def plot_bandstructure():
if "-h" in sys.argv:
print("usage: complot_bands.py [-g] [-f fname] [-el emin] [-eh emax]")
sys.exit()
if "-g" in sys.argv:
mode = "risb"
else:
mode = "tb"
bs = get_bands_symkpath(mode=mode)
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
if rank == 0:
bsplot = BSPlotter(bs)
if "-f" in sys.argv:
fname = sys.argv[sys.argv.index("-f")+1]
if ".pdf" not in fname:
fname += ".pdf"
else:
fname = "bndstr.pdf"
if "-el" in sys.argv:
emin = float(sys.argv[sys.argv.index("-el")+1])
else:
emin = numpy.min(bs.bands.values())
if "-eh" in sys.argv:
emax = float(sys.argv[sys.argv.index("-eh")+1])
else:
emax = numpy.max(bs.bands.values())
bsplot.save_plot(fname, img_format="pdf", ylim=(emin, emax), \
zero_to_efermi=False)
def get_mp_banddos():
check_matplotlib()
mpr = check_apikey()
print("input the mp-ID")
wait_sep()
in_str = wait()
mp_id = in_str
step_count = 1
proc_str = "Reading Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
data = mpr.get_entry_by_material_id(mp_id)
sepline()
print(data)
sepline()
step_count += 1
proc_str = "Reading Band Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
band = mpr.get_bandstructure_by_material_id(mp_id)
if band is None:
print("No data obtained online, stop now!")
os.exit(0)
step_count += 1
filename = mp_id + '_band.png'
proc_str = "Writing Data to " + filename + " File..."
bsp = BSPlotter(band)
procs(proc_str, step_count, sp='-->>')
bsp.save_plot(filename=filename, img_format="png")
step_count += 1
proc_str = "Reading DOS Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
dos = mpr.get_dos_by_material_id(mp_id)
if dos is None:
print("No data obtained online, stop now!")
step_count += 1
filename = mp_id + '_dos.png'
proc_str = "Writing Data to " + filename + " File..."
dsp = DosPlotter()
dsp.add_dos('Total', dos)
procs(proc_str, step_count, sp='-->>')
dsp.save_plot(filename=filename, img_format="png")
class BSPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
def test_bs_plot_data(self):
self.assertEqual(len(self.plotter.bs_plot_data()['distances'][0]), 16,
"wrong number of distances in the first branch")
self.assertEqual(len(self.plotter.bs_plot_data()['distances']), 10,
"wrong number of branches")
self.assertEqual(
sum([len(e) for e in self.plotter.bs_plot_data()['distances']]),
160, "wrong number of distances")
self.assertEqual(self.plotter.bs_plot_data()['ticks']['label'][5], "K",
"wrong tick label")
self.assertEqual(len(self.plotter.bs_plot_data()['ticks']['label']),
19, "wrong number of tick labels")
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# zero_to_efermi = True, ylim = None, smooth = False,
# vbm_cbm_marker = False, smooth_tol = None
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc('text', usetex=False)
plt = self.plotter.get_plot()
plt = self.plotter.get_plot(smooth=True)
plt = self.plotter.get_plot(vbm_cbm_marker=True)
self.plotter.save_plot("bsplot.png")
self.assertTrue(os.path.isfile("bsplot.png"))
os.remove("bsplot.png")
plt.close("all")
class BSPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
def test_bs_plot_data(self):
self.assertEqual(len(self.plotter.bs_plot_data()['distances'][0]), 16,
"wrong number of distances in the first branch")
self.assertEqual(len(self.plotter.bs_plot_data()['distances']), 10,
"wrong number of branches")
self.assertEqual(
sum([len(e) for e in self.plotter.bs_plot_data()['distances']]),
160, "wrong number of distances")
self.assertEqual(self.plotter.bs_plot_data()['ticks']['label'][5], "K",
"wrong tick label")
self.assertEqual(len(self.plotter.bs_plot_data()['ticks']['label']),
19, "wrong number of tick labels")
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# zero_to_efermi = True, ylim = None, smooth = False,
# vbm_cbm_marker = False, smooth_tol = None
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc('text', usetex=False)
plt = self.plotter.get_plot()
plt = self.plotter.get_plot(smooth=True)
plt = self.plotter.get_plot(vbm_cbm_marker=True)
self.plotter.save_plot("bsplot.png")
self.assertTrue(os.path.isfile("bsplot.png"))
os.remove("bsplot.png")
# !/usr/bin/env python
# -*- coding: utf-8 -*-
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter
vasprun = Vasprun("vasprun.xml")
bss = vasprun.get_band_structure(kpoints_filename="KPOINTS", line_mode=True)
plotter = BSPlotter(bss)
#plotter.save_plot("bandStructure.svg", img_format="svg")
#plotter.save_plot("bandStructure.png", img_format="png")
#plotter.save_plot("lim_bandStructure.svg", img_format="svg", ylim=(-.2, 1.4))
plotter.save_plot("MAPbI3-primitive.png", img_format="png", ylim=(-5, 5))
plotter.plot_brillouin()
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
reads in KPOINTS(with labels for high symmetry kpoints) and
vasprun.xml files and plots the band structure along the high
symmetry kpoints
"""
# To use matplotlib on Hipergator, uncomment the following 2 lines:
# import matplotlib
# matplotlib.use('Agg')
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter
if __name__ == "__main__":
# readin bandstructure from vasprun.xml and labeled KPOINTS
run = Vasprun("vasprun.xml", parse_projected_eigen=True)
bands = run.get_band_structure("KPOINTS",
line_mode=True,
efermi=run.efermi)
bsp = BSPlotter(bands)
# Blue lines are up spin, red lines are down spin
bsp.save_plot('band_diagram.eps', ylim=(-5, 5))
# bsp = BSPlotterProjected(bands)
# plt = bsp.get_projected_plots_dots( {'Fe':['s', 'p', 'd'],
# 'Sb':['s', 'p', 'd']})
# get_elt_projected_plots_color()
def band_structure():
check_matplotlib()
step_count=1
filename='vasprun.xml'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
vsr=Vasprun(filename)
step_count+=1
filename='KPOINTS'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
bands = vsr.get_band_structure(filename, line_mode=True, efermi=vsr.efermi)
step_count+=1
filename='OUTCAR'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
outcar=Outcar('OUTCAR')
mag=outcar.as_dict()['total_magnetization']
if vsr.is_spin:
proc_str="This Is a Spin-polarized Calculation."
procs(proc_str,0,sp='-->>')
tdos=vsr.tdos
SpinUp_gap=tdos.get_gap(spin=Spin.up)
cbm_vbm_up=tdos.get_cbm_vbm(spin=Spin.up)
SpinDown_gap=tdos.get_gap(spin=Spin.down)
cbm_vbm_down=tdos.get_cbm_vbm(spin=Spin.up)
if SpinUp_gap > min_gap and SpinDown_gap > min_gap:
is_metal=False
is_semimetal=False
elif SpinUp_gap > min_gap and SpinDown_gap < min_gap:
is_metal=False
is_semimetal=True
elif SpinUp_gap < min_gap and SpinDown_gap > min_gap:
is_metal=False
is_semimetal=True
elif SpinUp_gap < min_gap and SpinDown_gap < min_gap:
is_metal=True
is_semimetal=False
if is_metal:
proc_str="This Material Is a Metal."
procs(proc_str,0,sp='-->>')
if not is_metal and is_semimetal:
proc_str="This Material Is a Semimetal."
procs(proc_str,0,sp='-->>')
else:
proc_str="This Material Is a Semiconductor."
procs(proc_str,0,sp='-->>')
proc_str="Total magnetization is "+str(mag)
procs(proc_str,0,sp='-->>')
if mag > min_mag:
proc_str="SpinUp : vbm=%f eV cbm=%f eV gap=%f eV"%(cbm_vbm_up[1],cbm_vbm_up[0],SpinUp_gap)
procs(proc_str,0,sp='-->>')
proc_str="SpinDown: vbm=%f eV cbm=%f eV gap=%f eV"%(cbm_vbm_down[1],cbm_vbm_down[0],SpinUp_gap)
procs(proc_str,0,sp='-->>')
else:
proc_str="SpinUp : vbm=%f eV cbm=%f eV gap=%f eV"%(cbm_vbm_up[1],cbm_vbm_up[0],SpinUp_gap)
procs(proc_str,0,sp='-->>')
step_count+=1
filename="BAND.dat"
proc_str="Writting Band Structure Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
band_data_up=bands.bands[Spin.up]
band_data_down=bands.bands[Spin.down]
y_data_up=band_data_up.reshape(1,band_data_up.shape[0]*band_data_up.shape[1])[0]-vsr.efermi #shift fermi level to 0
y_data_down=band_data_down.reshape(1,band_data_down.shape[0]*band_data_down.shape[1])[0]-vsr.efermi #shift fermi level to 0
x_data=np.array(bands.distance*band_data_up.shape[0])
data=np.vstack((x_data,y_data_up,y_data_down)).T
head_line="#%(key1)+12s%(key2)+13s%(key3)+15s"%{'key1':'K-Distance','key2':'UpEnergy(ev)','key3':'DownEnergy(ev)'}
write_col_data(filename,data,head_line,band_data_up.shape[1])
else:
if vsr.parameters['LNONCOLLINEAR']:
proc_str="This Is a Non-Collinear Calculation."
else:
proc_str="This Is a Non-Spin Calculation."
procs(proc_str,0,sp='-->>')
cbm=bands.get_cbm()['energy']
vbm=bands.get_vbm()['energy']
gap=bands.get_band_gap()['energy']
if not bands.is_metal():
proc_str="This Material Is a Semiconductor."
procs(proc_str,0,sp='-->>')
proc_str="vbm=%f eV cbm=%f eV gap=%f eV"%(vbm,cbm,gap)
procs(proc_str,0,sp='-->>')
else:
proc_str="This Material Is a Metal."
procs(proc_str,0,sp='-->>')
step_count+=1
filename3="BAND.dat"
proc_str="Writting Band Structure Data to "+ filename3 +" File ..."
procs(proc_str,step_count,sp='-->>')
band_data=bands.bands[Spin.up]
y_data=band_data.reshape(1,band_data.shape[0]*band_data.shape[1])[0]-vsr.efermi #shift fermi level to 0
x_data=np.array(bands.distance*band_data.shape[0])
data=np.vstack((x_data,y_data)).T
head_line="#%(key1)+12s%(key2)+13s"%{'key1':'K-Distance','key2':'Energy(ev)'}
write_col_data(filename3,data,head_line,band_data.shape[1])
step_count+=1
bsp=BSPlotter(bands)
filename4="HighSymmetricPoints.dat"
proc_str="Writting Label infomation to "+ filename4 +" File ..."
procs(proc_str,step_count,sp='-->>')
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s"%{'key1':'index','key2':'label','key3':'position'}
line=head_line+'\n'
for i,label in enumerate(bsp.get_ticks()['label']):
new_line="%(key1)12d%(key2)+12s%(key3)12f\n"%{'key1':i,'key2':label,'key3':bsp.get_ticks()['distance'][i]}
line+=new_line
line+='\n'
write_col_data(filename4,line,'',str_data=True)
try:
step_count+=1
filename5="BAND.png"
proc_str="Saving Plot to "+ filename5 +" File ..."
procs(proc_str,step_count,sp='-->>')
bsp.save_plot(filename5, img_format="png")
except:
print("Figure output fails !!!")
class BSPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
self.assertEqual(len(self.plotter._bs), 1,
"wrong number of band objects")
with open(os.path.join(test_dir, "N2_12103_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.sbs_sc = BandStructureSymmLine.from_dict(d)
with open(os.path.join(test_dir, "C_48_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.sbs_met = BandStructureSymmLine.from_dict(d)
self.plotter_multi = BSPlotter([self.sbs_sc, self.sbs_met])
self.assertEqual(len(self.plotter_multi._bs), 2,
"wrong number of band objects")
self.assertEqual(self.plotter_multi._nb_bands, [96, 96],
"wrong number of bands")
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
def test_add_bs(self):
self.plotter_multi.add_bs(self.sbs_sc)
self.assertEqual(len(self.plotter_multi._bs), 3,
"wrong number of band objects")
self.assertEqual(self.plotter_multi._nb_bands, [96, 96, 96],
"wrong number of bands")
def test_get_branch_steps(self):
steps_idx = BSPlotter._get_branch_steps(self.sbs_sc.branches)
self.assertEqual(steps_idx, [0, 121, 132, 143],
"wrong list of steps idx")
def test_rescale_distances(self):
rescaled_distances = self.plotter_multi._rescale_distances(
self.sbs_sc, self.sbs_met)
self.assertEqual(
len(rescaled_distances),
len(self.sbs_met.distance),
"wrong lenght of distances list",
)
self.assertEqual(rescaled_distances[-1], 6.5191398067252875,
"wrong last distance value")
self.assertEqual(
rescaled_distances[148],
self.sbs_sc.distance[19],
"wrong distance at high symm k-point",
)
def test_interpolate_bands(self):
data = self.plotter.bs_plot_data()
d = data["distances"]
en = data["energy"]["1"]
int_distances, int_energies = self.plotter._interpolate_bands(d, en)
self.assertEqual(len(int_distances), 10,
"wrong lenght of distances list")
self.assertEqual(len(int_distances[0]), 100,
"wrong lenght of distances in a branch")
self.assertEqual(len(int_energies), 10,
"wrong lenght of distances list")
self.assertEqual(int_energies[0].shape, (16, 100),
"wrong lenght of distances list")
def test_bs_plot_data(self):
self.assertEqual(
len(self.plotter.bs_plot_data()["distances"]),
10,
"wrong number of sequences of branches",
)
self.assertEqual(
len(self.plotter.bs_plot_data()["distances"][0]),
16,
"wrong number of distances in the first sequence of branches",
)
self.assertEqual(
sum([len(e) for e in self.plotter.bs_plot_data()["distances"]]),
160,
"wrong number of distances",
)
lenght = len(
self.plotter.bs_plot_data(split_branches=False)["distances"][0])
self.assertEqual(
lenght, 144,
"wrong number of distances in the first sequence of branches")
lenght = len(
self.plotter.bs_plot_data(split_branches=False)["distances"])
self.assertEqual(
lenght, 2,
"wrong number of distances in the first sequence of branches")
self.assertEqual(self.plotter.bs_plot_data()["ticks"]["label"][5], "K",
"wrong tick label")
self.assertEqual(
len(self.plotter.bs_plot_data()["ticks"]["label"]),
19,
"wrong number of tick labels",
)
def test_get_ticks(self):
self.assertEqual(self.plotter.get_ticks()["label"][5], "K",
"wrong tick label")
self.assertEqual(
self.plotter.get_ticks()["distance"][5],
2.406607625322699,
"wrong tick distance",
)
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# zero_to_efermi = True, ylim = None, smooth = False,
# vbm_cbm_marker = False, smooth_tol = None
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc("text", usetex=False)
plt = self.plotter.get_plot()
self.assertEqual(plt.ylim(), (-4.0, 7.6348), "wrong ylim")
plt = self.plotter.get_plot(smooth=True)
plt = self.plotter.get_plot(vbm_cbm_marker=True)
self.plotter.save_plot("bsplot.png")
self.assertTrue(os.path.isfile("bsplot.png"))
os.remove("bsplot.png")
plt.close("all")
# test plotter with 2 bandstructures
plt = self.plotter_multi.get_plot()
self.assertEqual(len(plt.gca().get_lines()), 874,
"wrong number of lines")
self.assertEqual(plt.ylim(), (-10.0, 10.0), "wrong ylim")
plt = self.plotter_multi.get_plot(zero_to_efermi=False)
self.assertEqual(plt.ylim(), (-15.2379, 12.67141266), "wrong ylim")
plt = self.plotter_multi.get_plot(smooth=True)
self.plotter_multi.save_plot("bsplot.png")
self.assertTrue(os.path.isfile("bsplot.png"))
os.remove("bsplot.png")
plt.close("all")
# 3rd run to obtain Band structure
band = MPNonSCFSet.from_prev_calc(static_dir,
mode="line",
standardize=True,
user_incar_settings=myset)
band.write_input(band_dir)
run_vasp(cmd, band_dir)
os.system('cp ' + band_dir + '/vasprun.xml ./band-vasprun.xml')
os.system('cp ' + band_dir + '/KPOINTS ./')
v = BSVasprun("band-vasprun.xml")
bs = v.get_band_structure(kpoints_filename='KPOINTS', line_mode=True)
plt = BSPlotter(bs)
plt.get_plot(vbm_cbm_marker=True)
plt.save_plot(Name + '-band.png', ylim=[-4, 4], img_format='png')
v = Vasprun('dos-vasprun.xml')
tdos = v.tdos
cdos = v.complete_dos
spd_dos = cdos.get_spd_dos()
plotter = DosPlotter(sigma=0.1)
plotter.add_dos("Total DOS", tdos)
# plotter.add_dos("spd_dos", spd_dos)
plotter.save_plot(Name + '-dos.png', img_format='png', xlim=[-4, 4])
shutil.rmtree(band_dir)
shutil.rmtree(dos_dir)
shutil.rmtree(static_dir)
os.chdir('../')
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter, BSPlotterProjected
vr = Vasprun("nself/vasprun.xml")
bs = vr.get_band_structure(kpoints_filename="nself/KPOINTS", line_mode=True)
bsp = BSPlotter(bs)
#plt = bsp.get_elt_projected_plots(zero_to_efermi=False)
#plt.savefig("band_structure.png", format="png")
bsp.save_plot(filename="band_structure.png", img_format="png")
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
"""
reads in KPOINTS(with labels for high symmetry kpoints) and
vasprun.xml files and plots the band structure along the high
symmetry kpoints
"""
# To use matplotlib on Hipergator, uncomment the following 2 lines:
# import matplotlib
# matplotlib.use('Agg')
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotterProjected, BSPlotter
if __name__ == "__main__":
# readin bandstructure from vasprun.xml and labeled KPOINTS
run = Vasprun("vasprun.xml", parse_projected_eigen=True)
bands = run.get_band_structure("KPOINTS", line_mode=True,
efermi=run.efermi)
bsp = BSPlotter(bands)
# Blue lines are up spin, red lines are down spin
bsp.save_plot('band_diagram.eps', ylim=(-5, 5))
# bsp = BSPlotterProjected(bands)
# plt = bsp.get_projected_plots_dots( {'Fe':['s', 'p', 'd'],
# 'Sb':['s', 'p', 'd']})
# get_elt_projected_plots_color()
#!/usr/bin/env python
## Application: plot band structure by pymatgen
## Written by: Asst.Prof.Dr. Kittiphong Amnuyswat
## Updated: 20/04/2020
## Original: http://home.ustc.edu.cn/~lipai/scripts/vasp_scripts/python_plot_dos_band.html
import os
import sys
import datetime
import time
sys.path.append('/Volumes/kaswat200GB/GitHub/pyVASP/')
os.system('clear')
print("Current date and time: ",
datetime.datetime.now().strftime("%d-%m-%Y %H-%M-%S"))
print("")
from pymatgen.io.vasp import Vasprun, BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotter
localDir = os.getcwd()
temp = os.path.join(localDir, 'vasprun.xml')
v = BSVasprun(temp)
kpt = os.path.join(localDir, 'KPOINTS')
bs = v.get_band_structure(kpoints_filename=kpt, line_mode=True)
plt = BSPlotter(bs)
plt.get_plot(vbm_cbm_marker=True)
plt.save_plot('band.eps')
from __future__ import division, unicode_literals, print_function
"""
reads in KPOINTS(with labels for high symmetry kpoints) and
vasprun.xml files and plots the band structure along the high
symmetry kpoints
"""
# To use matplotlib on Hipergator, uncomment the following 2 lines:
# import matplotlib
# matplotlib.use('Agg')
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotterProjected, BSPlotter
if __name__ == "__main__":
# readin bandstructure from vasprun.xml and labeled KPOINTS
run = Vasprun("vasprun.xml", parse_projected_eigen=True)
bands = run.get_band_structure("KPOINTS", line_mode=True, efermi=run.efermi)
bsp = BSPlotter(bands)
# Blue lines are up spin, red lines are down spin
bsp.save_plot("band_diagram.eps", ylim=(-5, 5))
# bsp = BSPlotterProjected(bands)
# plt = bsp.get_projected_plots_dots( {'Fe':['s', 'p', 'd'],
# 'Sb':['s', 'p', 'd']})
# get_elt_projected_plots_color()
