Source code for pyprocar.scripts.scriptDosplot

# -*- 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={}, 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. 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=['plain','parametric', 'parametric_line', 'stack', 'stack_orbitals', 'stack_species'] modes_txt=' , '.join(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 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 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