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PAWpySeed
Parallel C/Python package for numerical analysis of PAW DFT wavefunctions
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PAWpySeed
Parallel C/Python package for numerical analysis of PAW DFT wavefunctions
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Public Member Functions | |
| def | __init__ (self, struct, pwf, cr, outcar, setup_projectors=False) |
| def | get_c_projectors_from_pps (self, pps) |
| def | make_c_projectors (self) |
| def | check_c_projectors (self) |
| def | get_state_realspace (self, b, k, s, dim=None) |
| def | write_state_realspace (self, b, k, s, fileprefix="", dim=None, return_wf=False) |
| def | write_density_realspace (self, filename="PYAECCAR", dim=None, return_wf=False) |
| def | get_symmops (self, symprec) |
| def | get_nosym_kpoints (self, init_kpts=None, symprec=1e-5, gen_trsym=True, fil_trsym=True) |
| def | get_kpt_mapping (self, allkpts, symprec=1e-5, gen_trsym=True) |
| def | kpts (self) |
| def | kws (self) |
| def | free_all (self) |
Static Public Member Functions | |
| def | from_files (struct="CONTCAR", pwf="WAVECAR", cr="POTCAR", vr="vasprun.xml", outcar="OUTCAR", setup_projectors=False) |
| def | from_directory (path, setup_projectors=False) |
| def | from_atomate_directory (path, setup_projectors=False) |
Public Attributes | |
| structure | |
| pwf | |
| cr | |
| dim | |
| projector_owner | |
| projector_list | |
| nums | |
| coords | |
| nband | |
| nwk | |
| nspin | |
| encut | |
| num_proj_els | |
| freed | |
| nosym_kpts | |
| orig_kptnums | |
| op_nums | |
| symmops | |
Class for storing and manipulating all electron wave functions in the PAW
formalism.
Attributes:
structure (pymatgen.core.structure.Structure): stucture of the material
that the wave function describes
pwf (PseudoWavefunction): Pseudowavefunction componenet
cr (CoreRegion): Contains the pseudopotentials, with projectors and
partials waves, for the structure
projector: ctypes object for interfacing with C code
wf_ptr (C pointer): pointer to the pswf_t C object for this wavefunction
dim (np.ndarray, length 3): dimension of the FFT grid used by VASP
and therefore for FFTs in this code
| def pawpyseed.core.wavefunction.Wavefunction.__init__ | ( | self, | |
| struct, | |||
| pwf, | |||
| cr, | |||
| outcar, | |||
setup_projectors = False |
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| ) |
Arguments:
struct (pymatgen.core.Structure): structure that the wavefunction describes
pwf (PseudoWavefunction): Pseudowavefunction component
cr (CoreRegion): Contains the pseudopotentials, with projectors and
partials waves, for the structure
outcar (pymatgen.io.vasp.outputs.Outcar): Outcar object for reading ngf
setup_projectors (bool, False): Whether to set up the core region
components of the wavefunctions (leave as False if passing this
object to Projector, which will do the setup automatically)
Returns:
Wavefunction object
| def pawpyseed.core.wavefunction.Wavefunction.check_c_projectors | ( | self | ) |
Check to see if the projector functions have been read in and set up. If not, do so.
| def pawpyseed.core.wavefunction.Wavefunction.free_all | ( | self | ) |
Frees all of the C structures associated with the Wavefunction object. After being called, this object is not usable.
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static |
Assumes VASP output has the default filenames and is located
in the directory specificed by path. Checks for
gzipped files created by atomate
Arguments:
path (str): VASP output directory
setup_projectors (bool, False): Whether to set up the core region
components of the wavefunctions (leave as False if passing this
object to Projector, which will do the setup automatically)
Returns:
Wavefunction object
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static |
Assumes VASP output has the default filenames and is located
in the directory specificed by path.
Arguments:
path (str): VASP output directory
setup_projectors (bool, False): Whether to set up the core region
components of the wavefunctions (leave as False if passing this
object to Projector, which will do the setup automatically)
Returns:
Wavefunction object
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static |
Construct a Wavefunction object from file paths.
Arguments:
struct (str): VASP POSCAR or CONTCAR file path
pwf (str): VASP WAVECAR file path
cr (str): VASP POTCAR file path
vr (str): VASP vasprun file path
outcar (str): VASP OUTCAR file path
Returns:
Wavefunction object
| def pawpyseed.core.wavefunction.Wavefunction.get_c_projectors_from_pps | ( | self, | |
| pps | |||
| ) |
Returns a point to a list of ppot_t objects in C,
to be used for high performance parts of the code
Args:
pps (dict of Pseudopotential objects): keys are integers,
values of Pseudopotential objects
Returns:
c_void_p object pointing to ppot_t list with each Pseudopotential,
ordered in the list by their numerical keys
| def pawpyseed.core.wavefunction.Wavefunction.get_kpt_mapping | ( | self, | |
| allkpts, | |||
symprec = 1e-5, |
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gen_trsym = True |
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| ) |
| def pawpyseed.core.wavefunction.Wavefunction.get_nosym_kpoints | ( | self, | |
init_kpts = None, |
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symprec = 1e-5, |
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gen_trsym = True, |
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fil_trsym = True |
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| ) |
| def pawpyseed.core.wavefunction.Wavefunction.get_state_realspace | ( | self, | |
| b, | |||
| k, | |||
| s, | |||
dim = None |
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| ) |
Returns the real and imaginary parts of a given band.
Args:
b (int): band number
k (int): kpoint number
s (int): spin number
dim (numpy array of 3 ints): dimensions of the FFT grid
Returns:
An array (x slow-indexed) where the first half of the values
are the real part and second half of the values are the
imaginary part
| def pawpyseed.core.wavefunction.Wavefunction.get_symmops | ( | self, | |
| symprec | |||
| ) |
| def pawpyseed.core.wavefunction.Wavefunction.kpts | ( | self | ) |
| def pawpyseed.core.wavefunction.Wavefunction.kws | ( | self | ) |
| def pawpyseed.core.wavefunction.Wavefunction.make_c_projectors | ( | self | ) |
Uses the CoreRegion objects in self and basis (if not None)
to construct C representations of the projectors and partial waves
for a structure. Also assigns numerical labels for each element and
returns a list of indices and positions which can be easily converted
to C lists for projection functions.
Arguments:
basis (None or Wavefunction): an additional structure from which
to include pseudopotentials. E.g. can be useful if a basis contains
some different elements than self.
Returns:
projector_list (C pointer): describes the pseudopotential data in C
selfnums (int32 numpy array): numerical element label for each site in
the structure
selfcoords (float64 numpy array): flattened list of coordinates of each site
in self
basisnums (if basis != None): same as selfnums, but for basis
basiscoords (if basis != None): same as selfcoords, but for basis
| def pawpyseed.core.wavefunction.Wavefunction.write_density_realspace | ( | self, | |
filename = "PYAECCAR", |
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dim = None, |
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return_wf = False |
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| ) |
Writes the AE charge density to a file. Returns it if desired.
Args:
b (int): band number
k (int): kpoint number
s (int): spin number
dim (numpy array of 3 ints): dimensions of the FFT grid
filename (string, "PYAECCAR"): charge density filename
return_wf (bool): whether to return the wavefunction
Returns:
(if return_wf==True) An array (x slow-indexed, as in VASP)
with the charge densities
The charge density is written with z the slow index.
| def pawpyseed.core.wavefunction.Wavefunction.write_state_realspace | ( | self, | |
| b, | |||
| k, | |||
| s, | |||
fileprefix = "", |
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dim = None, |
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return_wf = False |
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| ) |
Writes the real and imaginary parts of a given band to two files,
prefixed by fileprefix
Args:
b (int): band number (0-indexed!)
k (int): kpoint number (0-indexed!)
s (int): spin number (0-indexed!)
dim (numpy array of 3 ints): dimensions of the FFT grid
fileprefix (string, optional): first part of the file name
return_wf (bool): whether to return the wavefunction
Returns:
(if return_wf==True) An array (x slow-indexed) where the first half of the values
are the real part and second half of the values are the
imaginary part
The wavefunction is written with z the slow index.
| pawpyseed.core.wavefunction.Wavefunction.coords |
| pawpyseed.core.wavefunction.Wavefunction.cr |
| pawpyseed.core.wavefunction.Wavefunction.dim |
| pawpyseed.core.wavefunction.Wavefunction.encut |
| pawpyseed.core.wavefunction.Wavefunction.freed |
| pawpyseed.core.wavefunction.Wavefunction.nband |
| pawpyseed.core.wavefunction.Wavefunction.nosym_kpts |
| pawpyseed.core.wavefunction.Wavefunction.nspin |
| pawpyseed.core.wavefunction.Wavefunction.num_proj_els |
| pawpyseed.core.wavefunction.Wavefunction.nums |
| pawpyseed.core.wavefunction.Wavefunction.nwk |
| pawpyseed.core.wavefunction.Wavefunction.op_nums |
| pawpyseed.core.wavefunction.Wavefunction.orig_kptnums |
| pawpyseed.core.wavefunction.Wavefunction.projector_list |
| pawpyseed.core.wavefunction.Wavefunction.projector_owner |
| pawpyseed.core.wavefunction.Wavefunction.pwf |
| pawpyseed.core.wavefunction.Wavefunction.structure |
| pawpyseed.core.wavefunction.Wavefunction.symmops |
1.8.11