Merge branch '4-create-projected-dos' into 'master'

Resolve "Create projected DOS plot/reader"

Closes orest-d#4

See merge request schlipf/py4vasp!5

src/py4vasp/data/dos.py

@@ -1,34 +1,151 @@
+import re
+import functools
+import itertools
+import numpy as np
 import pandas as pd
 import cufflinks as cf
+from collections import namedtuple
 
 cf.go_offline()
 
 
 class Dos:
+ _Index = namedtuple("_Index", "spin, atom, orbital")
+ _Atom = namedtuple("_Atom", "indices, label")
+ _Orbital = namedtuple("_Orbital", "indices, label")
+ _Spin = namedtuple("_Spin", "indices, label")
+
  def __init__(self, vaspout):
  self._fermi_energy = vaspout["results/dos/efermi"][()]
  self._energies = vaspout["results/dos/energies"]
  self._dos = vaspout["results/dos/dos"]
  self._spin_polarized = self._dos.shape[0] == 2
+ self._has_partial_dos = vaspout["results/dos/jobpar"][()] == 1
+ if self._has_partial_dos:
+ self._init_partial_dos(vaspout)
 
- def read(self):
- if self._spin_polarized:
- data = {"up": self._dos[0, :], "down": self._dos[1, :]}
- else:
- data = {"total": self._dos[0, :]}
- data["energies"] = self._energies[:] - self._fermi_energy
- df = pd.DataFrame(data)
- df.fermi_energy = self._fermi_energy
- return df
+ def _init_partial_dos(self, vaspout):
+ self._partial_dos = vaspout["results/dos/dospar"]
+ ion_types = vaspout["results/positions/ion_types"]
+ ion_types = [type.decode().strip() for type in ion_types]
+ self._init_atom_dict(ion_types, vaspout["results/positions/number_ion_types"])
+ orbitals = vaspout["results/projectors/lchar"]
+ orbitals = [orb.decode().strip() for orb in orbitals]
+ self._init_orbital_dict(orbitals)
+ self._init_spin_dict()
+
+ def _init_atom_dict(self, ion_types, number_ion_types):
+ num_atoms = self._partial_dos.shape[1]
+ all_atoms = self._Atom(indices=range(num_atoms), label=None)
+ self._atom_dict = {"*": all_atoms}
+ start = 0
+ for type, number in zip(ion_types, number_ion_types):
+ _range = range(start, start + number)
+ self._atom_dict[type] = self._Atom(indices=_range, label=type)
+ for i in _range:
+ # create labels like Si_1, Si_2, Si_3 (starting at 1)
+ label = type + "_" + str(_range.index(i) + 1)
+ self._atom_dict[str(i + 1)] = self._Atom(indices=[i], label=label)
+ start += number
+ # atoms may be preceeded by :
+ for key in self._atom_dict.copy():
+ self._atom_dict[key + ":"] = self._atom_dict[key]
+
+ def _init_orbital_dict(self, orbitals):
+ num_orbitals = self._partial_dos.shape[2]
+ all_orbitals = self._Orbital(indices=range(num_orbitals), label=None)
+ self._orbital_dict = {"*": all_orbitals}
+ for i, orbital in enumerate(orbitals):
+ self._orbital_dict[orbital] = self._Orbital(indices=[i], label=orbital)
+ if "px" in self._orbital_dict:
+ self._orbital_dict["p"] = self._Orbital(indices=range(1, 4), label="p")
+ self._orbital_dict["d"] = self._Orbital(indices=range(4, 9), label="d")
+ self._orbital_dict["f"] = self._Orbital(indices=range(9, 16), label="f")
 
- def plot(self):
- df = self.read()
+ def _init_spin_dict(self):
+ labels = ["up", "down"] if self._spin_polarized else [None]
+ self._spin_dict = {
+ key: self._Spin(indices=[i], label=key) for i, key in enumerate(labels)
+ }
+
+ def plot(self, selection=None):
+ df = self.to_frame(selection)
  if self._spin_polarized:
- df.down = -df.down
+ for col in filter(lambda col: "down" in col, df):
+ df[col] = -df[col]
  default = {
  "x": "energies",
  "xTitle": "Energy (eV)",
  "yTitle": "DOS (1/eV)",
  "asFigure": True,
  }
  return df.iplot(**default)
+
+ def read(self, selection=None):
+ return self.to_dict(selection)
+
+ def to_dict(self, selection=None):
+ return {**self._read_data(selection), "fermi_energy": self._fermi_energy}
+
+ def to_frame(self, selection=None):
+ df = pd.DataFrame(self._read_data(selection))
+ df.fermi_energy = self._fermi_energy
+ return df
+
+ def _read_data(self, selection):
+ return {
+ **self._read_energies(),
+ **self._read_total_dos(),
+ **self._read_partial_dos(selection),
+ }
+
+ def _read_energies(self):
+ return {"energies": self._energies[:] - self._fermi_energy}
+
+ def _read_total_dos(self):
+ if self._spin_polarized:
+ return {"up": self._dos[0, :], "down": self._dos[1, :]}
+ else:
+ return {"total": self._dos[0, :]}
+
+ def _read_partial_dos(self, selection):
+ if selection is None:
+ return {}
+ self._raise_error_if_partial_Dos_not_available()
+ parts = self._parse_filter(selection)
+ return self._read_elements(parts)
+
+ def _raise_error_if_partial_Dos_not_available(self):
+ if not self._has_partial_dos:
+ raise ValueError(
+ "Filtering requires partial DOS which was not found in HDF5 file."
+ )
+
+ def _parse_filter(self, selection):
+ atom = self._atom_dict["*"]
+ selection = re.sub("\s*:\s*", ": ", selection)
+ for part in re.split("[ ,]+", selection):
+ if part in self._orbital_dict:
+ orbital = self._orbital_dict[part]
+ else:
+ atom = self._atom_dict[part]
+ orbital = self._orbital_dict["*"]
+ if ":" not in part: # exclude ":" because it starts a new atom
+ for spin in self._spin_dict.values():
+ yield atom, orbital, spin
+
+ def _read_elements(self, parts):
+ res = {}
+ for atom, orbital, spin in parts:
+ label = self._merge_labels([atom.label, orbital.label, spin.label])
+ index = self._Index(spin.indices, atom.indices, orbital.indices)
+ res[label] = self._read_element(index)
+ return res
+
+ def _merge_labels(self, labels):
+ return "_".join(filter(None, labels))
+
+ def _read_element(self, index):
+ sum_dos = lambda dos, i: dos + self._partial_dos[i]
+ zero_dos = np.zeros_like(self._energies[:])
+ return functools.reduce(sum_dos, itertools.product(*index), zero_dos)