class DosPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r",
encoding='utf-8') as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def test_add_dos_dict(self):
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 0)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 4)
def test_get_dos_dict(self):
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
for el in ["Li", "Fe", "P", "O"]:
self.assertIn(el, d)
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc('text', usetex=False)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
plt = self.plotter.get_plot()
self.plotter.save_plot("dosplot.png")
self.assertTrue(os.path.isfile("dosplot.png"))
os.remove("dosplot.png")
def get_odos(self, stack=True, xlim=[-10, 10], ylim=[0, 50], sigma=0.15):
dos_vasprun = Vasprun(os.path.join(self.path, "vasprun.xml"), parse_projected_eigen=True)
dos_data = dos_vasprun.complete_dos
plotter = DosPlotter(stack=stack, sigma=sigma)
o_dos = dos_data.get_spd_dos()
plotter.add_dos_dict(o_dos)
plotter.save_plot(f'{self.path}-odos.png', img_format=u'png', xlim=xlim, ylim=ylim)
class DosPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r",
encoding='utf-8') as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def test_add_dos_dict(self):
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 0)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
self.assertEqual(len(d), 4)
def test_get_dos_dict(self):
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
d = self.plotter.get_dos_dict()
for el in ["Li", "Fe", "P", "O"]:
self.assertIn(el, d)
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc('text', usetex=False)
self.plotter.add_dos_dict(self.dos.get_element_dos(),
key_sort_func=lambda x: x.X)
plt = self.plotter.get_plot()
self.plotter.save_plot("dosplot.png")
self.assertTrue(os.path.isfile("dosplot.png"))
os.remove("dosplot.png")
def get_sdos(self, dos_dict, stack=True, xlim=[-10, 10], ylim=None, sigma=0.15):
dos_vasprun = Vasprun(os.path.join(self.path, "vasprun.xml"), parse_projected_eigen=True)
dos_data = dos_vasprun.complete_dos
plotter = DosPlotter(stack=stack, sigma=sigma)
edos = dos_data.get_element_dos()
for key in dos_dict:
if type(dos_dict[key]) is list:
for index, item in enumerate(dos_dict[key]):
if index == 0:
temp = dos_data.get_site_dos(dos_data.structure[item])
else:
temp = temp + dos_data.get_site_dos(dos_data.structure[item])
plotter.add_dos(key, temp)
elif type(dos_dict[key]) is str:
temp = edos[Element(dos_dict[key])]
plotter.add_dos(key, temp)
elif type(dos_dict[key]) is int:
temp = dos_data.get_site_dos(dos_data.structure[dos_dict[key]])
plotter.add_dos(key, temp)
else:
print('Warning: invalid value')
if ylim is not None:
plotter.save_plot(f'{self.path}-dos.png', img_format=u'png', xlim=xlim, ylim=ylim)
else:
plotter.save_plot(f'{self.path}-dos.png', img_format=u'png', xlim=xlim)
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")
def total_dos():
check_matplotlib()
filename='vasprun.xml'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,1,sp='-->>')
vsr=Vasprun(filename,parse_eigen=False)
tdos=vsr.tdos
idos=vsr.idos
E=tdos.energies-tdos.efermi
if vsr.is_spin:
proc_str="This Is a Spin-polarized Calculation."
procs(proc_str,0,sp='-->>')
proc_str="Writting TDOS.dat File ..."
TDOSUP=tdos.densities[Spin.up]
TDOSDOWN=tdos.densities[Spin.down]
ETDOS=np.vstack((E,TDOSUP,TDOSDOWN))
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s"%{'key1':'Energy(eV)','key2':'SpinUp','key3':'SpinDown'}
write_col_data('TDOS.dat',ETDOS.T,head_line)
proc_str="Writting IDOS.dat File ..."
procs(proc_str,3,sp='-->>')
IDOSUP=idos.densities[Spin.up]
IDOSDOWN=idos.densities[Spin.down]
EIDOS=np.vstack((E,IDOSUP,IDOSDOWN))
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s"%{'key1':'Energy(eV)','key2':'IntSpinUp','key3':'IntSpinDown'}
write_col_data('IDOS.dat',EIDOS.T,head_line)
plt1=DosPlotter()
plt2=DosPlotter()
plt1.add_dos('Total DOS',tdos)
plt2.add_dos('Total DOS',idos)
try:
# plt1.show()
plt1.save_plot('TotalDOS.png', img_format="png")
# plt2.show()
plt2.save_plot('IntegratedDOS.png', img_format="png")
except:
print("pls use gnuplot to plot TDOS.dat and IDOS.dat")
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='-->>')
proc_str="Writting TDOS.dat File ..."
procs(proc_str,2,sp='-->>')
TDOS=tdos.densities[Spin.up]
ETDOS=np.vstack((E,TDOS))
head_line="#%(key1)+12s%(key2)+12s"%{'key1':'Energy(eV)','key2':'TotalDOS'}
write_col_data('TDOS.dat',ETDOS.T,head_line)
proc_str="Writting IDOS.dat File ..."
procs(proc_str,3,sp='-->>')
IDOS=idos.densities[Spin.up]
EIDOS=np.vstack((E,IDOS))
head_line="#%(key1)+12s%(key2)+13s"%{'key1':'Energy(eV)','key2':'IntegratedDOS'}
write_col_data('IDOS.dat',EIDOS.T,head_line)
plt1=DosPlotter()
plt2=DosPlotter()
plt1.add_dos('Total DOS',tdos)
plt2.add_dos('Integrated DOS',idos)
filename4="TotalDOS.png IntegratedDOS.png"
proc_str="Saving Plot to "+ filename4 +" File ..."
procs(proc_str,4,sp='-->>')
try:
# plt1.show()
plt1.save_plot('TotalDOS.png', img_format="png")
# plt2.show()
plt2.save_plot('IntegratedDOS.png', img_format="png")
except:
print("pls use gnuplot to plot TDOS.dat and IDOS.dat")
Plot DOS
"""
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
v = Vasprun('./vasprun.xml', parse_dos=True)
cdos = v.complete_dos
element_dos = cdos.get_element_dos()
plotter = DosPlotter()
plotter.add_dos_dict(element_dos)
plotter.save_plot('plots/dos.pdf', img_format='pdf', xlim=None, ylim=None)
# plotter.save_plot('spin-up_dos.pdf', img_format='pdf', xlim= None, ylim = [0,None]) # up-spin dos
"""
Plot Band
"""
from pymatgen.io.vasp import BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotter
v = BSVasprun('./vasprun.xml', parse_projected_eigen=True)
bs = v.get_band_structure(kpoints_filename='./KPOINTS', line_mode=True)
bsplot = BSPlotter(bs)
bsplot.get_plot(zero_to_efermi=True, ylim=[-5, 5]).savefig('plots/band.pdf')
# add some features
# 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('../')
wf = WorkFunctionAnalyzer(s.structure,
l.get_average_along_axis(1),
efermi,
shift=0)
loc_vac = wf.vacuum_locpot
for i in element_dos:
element_dos[i].efermi = loc_vac
plotter.add_dos_dict(element_dos)
plt = plotter.get_plot(xlim=[-9, 1])
plt.plot([efermi - loc_vac, efermi - loc_vac],
plt.ylim(),
'b--',
linewidth=2,
label='EF')
plt.xlabel('Energies - Vac(eV)')
plt.legend()
leg = plt.gca().get_legend()
ltext = leg.get_texts() # all the text.Text instance in the legend
plt.setp(ltext, fontsize=30)
plt.tight_layout()
plt.savefig('dos.png')
plt.show()
else:
plotter.add_dos_dict(element_dos)
plotter.show()
plotter.save_plot('vasp_dos.png', xlim=[-8, 7], img_format='png')
#!/nfshome/villa/anaconda3/bin/python
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter, DosPlotter
vaspout = Vasprun("./vasprun.xml")
# Initializes plotter with some optional args. Defaults are usually
# fine,
complete_dos = vaspout.complete_dos
plt = DosPlotter()
plt.add_dos_dict(complete_dos.get_spd_dos())
tdos = vaspout.tdos
# Adds a DOS with a label.
plt.add_dos("Total", tdos)
#plt.get_plot()
plt.save_plot('dos_mg.pdf', img_format='pdf', xlim=[-7, 6], ylim=[0, 20])
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
reads in vasprun.xml file and plots the density of states
"""
# 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 DosPlotter
if __name__ == "__main__":
# readin the density of states from vasprun.xml file
run = Vasprun("vasprun.xml", parse_projected_eigen=True)
complete_dos = run.complete_dos
print('cbm and vbm ', complete_dos.get_cbm_vbm())
print('gap = ', complete_dos.get_gap())
# get orbital projected DOS.
spd_dos = complete_dos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(spd_dos)
plotter.save_plot('dos.eps')
import os
import sys
import datetime
import time
import pandas as pd
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
from pymatgen.electronic_structure.plotter import DosPlotter
localDir = os.getcwd()
temp = os.path.join(localDir, 'vasprun.xml')
v = Vasprun(temp)
tdos = v.tdos
plotter = DosPlotter()
plotter.add_dos("Total DOS", tdos)
## plotter.show()
plotter.save_plot('TDOS.eps')
cdos = v.complete_dos
element_dos = cdos.get_element_dos()
plotter = DosPlotter()
plotter.add_dos_dict(element_dos)
## plotter.show()
plotter.save_plot('PDOS.eps')
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
reads in vasprun.xml file and plots the density of states
"""
# 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 DosPlotter
if __name__ == "__main__":
# readin the density of states from vasprun.xml file
run = Vasprun("vasprun.xml", parse_projected_eigen=True)
complete_dos = run.complete_dos
print('cbm and vbm ', complete_dos.get_cbm_vbm())
print('gap = ', complete_dos.get_gap())
# get orbital projected DOS.
spd_dos = complete_dos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(spd_dos)
plotter.save_plot('dos.eps')
