From d42a5739be64bfc74b383122b10bf0d1b0a3073d Mon Sep 17 00:00:00 2001
From: Lauri Himanen <lauri.himanen@gmail.com>
Date: Tue, 28 Apr 2020 16:42:04 +0300
Subject: [PATCH] Removed band path label detection. The
BandStructureNormalizer has the same functionality and will apply it for all
codes.
---
vaspparser/parser_vasprun.py | 158 +----------------------------------
1 file changed, 1 insertion(+), 157 deletions(-)
diff --git a/vaspparser/parser_vasprun.py b/vaspparser/parser_vasprun.py
index 50ce84c..e64031c 100644
--- a/vaspparser/parser_vasprun.py
+++ b/vaspparser/parser_vasprun.py
@@ -37,84 +37,12 @@ from nomadcore.unit_conversion.unit_conversion import convert_unit
eV2J = convert_unit_function("eV", "J")
eV2JV = np.vectorize(eV2J)
-
-
-def crystal_structure_from_cell(cell, eps=1e-4):
- """Return the crystal structure as a string calculated from the cell.
- """
- cellpar = ase.geometry.cell_to_cellpar(cell=cell)
- abc = cellpar[:3]
- angles = cellpar[3:] / 180 * pi
- a, b, c = abc
- alpha, beta, gamma = angles
- # According to:
- # https://www.physics-in-a-nutshell.com/article/6/symmetry-crystal-systems-and-bravais-lattices#the-seven-crystal-systems
- # If a=b=c and alpha=beta=gamma=90degrees we have cubic.
- if abc.ptp() < eps and abs(angles - pi / 2).max() < eps:
- return 'cubic'
- elif abc.ptp() < eps and abs(angles - pi / 3).max() < eps:
- return 'fcc'
- elif abc.ptp() < eps and abs(angles - np.arccos(-1 / 3)).max() < eps:
- return 'bcc'
- # If a=b!=c, alpha=beta=gamma=90deg, tetragonal.
- elif abs(a - b) < eps and abs(angles - pi / 2).max() < eps:
- return 'tetragonal'
- elif abs(angles - pi / 2).max() < eps:
- return 'orthorhombic'
- # if a = b != c , alpha = beta = 90deg, gamma = 120deg, hexagonal
- elif (abs(a - b) < eps
- and abs(gamma - pi / 3 * 2) < eps
- and abs(angles[:2] - pi / 2).max() < eps):
- return 'hexagonal'
- elif (c >= a and c >= b and alpha < pi / 2 and
- abs(angles[1:] - pi / 2).max() < eps):
- return 'monoclinic'
- else:
- raise ValueError('Cannot find crystal structure')
-
vasp_to_metainfo_type_mapping = {
'string': ['C'],
'int': ['i'],
'logical': ['b', 'C'],
'float': ['f']}
-special_points = {
- 'cubic': {'Γ': [0, 0, 0],
- 'M': [1 / 2, 1 / 2, 0],
- 'R': [1 / 2, 1 / 2, 1 / 2],
- 'X': [0, 1 / 2, 0]},
- 'fcc': {'Γ': [0, 0, 0],
- 'K': [3 / 8, 3 / 8, 3 / 4],
- 'L': [1 / 2, 1 / 2, 1 / 2],
- 'U': [5 / 8, 1 / 4, 5 / 8],
- 'W': [1 / 2, 1 / 4, 3 / 4],
- 'X': [1 / 2, 0, 1 / 2]},
- 'bcc': {'Γ': [0, 0, 0],
- 'H': [1 / 2, -1 / 2, 1 / 2],
- 'P': [1 / 4, 1 / 4, 1 / 4],
- 'N': [0, 0, 1 / 2]},
- 'tetragonal': {'Γ': [0, 0, 0],
- 'A': [1 / 2, 1 / 2, 1 / 2],
- 'M': [1 / 2, 1 / 2, 0],
- 'R': [0, 1 / 2, 1 / 2],
- 'X': [0, 1 / 2, 0],
- 'Z': [0, 0, 1 / 2]},
- 'orthorhombic': {'Γ': [0, 0, 0],
- 'R': [1 / 2, 1 / 2, 1 / 2],
- 'S': [1 / 2, 1 / 2, 0],
- 'T': [0, 1 / 2, 1 / 2],
- 'U': [1 / 2, 0, 1 / 2],
- 'X': [1 / 2, 0, 0],
- 'Y': [0, 1 / 2, 0],
- 'Z': [0, 0, 1 / 2]},
- 'hexagonal': {'Γ': [0, 0, 0],
- 'A': [0, 0, 1 / 2],
- 'H': [1 / 3, 1 / 3, 1 / 2],
- 'K': [1 / 3, 1 / 3, 0],
- 'L': [1 / 2, 0, 1 / 2],
- 'M': [1 / 2, 0, 0]}}
-
-
special_paths = {
'cubic': 'ΓXMΓRX,MR',
'fcc': 'ΓXWKΓLUWLK,UX',
@@ -125,81 +53,6 @@ special_paths = {
'monoclinic': 'ΓYHCEM1AXH1,MDZ,YD'}
-def get_special_points(cell, eps=1e-4):
- """Return dict of special points.
-
- The definitions are from a paper by Wahyu Setyawana and Stefano
- Curtarolo::
-
- http://dx.doi.org/10.1016/j.commatsci.2010.05.010
-
- lattice: str
- One of the following: cubic, fcc, bcc, orthorhombic, tetragonal,
- hexagonal or monoclinic.
- cell: 3x3 ndarray
- Unit cell.
- eps: float
- Tolerance for cell-check.
- """
-
- lattice = crystal_structure_from_cell(cell)
-
- cellpar = ase.geometry.cell_to_cellpar(cell=cell)
- abc = cellpar[:3]
- angles = cellpar[3:] / 180 * pi
- a, b, c = abc
- alpha, beta, gamma = angles
-
- # Check that the unit-cells are as in the Setyawana-Curtarolo paper:
- if lattice == 'cubic':
- assert abc.ptp() < eps and abs(angles - pi / 2).max() < eps
- elif lattice == 'fcc':
- assert abc.ptp() < eps and abs(angles - pi / 3).max() < eps
- elif lattice == 'bcc':
- angle = np.arccos(-1 / 3)
- assert abc.ptp() < eps and abs(angles - angle).max() < eps
- elif lattice == 'tetragonal':
- assert abs(a - b) < eps and abs(angles - pi / 2).max() < eps
- elif lattice == 'orthorhombic':
- assert abs(angles - pi / 2).max() < eps
- elif lattice == 'hexagonal':
- assert abs(a - b) < eps
- assert abs(gamma - pi / 3 * 2) < eps
- assert abs(angles[:2] - pi / 2).max() < eps
- elif lattice == 'monoclinic':
- assert c >= a and c >= b
- assert alpha < pi / 2 and abs(angles[1:] - pi / 2).max() < eps
- if lattice != 'monoclinic':
- return special_points[lattice]
-
- # Here, we need the cell:
- eta = (1 - b * np.cos(alpha) / c) / (2 * np.sin(alpha)**2)
- nu = 1 / 2 - eta * c * np.cos(alpha) / b
- return {'Γ': [0, 0, 0],
- 'A': [1 / 2, 1 / 2, 0],
- 'C': [0, 1 / 2, 1 / 2],
- 'D': [1 / 2, 0, 1 / 2],
- 'D1': [1 / 2, 0, -1 / 2],
- 'E': [1 / 2, 1 / 2, 1 / 2],
- 'H': [0, eta, 1 - nu],
- 'H1': [0, 1 - eta, nu],
- 'H2': [0, eta, -nu],
- 'M': [1 / 2, eta, 1 - nu],
- 'M1': [1 / 2, 1 - eta, nu],
- 'M2': [1 / 2, eta, -nu],
- 'X': [0, 1 / 2, 0],
- 'Y': [0, 0, 1 / 2],
- 'Y1': [0, 0, -1 / 2],
- 'Z': [1 / 2, 0, 0]}
-
-
-def findLabel(labels, value):
- for k, v in labels.items():
- if np.all(np.abs(v-value) < 1.e-5):
- return k
- return "?"
-
-
def secondsFromEpoch(date):
epoch = datetime(1970, 1, 1)
ts = date-epoch
@@ -603,7 +456,7 @@ class VasprunContext(object):
kpt = np.reshape(
self.kpoints, (nsegments, divisions, 3))
energies = np.reshape(
- ev, (self.ispin, nsegments, divisions, bands.shape[0]))
+ ev, (self.ispin, nsegments, divisions, bands.shape[0]))
occ = np.reshape(
occupation, (self.ispin, nsegments, divisions, bands.shape[0]))
for isegment in range(nsegments):
@@ -623,12 +476,6 @@ class VasprunContext(object):
backend.closeNonOverlappingSection("section_k_band")
backend.openNonOverlappingSection(
"section_k_band_normalized")
- specialPoints = {}
- try:
- specialPoints = get_special_points(
- convert_unit_function("m", "angstrom")(self.cell))
- except Exception as e:
- self.logger.warn("failed to get special points/xtal structure", exc_info=e)
for isegment in range(nsegments):
backend.openNonOverlappingSection(
"section_k_band_segment_normalized")
@@ -640,9 +487,6 @@ class VasprunContext(object):
"band_k_points_normalized", kpt[isegment])
backend.addArrayValues("band_segm_start_end_normalized", np.asarray(
[kpt[isegment, 0], kpt[isegment, divisions - 1]]))
- backend.addValue("band_segm_labels_normalized",
- [findLabel(specialPoints, kpt[isegment, 0]),
- findLabel(specialPoints, kpt[isegment, divisions - 1])])
backend.closeNonOverlappingSection(
"section_k_band_segment_normalized")
--
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