -0.0071224503923133595, -0.007122450392313428], [-0.007122450392313417, 2.033704999999999, 2.0337049999999994], [2.0337049999999994, -0.007122450392313366, 2.0337049999999994], [2.0337049999999994, 2.033704999999999, -0.007122450392313428]], "elements": ["Al", "Al", "Al", "Al"], "abc": [4.08165, 4.08165, 4.08165], "angles": [90.0, 90.0, 90.0], "cartesian": true, "props": ["", "", "", ""]}}]
16 changes: 16 additions & 0 deletions jarvis/examples/lammps/Al_test/ELASTIC/data
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
datafile (written by JARVIS-Tools)

4 atoms
1 atom types
0.0 4.06741 xlo xhi
0.0 4.06741 ylo yhi
0.0 4.06741 zlo zhi
0.0 0.0 0.0 xy xz yz


Atoms

1 1 0.000000 0.0 0.0 0.0
2 1 0.000000 0.0 2.033705 2.033705
3 1 0.000000 2.033705 0.0 2.033705
4 1 0.000000 2.033705 2.033705 0.0
27 changes: 27 additions & 0 deletions jarvis/examples/lammps/Al_test/ELASTIC/data0
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LAMMPS data file via write_data, version 19 Oct 2016, timestep = 7

4 atoms
1 atom types

-7.1224503923134168e-03 4.0745324503923124e+00 xlo xhi
-7.1224503923133656e-03 4.0745324503923115e+00 ylo yhi
-7.1224503923134281e-03 4.0745324503923124e+00 zlo zhi
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 xy xz yz

Masses

1 26.982

Atoms # charge

1 1 0.0000000000000000e+00 -7.1224503923134168e-03 -7.1224503923133595e-03 -7.1224503923134281e-03 0 0 0
2 1 0.0000000000000000e+00 -7.1224503923134168e-03 2.0337049999999990e+00 2.0337049999999994e+00 0 0 0
3 1 0.0000000000000000e+00 2.0337049999999994e+00 -7.1224503923133656e-03 2.0337049999999994e+00 0 0 0
4 1 0.0000000000000000e+00 2.0337049999999994e+00 2.0337049999999990e+00 -7.1224503923134281e-03 0 0 0

Velocities

1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
1 change: 1 addition & 0 deletions jarvis/examples/lammps/Al_test/ELASTIC/in.main
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include inelast.mod
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