import ase
import numpy as np
import types
import warnings
from ase.calculators import calculator
from ase.utils import basestring
from typing import Union, List
[docs]def algo(calc, val):
""" specify the electronic minimisation algorithm (as of VASP.4.5) (string)
http://cms.mpi.univie.ac.at/wiki/index.php/ALGO
"""
assert isinstance(val, str)
assert val.lower() in [
x.lower()
for x in [
"Normal",
"VeryFast",
"Fast",
"Conjugate",
"All",
"Damped",
"Subrot",
"Eigenval",
"None",
"Nothing",
"CHI",
"GW0",
"GW",
"scGW0",
"scGW",
]
]
[docs]def atoms(calc, val):
"""The Atoms object. (ase.atoms.Atoms)."""
assert isinstance(val, ase.atoms.Atoms)
[docs]def eb_k(calc, val):
"""The relative permittivity of the solvent used in the VASPsol code. (float)
https://github.com/henniggroup/VASPsol/blob/master/docs/USAGE.md
"""
assert isinstance(val, float)
[docs]def ediff(calc, val):
"""EDIFF specifies the global break condition for the electronic loop. (float)
http://cms.mpi.univie.ac.at/wiki/index.php/EDIFF
"""
assert isinstance(val, float) or val == 0
[docs]def ediffg(calc, val):
"""EDIFFG defines the break condition for the ionic relaxation loop. (float)
If EDIFFG < 0, it defines a force criteria.
http://cms.mpi.univie.ac.at/wiki/index.php/EDIFFG
"""
assert isinstance(val, float) or val == 0
[docs]def encut(calc, val):
"""Planewave cutoff in eV. (float)
http://cms.mpi.univie.ac.at/wiki/index.php/ENCUT
"""
assert val > 0, "encut must be greater than zero."
assert isinstance(val, int) or isinstance(
val, float
), "encut should be an int or float." " You provided {} ({}).".format(
val, type(val)
)
[docs]def ialgo(calc, val):
"""
`IALGO <http://cms.mpi.univie.ac.at/wiki/index.php/IALGO>`_ selects the
algorithm used to optimize the orbitals.
"""
print("You are advised to use the algo key instead of ialgo.")
assert isinstance(val, int)
assert val in [
-1,
2,
3,
4,
5,
6,
7,
8,
15,
16,
17,
18,
28,
38,
44,
45,
46,
47,
48,
53,
54,
55,
56,
57,
58,
]
[docs]def ibrion(calc, val):
"""`IBRION <http://cms.mpi.univie.ac.at/wiki/index.php/IBRION>`_
determines the algorithm to update geometry during relaxtion. (int)
"""
assert val in [-1, 0, 1, 2, 3, 5, 6, 7, 8, 44]
[docs]def icharg(calc, val):
"""Determines how VASP constructs the
`initial charge density <http://cms.mpi.univie.ac.at/wiki/index.php/ICHARG>`_.
===== ===================================================
Value Meaning
===== ===================================================
0 calculate from initial wave functions
1 read from the CHGCAR
2 (default) Superposition of atomic charge densities
11 for band-structure plots
===== ===================================================
Parameters
----------
val : int
new value
"""
assert isinstance(val, int)
[docs]def images(calc, val):
"""
`The number of images <http://cms.mpi.univie.ac.at/wiki/index.php/IMAGES>`_
for a nudge elastic band (NEB) calculation not counting the end points.
Parameters
----------
val : int
new value
"""
assert isinstance(val, int)
assert val == len(calc.neb) - 2
[docs]def isif(calc, val):
"""ISIF determines what is changed during relaxations.
====== =========== =============== ======= ============ =============
ISIF calculate calculate relax change change
force stress tensor ions cell shape cell volume
====== =========== =============== ======= ============ =============
0 yes no yes no no
1 yes trace only yes no no
2 yes yes yes no no
3 yes yes yes yes yes
4 yes yes yes yes no
5 yes yes no yes no
6 yes yes no yes yes
7 yes yes no no yes
====== =========== =============== ======= ============ =============
Parameters
----------
val : int
new value
"""
assert val in [0, 1, 2, 3, 4, 5, 6, 7]
[docs]def ismear(calc, val):
"""
`ISMEAR <http://cms.mpi.univie.ac.at/wiki/index.php/ISMEAR>`_ determines
how the partial occupancies are set.
Parameters
----------
val : int
new value
"""
assert val in [-5, -4, -3, -2, -1, 0, 1, 2]
[docs]def ispin(calc, val):
"""`Control spin-polarization
<http://cms.mpi.univie.ac.at/wiki/index.php/ISPIN>`_.
===== ==============================
Value Meaning
===== ==============================
1 default, no spin polarization
2 spin-polarization.
===== ==============================
Parameters
----------
val : int
new value
"""
assert val in [1, 2]
[docs]def isym(calc, val):
"""ISYM determines the way VASP treats symmetry.
http://cms.mpi.univie.ac.at/wiki/index.php/ISYM
"""
assert val in [-1, 0, 1, 2, 3]
[docs]def ivdw(calc, val):
"""`IVDW <http://cms.mpi.univie.ac.at/vasp/vasp/IVDW_approximate_vdW_correction_methods.html>`_
determines the approximate vdW correction methods used.
===== ================================================================================================
Value Meaning
===== ================================================================================================
0 no correction
1|10 DFT-D2 method of Grimme (available as of VASP.5.2.11)
11 zero damping DFT-D3 method of Grimme (available as of VASP.5.3.4)
12 DFT-D3 method with Becke-Jonson damping (available as of VASP.5.3.4)
2 Tkatchenko-Scheffler method (available as of VASP.5.3.3)
21 Tkatchenko-Scheffler method with iterative Hirshfeld partitioning (available as of VASP.5.3.5)
202 Many-body dispersion energy method (MBD@rSC) (available as of VASP.5.4.1)
4 dDsC dispersion correction method (available as of VASP.5.4.1)
===== ================================================================================================
Parameters
----------
val : int
new value
"""
assert val in [0, 1, 10, 11, 12, 2, 21, 202, 4]
[docs]def ldau(calc, val):
"""`LDAU <http://cms.mpi.univie.ac.at/wiki/index.php/LDAU>`_
switches on the L(S)DA+U.
Parameters
----------
val : bool
new value
"""
assert val in [True, False, None]
[docs]def ldau_luj(calc, val):
"""
Dictionary of DFT+U parameters::
ldau_luj={'Mn': {'L': 2, 'U': 0.0, 'J': 0.0},
'O': {'L': -1, 'U': 0.0, 'J': 0.0}},
"""
assert isinstance(val, dict)
# this may not be the case for site-specific U. I think we need
# setups for that.
assert len(val.keys()) == len(set([a.symbol for a in calc.get_atoms()]))
[docs]def ldauprint(calc, val):
"""`LDAUPRINT <http://cms.mpi.univie.ac.at/wiki/index.php/LDAUPRINT>`_
controls the verbosity of the L(S)DA+U routines.
===== ==============================================================
Value Meaning
===== ==============================================================
0 silent.
1 Write occupancy matrix to the OUTCAR file.
2 same as LDAUPRINT=1, plus potential matrix dumped to vasp_stdout
===== ==============================================================
Parameters
----------
val : int
new value
"""
assert val in [0, 1, 2]
[docs]def ldautype(calc, val):
"""`LDAUTYPE <http://cms.mpi.univie.ac.at/wiki/index.php/LDAUTYPE>`_
specifies which type of L(S)DA+U approach will be used.
``LDAUTYPE=1``: Rotationally invariant LSDA+U [1]
``LDAUTYPE=2``: Simplified (rotationally invariant) LSDA+U [2]
1. A. I. Liechtenstein, V. I. Anisimov and J. Zaane, Phys. Rev. B
**52**, R5467 (1995).
2. S. L. Dudarev, G. A. Botton, S. Y. Savrasov, C. J. Humphreys
and A. P. Sutton, Phys. Rev. B **57**, 1505 (1998).
Parameters
----------
val : int
new value
"""
[docs]def lmaxmix(calc, val):
"""`LMAXMIX <http://cms.mpi.univie.ac.at/wiki/index.php/LMAXMIX>`_
the max l-quantum number the charge densities used.
Mostly used for DFT+U.
4 for d-electrons (or 6 for f-elements)
Parameters
----------
val : int
new value
"""
assert val in [2, 4, 6]
[docs]def kpts(calc, val):
"""Sets k-points. Not a Vasp keyword. (list or dict)"""
assert isinstance(val, list) or isinstance(
val, dict
), "kpts must be a list or a dict."
if isinstance(val, dict):
assert (
len([1 for key in val if key in ["size", "spacing", "auto", "list"]]) == 1
), "kpts dict must only contain one of the keys size/spacing/auto/list"
if isinstance(val, list):
assert len(val) == 3 or (
len(np.array(val).shape) == 2 and np.array(val).shape[1] == 3
), """kpts list must be either three ints specifying divisions or an
explicit list of k-points"""
[docs]def kspacing(calc, val):
"""`KSPACING <http://cms.mpi.univie.ac.at/vasp/vasp/KSPACING_tag_KGAMMA_tag.html>`_
determines the number of k-points if the KPOINTS file is not present.
Parameters
----------
val : float
new value
"""
assert isinstance(val, float)
[docs]def kgamma(calc, val):
""" Determines whether the grid is Gamma- or Monkhorst-Pack
if the kspacing tag was used.
Parameters
----------
val : bool
new value
"""
assert isinstance(val, bool)
[docs]def lcharg(calc, val):
"""`LCHARG <http://cms.mpi.univie.ac.at/wiki/index.php/LCHARG>`_
determines whether CHGCAR and CHG are written.
Parameters
----------
val : bool
new value
"""
assert val in [True, False]
[docs]def lorbit(calc, val):
"""`Determines whether the PROCAR or PROOUT files are written
<http://cms.mpi.univie.ac.at/wiki/index.php/LORBIT>`_.
Parameters
----------
val : int
new value
"""
if val < 10:
assert "rwigs" in calc.parameters
assert isinstance(val, int)
[docs]def lsol(calc, val):
"""`LSOL <https://github.com/henniggroup/VASPsol/blob/master/docs/USAGE.md>`_
determines whether the VASPsol is activated.
Parameters
----------
val : bool
new value
"""
assert val in [True, False]
[docs]def lreal(calc, val):
"""`LREAL <http://cms.mpi.univie.ac.at/wiki/index.php/LREAL>`_
determines whether the projection operators are evaluated in real-space
or in reciprocal space.
Parameters
----------
val : bool/string
new value
"""
assert val in [True, False, "On", "Auto", "O", "A"]
[docs]def lwave(calc, val):
"""`LWAVE <http://cms.mpi.univie.ac.at/wiki/index.php/LWAVE>`_
determines whether the WAVECAR is written.
Parameters
----------
val : bool
new value
"""
assert val in [True, False]
[docs]def magmom(calc: calculator, val: Union[List[int], np.ndarray]):
"""`MAGMOM <http://cms.mpi.univie.ac.at/wiki/index.php/MAGMOM>`_
specifies the initial magnetic moment for each atom.
Raises
------
TypeError
if the input value is neither a list nor a numpy array
ValueError
if the length of the input list does not match the number
of atoms of the structure associated with the calculator
"""
if not isinstance(val, (list, np.ndarray)):
raise TypeError(
"magmom must be a list or a numpy array yet"
" type(magmom)= {}\nmagmom: {}".format(type(val), val)
)
if len(val) != len(calc.atoms):
raise ValueError(
"Number of elements in magmom ({}) does not match the"
" number of atoms in the structure associated with the"
" calculator ({})".format(len(val), len(calc.atoms))
)
[docs]def maxmix(calc, val):
"""`MAXMIX <http://cms.mpi.univie.ac.at/wiki/index.php/MAXMIX>`_
specifies the maximum number steps stored in Broyden mixer (IMIX=4).
Parameters
----------
val : int
new value
"""
assert isinstance(val, int)
[docs]def nbands(calc, val):
"""`NBANDS <http://cms.mpi.univie.ac.at/wiki/index.php/NBANDS>`_
determines the actual number of bands in the calculation.
Parameters
----------
val : int
new value
"""
assert isinstance(val, int) or isinstance(val, long)
s = "nbands = {} which is less than {}."
assert val > calc.get_num_valence() / 2, s.format(val, calc.get_num_valence() / 2)
[docs]def ncore(calc, val):
"""`NCORE <http://cms.mpi.univie.ac.at/wiki/index.php/NCORE>`_
determines the number of compute cores that work on an individual orbital.
Parameters
----------
val : int
new value
"""
assert isinstance(val, int)
def nelm(calc, val):
"""`NELM <http://cms.mpi.univie.ac.at/wiki/index.php/NELM>`_
sets the maximum number of electronic SC (selfconsistency) steps which may
be performed.
Parameters
----------
val : int
new value
"""
assert isinstance(val, int)
[docs]def nupdown(calc, val):
"""`NUPDOWN <http://cms.mpi.univie.ac.at/vasp/vasp/NUPDOWN.html>`_
sets the difference between the number of spin up and down electrons.
This fixes the bulk magnetic moment. The VASP manual specifies this should
be an integer, but it appears floats work too.
Parameters
----------
val : int/float
new value
"""
assert isinstance(val, int) or isinstance(val, float)
[docs]def nsw(calc, val):
"""`NSW <http://cms.mpi.univie.ac.at/wiki/index.php/NSW>`_
sets the maximum number of ionic steps.
Parameters
----------
val : int
new value
"""
assert isinstance(val, int)
[docs]def potim(calc, val):
"""`POTIM <http://cms.mpi.univie.ac.at/wiki/index.php/POTIM>`_
sets the time step (MD) or step width scaling (ionic relaxations).
Parameters
----------
val : float
new value
"""
assert isinstance(val, float)
[docs]def pp(calc, val):
"""
Determines where POTCARS are retrieved from.
Parameters
----------
val : string
new value
"""
assert val in ["PBE", "LDA", "GGA"]
[docs]def prec(calc, val):
"""Specifies the `precision vasp_mode <http://cms.mpi.univie.ac.at/wiki/index.php/PREC>`_.
Parameters
----------
val : string
new value
"""
assert val in ["Low", "Medium", "High", "Normal", "Accurate", "Single"]
[docs]def rwigs(calc, val):
"""`RWIGS <http://cms.mpi.univie.ac.at/wiki/index.php/RWIGS>`_
specifies the Wigner-Seitz radius for each atom type.
in vasp.py you enter a dictionary of::
{sym: radius}
Parameters
----------
val : list
new value
"""
assert isinstance(val, list)
assert calc.parameters.get("lorbit", 0) < 10, "lorbit >= 10, rwigs is ignored."
[docs]def setups(calc, val):
"""Sets up special setups for the POTCARS (list of (symbol/int, suffix)).
The first element of each pair of the list is either an integer
index of the atom for the special setup, or a chemical symbol for
all atoms of that type. The second element of the pair is a suffix
to be appended to the symbol. For example, to use the O_s potcar
set setups to: [['O', '_s']].
This is not a vasp keyword.
"""
assert isinstance(val, dict)
for k, v in val.items():
assert isinstance(k, str) and isinstance(v, str)
[docs]def sigma(calc, val):
"""SIGMA determines the width of the smearing in eV. (float)"""
assert isinstance(val, float)
assert val > 0
[docs]def spring(calc, val):
"""The Spring constant in the elastic band method. -5 = NEB.
http://cms.mpi.univie.ac.at/wiki/index.php/SPRING
"""
assert isinstance(val, int) or isinstance(val, float)
if calc.parameters.get("ibrion") not in [1, 3]:
warnings.warn("ibrion should be 1 or 3.")
[docs]def xc(calc, val):
"""Set exchange-correlation functional. (string)"""
from storq.vasp.core import Vasp
assert val.lower() in Vasp.xc_defaults.keys(), "xc ({}) not in {}.".format(
val, Vasp._xc_defaults.keys()
)
[docs]def addgrid(calc, val):
"""ADDGRID gives an extra grid for the evaluation of augmentation charges."""
assert val in [True, False]
[docs]def luse_vdw(calc, val):
"""luse_vdw turns on vdW-DF by Langreth and Lundqvist"""
assert val in [True, False]
[docs]def aggac(calc, val):
"""Fraction of gradient correction to correlation in a hybrid calculation"""
assert isinstance(val, float)
aggac = calc.parameters.get("aggac", None)
if aggac is not None and not np.isclose(aggac, 0.0):
warnings.warn("aggac must be 0.0.")
[docs]def gga(calc, val):
"""Grants access to certain special GGAs """
assert isinstance(val, basestring) or val == 91
[docs]def nsim(calc, val):
"""Sets block size for the RMM-DIIS algorithm"""
assert isinstance(val, int) and val > 0
[docs]def kpar(calc, val):
"""Control parallelization over k-points"""
assert isinstance(val, int) and val > 0
[docs]def npar(calc, val):
"""Determines how many bands are run in parallel"""
assert isinstance(val, int) and val > 0
[docs]def amin(calc, val):
"""Initial value of the linear mixing parameter. """
assert isinstance(val, float) and val > 0
[docs]def amix(calc, val):
"""Linear mixing parameter. """
assert isinstance(val, float) and val > 0
[docs]def bmix(calc, val):
"""Controls deviation from linear mixing. """
assert isinstance(val, float) and val > 0
[docs]def nelm(calc, val):
"""Maximum number of allowed iterations in the SCF-cycle. """
assert isinstance(val, int) and val > 0
[docs]def nelmin(calc, val):
"""Minimum number of iterations in the SCF-cycle. """
assert isinstance(val, int) and val > 0
[docs]def nelmdl(calc, val):
"""Number of non-SCF steps. """
assert isinstance(val, int) and val != 0
[docs]def lvtot(calc, val):
"""Controls whether the local potential is written. """
assert isinstance(val, bool)
[docs]def lvhar(calc, val):
"""If True only the electrostatic part of the local potential is written. """
assert isinstance(val, bool)
[docs]def istart(calc, val):
"""Controls the restarting behaviour of VASP. """
assert isinstance(val, int) and val in [0, 1, 2, 3]
[docs]def symprec(calc, val):
"""Controls symmetry-detection precision. """
assert isinstance(val, float) and val < 1.0e-3
[docs]def ldipol(calc, val):
"""Turns dipole corrections on for potential and forces. """
assert isinstance(val, bool)
[docs]def idipol(calc, val):
"""Turns dipole corrections for total energy on along specified axis. """
assert isinstance(val, int) and val in [1, 2, 3, 4]
[docs]def dipol(calc, val):
"""Specifies the center of the cell used for the calculation of the dipole moment. """
assert (isinstance(val, list) or isinstance(val, np.ndarray)) and np.all(
np.logical_and(0.0 <= np.asarray(val), np.asarray(val) <= 1.0)
)
[docs]def keywords():
"""Return list of keywords we vasp_validate.
Returns a lisp list for Emacs.
"""
import vasp_validate
f = [
vasp_validate.__dict__.get(a)
for a in dir(vasp_validate)
if isinstance(vasp_validate.__dict__.get(a), types.FunctionType)
]
names = [x.__name__ for x in f]
names.remove("keywords")
return "(" + " ".join(['"{}"'.format(x) for x in names]) + ")"
[docs]def keyword_alist():
"""Returns an alist of (keyword . "first doc string").
Returns the alist for use in Emacs.
"""
import vasp_validate
f = [
vasp_validate.__dict__.get(a)
for a in dir(vasp_validate)
if isinstance(vasp_validate.__dict__.get(a), types.FunctionType)
]
names = [x.__name__ for x in f]
names.remove("keywords")
names.remove("keyword_alist")
docstrings = [vasp_validate.__dict__[name].__doc__.split("\n")[0] for name in names]
cons_cells = [
'("{}" "{}")'.format(key, doc) for key, doc in zip(names, docstrings)
]
return "(" + "".join(cons_cells) + ")"