# -*- coding: utf-8 -*-
__author__ = "Pedram Tavadze and Logan Lang"
__maintainer__ = "Pedram Tavadze and Logan Lang"
__email__ = "petavazohi@mail.wvu.edu, lllang@mix.wvu.edu"
__date__ = "March 31, 2020"
import os
from typing import List, Tuple
import yaml
import numpy as np
import matplotlib.pyplot as plt
from pyprocar.utils import welcome, ROOT
from pyprocar.utils.info import orbital_names
from pyprocar import io
from pyprocar.plotter import DOSPlot
from pyprocar.cfg import ConfigFactory, ConfigManager, PlotType
[docs]
def dosplot(
code:str="vasp",
dirname:str=None,
mode:str="plain",
orientation:str="horizontal",
spins:List[int]=None,
atoms:List[int]=None,
orbitals:List[int]=None,
items:dict={},
normalize_dos_mode:str=None,
fermi:float=None,
fermi_shift:float=0,
elimit:List[float]=None,
dos_limit:List[float]=None,
savefig:str=None,
labels:List[str]=None,
projection_mask=None,
ax:plt.Axes=None,
show:bool=True,
print_plot_opts:bool=False,
export_data_file:str=None,
export_append_mode:bool=True,
**kwargs
):
"""
This function plots the density of states in different formats
Parameters
----------
filename : str, optional (default ``'vasprun.xml'``)
The most important argument needed dosplot is
**filename**. **filename** defines the path to `vasprun.xml`
from the density of states calculation. If plotting is being
carried out in the directory of the calculation, one does not
need to specify this argument.
e.g. ``filename='~/SrVO3/DOS/vasprun.xml'``
dirname : str, optional (default ``'vasprun.xml'``)
This is used for qe and lobster codes. It specifies the directory the dosplot
calculation was performed.
e.g. ``dirname='~/SrVO3/dos'``
mode : str, optional (default ``'plain'``)
**mode** defines the mode of the plot. This parameter will be
explained in details with exmaples in the tutorial.
options are ``'plain'``, ``'parametric'``,
``'parametric_line'``, ``'stack'``,
``'stack_orbitals'``, ``'stack_species'``.
e.g. ``mode='stack'``
orientation : str, optional (default ``horizontal'``)
The orientation of the DOS plot. options are
``'horizontal', 'vertical'``
e.g. ``orientation='vertical'``
spins : list int, optional
``spins`` defines plotting of different spins channels present
in the calculation, If the calculation is spin non-polorized
the spins will be set by default to ``spins=[0]``. if the
calculation is spin polorized this parameter can be set to 0
or 1 or both.
e.g. ``spins=[0, 1]``
atoms : list int, optional
``atoms`` define the projection of the atoms in the Density of
States. In other words it selects only the contribution of the
atoms provided. Atoms has to be a python list(or numpy array)
containing the atom indices. Atom indices has to be order of
the input files of DFT package. ``atoms`` is only relevant in
``mode='parametric'``, ``mode='parametric_line'``,
``mode='stack_orbitals'``. keep in mind that python counting
starts from zero.
e.g. for SrVO\ :sub:`3`\ we are choosing only the oxygen
atoms. ``atoms=[2, 3, 4]``, keep in mind that python counting
starts from zero, for a **POSCAR** similar to following::
Sr1 V1 O3
1.0
3.900891 0.000000 0.000000
0.000000 3.900891 0.000000
0.000000 0.000000 3.900891
Sr V O
1 1 3
direct
0.500000 0.500000 0.500000 Sr atom 0
0.000000 0.000000 0.000000 V atom 1
0.000000 0.500000 0.000000 O atom 2
0.000000 0.000000 0.500000 O atom 3
0.500000 0.000000 0.000000 O atom 4
if nothing is specified this parameter will consider all the
atoms present.
orbitals : list int, optional
``orbitals`` define the projection of orbitals in the density
of States. In other words it selects only the contribution of
the orbitals provided. Orbitals has to be a python list(or
numpy array) containing the Orbital indices. Orbitals indices
has to be order of the input files of DFT package. The
following table represents the indecies for different orbitals
in **VASP**.
.. code-block::
:linenos:
+-----+-----+----+----+-----+-----+-----+-----+-------+
| s | py | pz | px | dxy | dyz | dz2 | dxz | x2-y2 |
+-----+-----+----+----+-----+-----+-----+-----+-------+
| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
+-----+-----+----+----+-----+-----+-----+-----+-------+
``orbitals`` is only relavent in ``mode='parametric'``,
``mode='parametric_line'``, ``mode='stack_species'``.
e.g. ``orbitals=[1,2,3]`` will only select the p orbitals
while ``orbitals=[4,5,6,7,8]`` will select the d orbitals.
If nothing is specified pyprocar will select all the present
orbitals.
normalize_dos_mode : str, optional
This defines the mode of the normalization of the density of states. The default is None.
If None, the density of states will not be normalized.
elimit : list float, optional
Energy window limit asked to plot. ``elimit`` has to be a two
element python list(or numpy array).
e.g. ``elimit=[-2, 2]``
The default is set to the minimum and maximum of the energy
window.
dos_limit : list float, optional
``dos_limit`` defines the density of states axis limits on the
graph. It is automatically set to select 10% higher than the
maximum of density of states in the specified energy window.
e.g. ``dos_limit=[0, 30]``
labels : list str, optional
``labels`` is a list of strings that will be used as the
legend of the plot. The length of the list should be equal to
the number of curves being plotted. If not provided the
default labels will be used.
savefig : str , optional (default None)
``savefig`` defines the file that the plot is going to be
saved in. ``savefig`` accepts all the formats accepted by
matplotlib such as png, pdf, jpg, ...
If not provided the plot will be shown in the
interactive matplotlib mode.
e.g. ``savefig='DOS.png'``, ``savefig='DOS.pdf'``
plot_total : bool, optional (default ``True``)
If the total density of states is plotted as well as other
options. The entry should be python boolian.
e.g. ``plot_total=True``
code : str, optional (default ``'vasp'``)
Defines the Density Functional Theory code used for the
calculation. The default of this argument is vasp, so if the
cal is done in vasp one does not need to define this argumnet.
e.g. ``code=vasp``, ``code=elk``, ``code=abinit``
items : dict, optional
``items`` is only relavent for ``mode='stack'``. stack will
plot the items defined with stacked filled areas under
curve. For clarification visit the examples in the
tutorial. ``items`` need to be provided as a python
dictionary, with keys being specific species and values being
projections of ``orbitals``. The following examples can
clarify the python lingo.
e.g. ``items={'Sr':[0],'O':[1,2,3],'V':[4,5,6,7,8]}`` or
``items=dict(Sr=[0],O=[1,2,3],V=[4,5,6,7,8])``. The two
examples are equivalent to each other. This will plot the
following curves stacked on top of each other. projection of s
orbital in Sr, projection of p orbitals in O and projection of
d orbitals in V.
The default is set to take every atom and every orbital. Which
will be equivalent to ``mode='stack_species'``
fermi : float, optional
``fermi`` defines the fermi energy. If not provided the
fermi energy will be read from the calculation directory
ax : matplotlib ax object, optional
``ax`` is a matplotlib axes. In case one wants to put plot
generated from this plot in a different figure and treat the
output as a subplot in a larger plot.
e.g. ::
>>> # Creates a figure with 3 rows and 2 colomuns
>>> fig, axs = plt.subplots(3, 2)
>>> x = np.linspace(-np.pi, np.pi, 1000)
>>> y = np.sin(x)
>>> axs[0, 0].plot(x, y)
>>> pyprocar.dosplot(mode='plain',ax=axs[2, 2]),elimit=[-2,2])
>>> plt.show()
plt_show : bool, optional (default ``True``)
whether to show the generated plot or skip to the saving.
e.g. ``plt_show=True``
export_data_file : str, optional
The file name to export the data to. If not provided the
data will not be exported.
export_append_mode : bool, optional
Boolean to append the mode to the file name. If not provided the
data will be overwritten.
print_plot_opts: bool, optional
Boolean to print the plotting options
Returns
-------
fig : matplotlib figure
The generated figure
ax : matplotlib ax object
The generated ax for this density of states.
If one chooses ``plt_show=False``, one can modify the plot
using this returned object.
e.g. ::
>>> fig, ax = pyprocar.dosplot(mode='plain', plt_show=False)
>>> ax.set_ylim(-2,2)
>>> fig.show()
"""
default_config = ConfigFactory.create_config(PlotType.DENSITY_OF_STATES)
config=ConfigManager.merge_configs(default_config, kwargs)
modes_txt=' , '.join(config.modes)
message=f"""
--------------------------------------------------------
There are additional plot options that are defined in a configuration file.
You can change these configurations by passing the keyword argument to the function
To print a list of plot options set print_plot_opts=True
Here is a list modes : {modes_txt}
--------------------------------------------------------"""
print(message)
if print_plot_opts:
for key,value in default_config.as_dict().items():
print(key,':',value)
if orientation[0].lower() == 'h':
orientation = 'horizontal'
elif orientation[0].lower() == 'v':
orientation = 'vertical'
parser = io.Parser(code = code, dir = dirname)
dos = parser.dos
structure = parser.structure
codes_with_scf_fermi = ['qe', 'elk']
if code in codes_with_scf_fermi and fermi is None:
fermi = dos.efermi
if fermi is not None:
dos.energies -= fermi
dos.energies += fermi_shift
fermi_level = fermi_shift
energy_label=r"Energy - E$_F$ (eV)"
else:
energy_label=r"Energy (eV)"
print("""
WARNING : `fermi` is not set! Set `fermi={value}`. The plot did not shift the energy by the Fermi energy.
----------------------------------------------------------------------------------------------------------
""")
if normalize_dos_mode:
dos.normalize_dos(mode=normalize_dos_mode)
if elimit is None:
elimit = [dos.energies.min(), dos.energies.max()]
edos_plot = DOSPlot(dos = dos, structure = structure, ax=ax, orientation = orientation, config=config)
if mode == "plain":
values_dict = edos_plot.plot_dos(spins=spins)
elif mode == "parametric":
if atoms is None:
atoms = list(np.arange(edos_plot.structure.natoms, dtype=int))
if spins is None:
spins = list(np.arange(len(edos_plot.dos.total)))
if orbitals is None:
orbitals = list(np.arange(len(edos_plot.dos.projected[0][0]), dtype=int))
values_dict = edos_plot.plot_parametric(
atoms=atoms,
principal_q_numbers=[-1],
orbitals=orbitals,
spins=spins)
elif mode == "parametric_line":
if atoms is None:
atoms = list(np.arange(edos_plot.structure.natoms, dtype=int))
if spins is None:
spins = list(np.arange(len(edos_plot.dos.total)))
if orbitals is None:
orbitals = list(np.arange(len(edos_plot.dos.projected[0][0]), dtype=int))
edos_plot.plot_parametric_line(
atoms=atoms,
principal_q_numbers=[-1],
spins=spins,
orbitals=orbitals,
)
elif mode == "stack_species":
edos_plot.plot_stack_species(
spins=spins,
orbitals=orbitals,
)
elif mode == "stack_orbitals":
edos_plot.plot_stack_orbitals(
spins=spins,
atoms=atoms,
)
elif mode == "stack":
edos_plot.plot_stack(
spins=spins,
items=items,
)
elif mode == "overlay_species":
edos_plot.plot_stack_species(
spins=spins,
orbitals=orbitals,
overlay_mode=True
)
elif mode == "overlay_orbitals":
edos_plot.plot_stack_orbitals(
spins=spins,
atoms=atoms,
overlay_mode=True
)
elif mode == "overlay":
edos_plot.plot_stack(
spins=spins,
items=items,
overlay_mode=True
)
else:
raise ValueError("The mode needs to be in the List [plain,parametric,parametric_line,stack_species,stack_orbitals,stack]")
if fermi is not None:
edos_plot.draw_fermi(fermi_level, orientation = orientation)
if orientation == 'horizontal':
edos_plot.set_xlabel(label=energy_label)
edos_plot.set_ylabel(label="DOS")
if elimit is not None:
edos_plot.set_xlim(elimit)
if dos_limit is not None:
edos_plot.set_ylim(dos_limit)
elif orientation == 'vertical':
edos_plot.set_xlabel(label="DOS")
edos_plot.set_ylabel(label=energy_label)
if elimit is not None:
edos_plot.set_ylim(elimit)
if dos_limit is not None:
edos_plot.set_xlim(dos_limit)
edos_plot.grid()
if labels:
labels=labels
else:
labels=edos_plot.labels
edos_plot.legend(labels)
if savefig is not None:
edos_plot.save(savefig)
if show:
edos_plot.show()
if export_data_file is not None:
if export_append_mode:
file_basename,file_type=export_data_file.split('.')
filename=f"{file_basename}_{mode}.{file_type}"
else:
filename=export_data_file
edos_plot.export_data(filename)
return edos_plot.fig, edos_plot.ax