def plot_orb_projected_bands(orbitals, fmt='pdf', ylim=(-5, 5)):
"""
Plot a separate band structure for each orbital of each element in
orbitals.
Args:
orbitals (dict): dictionary of the form
{element: [orbitals]},
e.g. {'Mo': ['s', 'p', 'd'], 'S': ['p']}
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
bs = vasprun.get_band_structure('KPOINTS', line_mode=True)
bspp = BSPlotterProjected(bs)
ax = bspp.get_projected_plots_dots(orbitals, ylim=ylim).gcf().gca()
ax.set_xticklabels([r'$\mathrm{%s}$' % t for t in ax.get_xticklabels()])
ax.set_yticklabels([r'$\mathrm{%s}$' % t for t in ax.get_yticklabels()])
if fmt == "None":
return ax
else:
plt.savefig('orb_projected_bands.{}'.format(fmt))
plt.close()
def setUp(self):
with open(os.path.join(PymatgenTest.TEST_FILES_DIR,
"Cu2O_361_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
class BSPlotterProjectedTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_methods(self):
self.plotter.get_elt_projected_plots().close()
self.plotter.get_elt_projected_plots_color().close()
self.plotter.get_projected_plots_dots({'Cu': ['d', 's'], 'O': ['p']})
self.plotter.get_projected_plots_dots_patom_pmorb(
{
'Cu': ['dxy', 's', 'px'],
'O': ['px', 'py', 'pz']
}, {
'Cu': [3, 5],
'O': [1]
})
class BSPlotterProjectedTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_methods(self):
self.plotter.get_elt_projected_plots().close()
self.plotter.get_elt_projected_plots_color().close()
self.plotter.get_projected_plots_dots({
"Cu": ["d", "s"],
"O": ["p"]
}).close()
self.plotter.get_projected_plots_dots_patom_pmorb(
{
"Cu": ["dxy", "s", "px"],
"O": ["px", "py", "pz"]
},
{
"Cu": [3, 5],
"O": [1]
},
).close()
class BSPlotterProjectedTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_methods(self):
self.plotter.get_elt_projected_plots()
self.plotter.get_elt_projected_plots_color()
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
def plot_elt_projected_bands(ylim=(-5, 5), fmt="pdf"):
"""
Plot separate band structures for each element where the size of the
markers indicates the elemental character of the eigenvalue.
Args:
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun("vasprun.xml", parse_projected_eigen=True)
bs = vasprun.get_band_structure("KPOINTS", line_mode=True)
bspp = BSPlotterProjected(bs)
bspp.get_elt_projected_plots(ylim=ylim).savefig("elt_projected_bands.{}".format(fmt))
plt.close()
def plot_elt_projected_bands(ylim=(-5, 5), fmt='pdf'):
"""
Plot separate band structures for each element where the size of the
markers indicates the elemental character of the eigenvalue.
Args:
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
bs = vasprun.get_band_structure('KPOINTS', line_mode=True)
bspp = BSPlotterProjected(bs)
bspp.get_elt_projected_plots(ylim=ylim).savefig(
'elt_projected_bands.{}'.format(fmt))
plt.close()
def plot_orb_projected_bands(orbitals, fmt="pdf", ylim=(-5, 5)):
"""
Plot a separate band structure for each orbital of each element in
orbitals.
Args:
orbitals (dict): dictionary of the form
{element: [orbitals]},
e.g. {'Mo': ['s', 'p', 'd'], 'S': ['p']}
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun("vasprun.xml", parse_projected_eigen=True)
bs = vasprun.get_band_structure("KPOINTS", line_mode=True)
bspp = BSPlotterProjected(bs)
bspp.get_projected_plots_dots(orbitals, ylim=ylim).savefig("orb_projected_bands.{}".format(fmt))
plt.close()
def plot_bs_elt_projected(bs, **kwargs):
"""
Get element projected BS color plot with pymatgen. Note that vasprun.xml needs to
be parsed with parse_projected_eigen set to True.
Parameters
----------
bs :
BandStructureSymmLine object, most likely generated from Vasprun or BSVasprun.
**kwargs : (dict)
Arguments for the get_elt_projected_plots_color function in BSPlotter in pymatgen.
Returns
-------
plt :
Matplotlib object.
"""
plotter = BSPlotterProjected(bs)
plt = plotter.get_elt_projected_plots_color(**kwargs)
return plt
def plot_orb_projected_bands(orbitals, fmt='pdf', ylim=(-5, 5)):
"""
Plot a separate band structure for each orbital of each element in
orbitals.
Args:
orbitals (dict): dictionary of the form
{element: [orbitals]},
e.g. {'Mo': ['s', 'p', 'd'], 'S': ['p']}
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
bs = vasprun.get_band_structure('KPOINTS', line_mode=True)
bspp = BSPlotterProjected(bs)
bspp.get_projected_plots_dots(orbitals, ylim=ylim).savefig(
'orb_projected_bands.{}'.format(fmt))
plt.close()
def plot_color_projected_bands(ylim=(-5, 5), fmt="pdf"):
"""
Plot a single band structure where the color of the band indicates
the elemental character of the eigenvalue.
Args:
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun("vasprun.xml", parse_projected_eigen=True)
bs = vasprun.get_band_structure("KPOINTS", line_mode=True)
bspp = BSPlotterProjected(bs)
plot = bspp.get_elt_projected_plots_color()
fig = plot.gcf()
ax = fig.gca()
ax.set_xticklabels([r"$\mathrm{%s}$" % t for t in ax.get_xticklabels()])
ax.set_ylim(ylim)
fig.savefig("color_projected_bands.{}".format(fmt))
plt.close()
def plot_color_projected_bands(ylim=(-5, 5), fmt='pdf'):
"""
Plot a single band structure where the color of the band indicates
the elemental character of the eigenvalue.
Args:
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
bs = vasprun.get_band_structure('KPOINTS', line_mode=True)
bspp = BSPlotterProjected(bs)
plot = bspp.get_elt_projected_plots_color()
fig = plot.gcf()
ax = fig.gca()
ax.set_xticklabels([r'$\mathrm{%s}$' % t for t in ax.get_xticklabels()])
ax.set_ylim(ylim)
fig.savefig('color_projected_bands.{}'.format(fmt))
plt.close()
def plot_elt_projected_bands(ylim=(-5, 5), fmt='pdf'):
"""
Plot separate band structures for each element where the size of the
markers indicates the elemental character of the eigenvalue.
Args:
ylim (tuple): minimum and maximum energies for the plot's
y-axis.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
bs = vasprun.get_band_structure('KPOINTS', line_mode=True)
bspp = BSPlotterProjected(bs)
ax = bspp.get_elt_projected_plots(ylim=ylim).gcf().gca()
ax.set_xticklabels([r'$\mathrm{%s}$' % t for t in ax.get_xticklabels()])
ax.set_yticklabels([r'$\mathrm{%s}$' % t for t in ax.get_yticklabels()])
if fmt == "None":
return ax
else:
plt.savefig('elt_projected_bands.{}'.format(fmt))
plt.close()
class BSPlotterProjectedTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_methods(self):
self.plotter.get_elt_projected_plots().close()
self.plotter.get_elt_projected_plots_color().close()
self.plotter.get_projected_plots_dots({'Cu': ['d', 's'], 'O': ['p']})
self.plotter.get_projected_plots_dots_patom_pmorb(
{'Cu': ['dxy', 's', 'px'], 'O': ['px', 'py', 'pz']},
{'Cu': [3, 5], 'O': [1]}
)
from pymatgen.io.vasp.outputs import BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotterProjected
import os
import pickle
vasp_dir = os.path.dirname(os.path.abspath(__file__))
vasp_run = BSVasprun(os.path.join(vasp_dir,"vasprun.xml"),parse_projected_eigen=True)
bs = vasp_run.get_band_structure(line_mode=True)
bsp = BSPlotterProjected(bs)
p = bsp.get_color_grouped([{'elements':['Ag','Se'],'color':[255,140,0]},
{'elements':['C','H'],'color':[0,0,0]}],ylim=[-3,4])
p.savefig('color_band.pdf')
#pickle.dump(bs, open("band_structure.dat", "w"))
def test_proj_bandstructure_plot(self):
# make sure that it can be plotted!
BSPlotterProjected(self.bs_spin).get_elt_projected_plots()
BSPlotterProjected(self.bs_spin).get_projected_plots_dots({"Si": ["3s"]})
Integrateddos = dosplotter.add_dos('Integrated DOS', idos)
#Pdos = dosplotter.add_dos('Partial DOS',pdos)
#Spd_dos = dosplotter.add_dos('spd DOS',spd_dos)
#Element_dos = dosplotter.add_dos('Element DOS',element_dos)
#Element_spd_dos = dosplotter.add_dos('Element_spd DOS',element_spd_dos)
dos_dict = {
'Total DOS': tdos,
'Integrated DOS': idos
} #'Partial DOS':pdos,'spd DOS':spd_dos,'Element DOS':element_dos}#'Element_spd DOS':element_spd_dos
add_dos_dict = dosplotter.add_dos_dict(dos_dict)
get_dos_dict = dosplotter.get_dos_dict()
#dos_plot = dosplotter.get_plot()
##dosplotter.save_plot("MAPbI3_dos",img_format="png")
##dos_plot.show()
bsplotter = BSPlotter(bs)
bsplotterprojected = BSPlotterProjected(bs)
bs_plot_data = bsplotter.bs_plot_data()
#bs_plot = bsplotter.get_plot()
#bsplotter.save_plot("MAPbI3_bs",img_format="png")
#bsplotter.show()
ticks = bsplotter.get_ticks()
#print ticks
bsdos = BSDOSPlotter(
tick_fontsize=10,
egrid_interval=20,
legend_fontsize=28,
dos_projection="orbitals",
bs_legend=None,
fig_size=(110, 85)) #bs_projection="HPbCIN",dos_projection="HPbCIN")
#projected_plots_dots = bsplotterprojected.get_projected_plots_dots({'Pb':['s','p'],'I':['s','p']})
elements = bsplotterprojected.get_elt_projected_plots(vbm_cbm_marker=True)
v = BSVasprun("./vasprun.xml", parse_projected_eigen=True)
bs = v.get_band_structure(line_mode=True)
#print (bs.is_metal())
#print (bs.get_band_gap())
#print (bs.get_direct_band_gap())
#print (bs.get_projections_on_elements_and_orbitals({'As':['s','p','d']}))
#promenade = HighSymmKpath.get_kpoints
#print promenade
#get_kpoints(bs,line_density=20, coords_are_cartesian=True)
BSPlotter(bs).show()
#BSPlotter(bs).plot_brillouin()
#BSPlotter(bs).save_plot(filename="normal-bandstructure.pdf",img_format="pdf",zero_to_efermi=True)
bsproj = BSPlotterProjected(bs).get_projected_plots_dots_patom_pmorb(
dictio={'As': ['px', 'py', 'pz']},
dictpa={'As': [5, 6, 7, 8]},
sum_atoms={'As': [5, 6, 7, 8]},
sum_morbs={'As': ['px', 'py', 'pz']})
bsproj.show()
# trying new things here
#bandstruct = BSDOSPlotter(bs_projection="As", dos_projection=None, vb_energy_range=2, cb_energy_range=2, egrid_interval=0.5, rgb_legend=True)
#BSDOSPlotterProjected(bandstruct)
# #plt.show()
# plt.savefig(sys.argv[1] + ".pdf", format="pdf")
#!/bin/env python3 """Alexandre Olivieri ([email protected]) Simple plot generation from the vasprun.xml and KPOINTS files.""" from pymatgen.io.vasp import BSVasprun from pymatgen.electronic_structure.plotter import BSPlotterProjected from matplotlib import pyplot as plt VRUN = BSVasprun('vasprun.xml', parse_projected_eigen=True) BS = VRUN.get_band_structure(kpoints_filename='KPOINTS', line_mode=True) BANDPLOTTER = BSPlotterProjected(BS) plot = BANDPLOTTER.get_projected_plots_dots_patom_pmorb( {'O':['p'], 'Nb':['dyz', 'dx2', 'dz2']}, {'O':['all'], 'Nb':['all']}, sum_atoms={'O':['all'], 'Nb':['all']}, sum_morbs={'O':['p']}, num_column=3 ) plot.savefig('bandstructure.pdf', dpi=1000)
from pymatgen.electronic_structure.plotter import BSPlotterProjected
from pymatgen.io.vasp.outputs import BSVasprun, Element
path = '/home/jinho93/interface/pzt-bso/loose/opti/band/'
vrun = BSVasprun(path + 'vasprun.xml', True, True)
bs = vrun.get_band_structure(path + 'KPOINTS')
plotter = BSPlotterProjected(bs)
#plt = plotter.get_elt_projected_plots_color(elt_ordered=[Element.O, Element.Hf])
#plt = plotter.get_plot(ylim=(-8, 5), vbm_cbm_marker=True)
plt = plotter.get_elt_projected_plots_color(
elt_ordered=[Element.Ti, Element.Sn, Element.O])
plt.ylim((-5, 6))
plt.show()
