# -*- coding: utf-8 -*-
"""Setup DFTB+"""
import logging
from pathlib import Path
import textwrap
import numpy as np
import pandas
import seekpath
import dftbplus_step
import seamm
import seamm.data
from seamm_util import Q_, units_class
import seamm_util.printing as printing
from seamm_util.printing import FormattedText as __
from .base import DftbBase
logger = logging.getLogger(__name__)
job = printing.getPrinter()
printer = printing.getPrinter("DFTB+")
[docs]
def fix_label(label):
"Convert a label such as GAMMA to the greek letter."
if label == "GAMMA":
return "\N{GREEK CAPITAL LETTER GAMMA}"
else:
return label
[docs]
class BandStructure(DftbBase):
def __init__(
self, flowchart=None, title="Band Structure", extension=None, logger=logger
):
"""Initialize the node"""
logger.debug("Creating BandStructure {}".format(self))
super().__init__(flowchart=flowchart, title=title, extension=extension)
self._calculation = "band structure"
self._model = None
self._metadata = dftbplus_step.metadata
self.parameters = dftbplus_step.BandStructureParameters()
self.description = ["Band Structure for DFTB+"]
self.sym_points = None # Points along graphs of symmetry lines
self.sym_labels = None # Labels of the symmetry lines
self.path = None # Coordinates along the path
self.energy_step = None # The step that got the energy and density
@property
def header(self):
"""A printable header for this section of output"""
return "Step {}: {}".format(".".join(str(e) for e in self._id), self.title)
@property
def version(self):
"""The semantic version of this module."""
return dftbplus_step.__version__
@property
def git_revision(self):
"""The git version of this module."""
return dftbplus_step.__git_revision__
[docs]
def description_text(self, P=None):
"""Prepare information about what this node will do"""
if not P:
P = self.parameters.values_to_dict()
text = "Calculate the band structure with {nPoints} points."
return self.header + "\n" + __(text, indent=4 * " ").__str__()
[docs]
def analyze(self, indent="", data={}, out=[]):
"""Parse the output and generating the text output and store the
data in variables for other stages to access
"""
# Print the key results
text = "Prepared the band structure graph."
# Prepare the band structure graph(s)
if "fermi_level" in self.energy_step.results:
Efermi = list(
Q_(self.energy_step.results["fermi_level"], "hartree")
.to("eV")
.magnitude
)
else:
raise RuntimeError("Serious problem in the Band Structure: no Fermi level!")
# Need the DOS information either from a preceding DOS step or the energy step
step = self.find_previous_step(dftbplus_step.DOS)
if step is None:
step = self.energy_step
else:
# Is it after the energy step?
dos_id = int(step._id[-1])
energy_id = int(self.energy_step._id[-1])
if dos_id < energy_id:
step = self.energy_step
dos_path = Path(step.directory) / "DOS.csv"
if dos_path.exists():
DOS = pandas.read_csv(dos_path, index_col=0)
else:
DOS = None
wd = Path(self.directory)
self.band_structure(
wd / "band.out",
self.sym_points,
self.sym_labels,
Efermi=Efermi,
DOS=DOS,
)
printer.normal(__(text, **data, indent=self.indent + 4 * " "))
# Put any requested results into variables or tables
self.store_results(
data=data,
properties=dftbplus_step.properties,
results=self.parameters["results"].value,
create_tables=self.parameters["create tables"].get(),
)
[docs]
def kpoints(self, nPoints):
"""Create the lines of kpoints for DFTB+."""
system, configuration = self.get_system_configuration(None)
cell_data = configuration.primitive_cell()
# Get the lines
seekpath_output = seekpath.get_path(cell_data[0:3], with_time_reversal=True)
# Get the total length of the path.
total_length = 0.0
for start_label, stop_label in seekpath_output["path"]:
start_coord = np.array(seekpath_output["point_coords"][start_label])
stop_coord = np.array(seekpath_output["point_coords"][stop_label])
start_coord_abs = np.dot(
start_coord, seekpath_output["reciprocal_primitive_lattice"]
)
stop_coord_abs = np.dot(
stop_coord, seekpath_output["reciprocal_primitive_lattice"]
)
segment_length = np.linalg.norm(stop_coord_abs - start_coord_abs)
total_length += segment_length
# And extra points needed -- 1 at start, and one at each break
last_label = ""
extra_points = 0
for start_label, stop_label in seekpath_output["path"]:
if start_label != last_label:
extra_points += 1
last_label = stop_label
n = nPoints - extra_points
result = []
last_label = ""
total = 0
self.sym_points = points = []
self.sym_labels = labels = []
self.path = path = []
for start_label, stop_label in seekpath_output["path"]:
start_coord = np.array(seekpath_output["point_coords"][start_label])
stop_coord = np.array(seekpath_output["point_coords"][stop_label])
start_coord_abs = np.dot(
start_coord, seekpath_output["reciprocal_primitive_lattice"]
)
stop_coord_abs = np.dot(
stop_coord, seekpath_output["reciprocal_primitive_lattice"]
)
segment_length = np.linalg.norm(stop_coord_abs - start_coord_abs)
# See if we needed an added point at the start
if start_label != last_label:
x, y, z = start_coord.tolist()
result.append(f" 1 {x:7.4f} {y:7.4f} {z:7.4f} # {start_label}")
total += 1
points.append(total)
labels.append(fix_label(start_label))
path.append(f"{x:6.3f} {y:6.3f} {z:6.3f}")
last_label = stop_label
num_points = max(2, int(round(n * segment_length / total_length)))
x, y, z = stop_coord.tolist()
result.append(f"{num_points:4} {x:7.4f} {y:7.4f} {z:7.4f} # {stop_label}")
delta = (stop_coord - start_coord) / num_points
for i in range(num_points):
start_coord += delta
x, y, z = start_coord.tolist()
path.append(f"{x:6.3f} {y:6.3f} {z:6.3f}")
total += num_points
points.append(total)
labels.append(fix_label(stop_label))
result.append("}")
result = textwrap.indent("\n".join(result), 8 * " ")
return "Klines {\n" + result
