def test_vasprun_bs(self):
bsv = BSVasprun(os.path.join(test_dir, "vasprun.xml"),
parse_projected_eigen=True,
parse_potcar_file=True)
bs = bsv.get_band_structure(kpoints_filename=os.path.join(test_dir, "KPOINTS.band"),
line_mode=True)
bs.get_projection_on_elements()
def plot_bs(vasprun_path: str):
try:
v = BSVasprun(vasprun_path)
except xml.etree.ElementTree.ParseError:
print("\tskipped due to parse error")
return
bs = v.get_band_structure(kpoints_filename="KPOINTS", line_mode=True)
plt = BSPlotter(bs)
plt.show()
def test_vasprun_bs(self):
bsv = BSVasprun(
os.path.join(PymatgenTest.TEST_FILES_DIR, "vasprun.xml"),
parse_projected_eigen=True,
parse_potcar_file=True,
)
bs = bsv.get_band_structure(
kpoints_filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "KPOINTS.band"), line_mode=True
)
bs.get_projection_on_elements()
def write_nn_input_coord_based(structure: IStructure,
sgnum: int,
index: int,
all_hs_path: str,
vasprun_path: str,
write_dir: str, ):
try:
bsvasprun = BSVasprun(vasprun_path)
except xml.etree.ElementTree.ParseError:
print("\tskipped due to parse error")
return
kpoints = [tuple(vector) for vector in bsvasprun.actual_kpoints] # (kpoints, 1)
bandstructure = bsvasprun.get_band_structure(kpoints_filename="KPOINTS", line_mode=True)
bands = bandstructure.bands[Spin.up].T # (kpoints, bands)
# connect two array
kpoints_to_bands = dict(zip(kpoints, bands))
# all possible high symmetry kpoints
all_hspoints = [tuple(vector) for vector in all_hspoints_from_file(all_hs_path)]
# high symmetry kpoints in this structure
cur_hspoints = [tuple(kpoints) for kpoints in HighSymmKpath(structure).kpath["kpoints"].values()]
# filter out bands of intermediate kpoints (cur_hspoints, bands)
cur_hspoints_to_bands = {
kpoints:
kpoints_to_bands[kpoints]
for kpoints in cur_hspoints
if kpoints in kpoints_to_bands
}
# pad zeros to missing high symmetry points (all_hspoints, bands)
all_hspoints_to_bands = {
hspoints:
cur_hspoints_to_bands[hspoints].tolist()
if (hspoints in cur_hspoints_to_bands) else
[0] * bands.shape[1]
for hspoints in all_hspoints
}
all_bands = numpy.array(list(all_hspoints_to_bands.values())).T.tolist() # (bands, all_hspoints)
input_dict = {"number": sgnum, "bands": all_bands}
file_path = write_dir + "theo_input_data_{}_{}.json".format(sgnum, index)
with open(file_path, "w") as file:
json.dump(input_dict, file, indent=4)
def wave(**kwargs):
"""Extract wavefunction coefficients from a WAVECAR"""
from pymatgen.io.vasp import BSVasprun
from amset.constants import defaults
from amset.electronic_structure.common import get_ibands
from amset.tools.common import echo_ibands
from amset.wavefunction.io import write_coefficients
output = kwargs.pop("output")
planewave_cutoff = kwargs.pop("planewave_cutoff")
pawpyseed = kwargs.pop("pawpyseed")
energy_cutoff = kwargs.pop("energy_cutoff")
if not energy_cutoff:
energy_cutoff = defaults["energy_cutoff"]
if kwargs["directory"]:
vasprun_file = Path(kwargs["directory"]) / "vasprun.xml"
else:
vasprun_file = kwargs["vasprun"]
try:
vr = BSVasprun(vasprun_file)
except FileNotFoundError:
vr = BSVasprun(str(vasprun_file) + ".gz")
bs = vr.get_band_structure()
ibands = get_ibands(energy_cutoff, bs)
click.echo("******* Getting wavefunction coefficients *******\n")
echo_ibands(ibands, bs.is_spin_polarized)
click.echo("")
if pawpyseed:
coeffs, gpoints, kpoints = _wavefunction_pawpy(bs, ibands,
planewave_cutoff,
**kwargs)
else:
coeffs, gpoints = _wavefunction_vasp(ibands, planewave_cutoff,
**kwargs)
kpoints = np.array([k.frac_coords for k in bs.kpoints])
structure = vr.final_structure
click.echo("Writing coefficients to {}".format(output))
write_coefficients(coeffs, gpoints, kpoints, structure, filename=output)
def dump_wavefunction(**kwargs):
"""Extract wavefunction coefficients from a WAVECAR"""
from amset.electronic_structure.wavefunction import (
get_wavefunction,
get_wavefunction_coefficients,
dump_coefficients,
)
from amset.electronic_structure.common import get_ibands
from amset.constants import defaults
from pymatgen.io.vasp import BSVasprun
output = kwargs.pop("output")
planewave_cutoff = kwargs.pop("planewave_cutoff")
energy_cutoff = kwargs.pop("energy_cutoff")
if not energy_cutoff:
energy_cutoff = defaults["energy_cutoff"]
wf = get_wavefunction(**kwargs)
if kwargs["directory"]:
kwargs["vasprun"] = Path(kwargs["directory"]) / "vasprun.xml"
vr = BSVasprun(kwargs["vasprun"])
bs = vr.get_band_structure()
ibands = get_ibands(energy_cutoff, bs)
click.echo("******* Getting wavefunction coefficients *******")
click.echo("\nIncluding:")
for spin, spin_bands in ibands.items():
min_b = spin_bands.min() + 1
max_b = spin_bands.max() + 1
click.echo(" Spin-{} bands {}—{}".format(spin.name, min_b, max_b))
click.echo("")
coeffs = get_wavefunction_coefficients(wf,
bs,
iband=ibands,
encut=planewave_cutoff)
click.echo("Writing coefficients to {}".format(output))
dump_coefficients(coeffs, wf.kpts, wf.structure, filename=output)
def write_nn_input_label_based(sgnum: int,
index: int,
all_hs_path: str,
vasprun_path: str,
write_dir: str, ):
try:
bsvasprun = BSVasprun(vasprun_path)
except xml.etree.ElementTree.ParseError:
print("\tskipped due to parse error")
return
bandstructure = bsvasprun.get_band_structure(kpoints_filename="KPOINTS", line_mode=True)
bands = bandstructure.bands[Spin.up].T # (kpoints, bands)
# all possible high symmetry labels
all_hslabels = all_hslabels_from_file(all_hs_path)
# filter out bands of intermediate kpoints (cur_hslabels, bands)
cur_hslabels_to_bands = {}
for kpath in bandstructure.branches:
cur_hslabels_to_bands[kpath["name"].split("-")[0]] = bands[kpath["start_index"]]
cur_hslabels_to_bands[kpath["name"].split("-")[1]] = bands[kpath["end_index"]]
# pad zeros to missing high symmetry labels (all_hspoints, bands)
all_hslabels_to_bands = {
hslabels:
cur_hslabels_to_bands[hslabels].tolist()
if (hslabels in cur_hslabels_to_bands) else
[0] * bands.shape[1]
for hslabels in all_hslabels
}
all_bands = numpy.array(list(all_hslabels_to_bands.values())).T.tolist() # (bands, all_hslabels)
input_dict = {"number": sgnum, "bands": all_bands}
file_path = write_dir + "theo_input_data_{}_{}.json".format(sgnum, index)
with open(file_path, "w") as file:
json.dump(input_dict, file, indent=4)
df_Asite['formula_%s' % (Asite_element)][idx + 1] = formula
df_Asite['total_E_%s' % (Asite_element)][idx + 1] = tot_E
df_Asite['tot_mag_%s' % (Asite_element)][idx + 1] = tot_mag
df_Asite['DHf_%s' % (Asite_element)][idx + 1] = fE
df_Asite['Ehull_ref_%s' % (Asite_element)][idx + 1] = entries[idx]['e_above_hull']
df_Asite['Volume_%s' % (Asite_element)][idx + 1] = volume
except FileNotFoundError:
# print('%03d_%s/2nd files are not found' % (idx + 1.0, formula))
f.writelines('%s files are not found\n' % (file_path))
continue
try:
bsv = BSVasprun(file_path + 'DOS/vasprun.xml', parse_projected_eigen = True)
bs = bsv.get_band_structure(kpoints_filename = file_path + 'DOS/KPOINTS', line_mode = True)
vbm = bs.as_dict()['vbm']['energy']
e_fermi = bs.as_dict()['efermi']
cbm = bs.as_dict()['cbm']['energy']
df_bulk.VBM[idx+1] = vbm
df_bulk.E_fermi[idx+1] = e_fermi
df_bulk.CBM[idx+1] = cbm
bg = bs.get_band_gap()['energy']
bgpath = bs.get_band_gap()['transition']
if bs.get_band_gap()['direct'] == True:
bgtype = 'Direct'
elif bs.get_band_gap()['direct'] == False:
bgtype = 'Indirect'
def Get_bandstruct(self, filepath):
''' Calculate band structure '''
vaspband = BSVasprun(filepath + "vasprun.xml")
bandstru = vaspband.get_band_structure(kpoints_filename=filepath+"KPOINTS",line_mode=True)
return bandstru
dos.write_input(dos_dir)
run_vasp(cmd, dos_dir)
os.system('cp ' + dos_dir + '/vasprun.xml ./dos-vasprun.xml')
# 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)
completeDos = vasprun.complete_dos
element_dos = completeDos.get_element_dos()
plotter = DosPlotter()
plotter.add_dos_dict(element_dos)
plotter.add_dos('Total DOS', tdos)
plotter.show()
spd_dos = completeDos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(spd_dos)
plotter.add_dos('Total DOS', tdos)
plotter.show()
bsvasprun_file = './AlEuO3_Perovskite_BS/vasprun.xml'
kpoint_file = './AlEuO3_Perovskite_BS/KPOINTS'
bsvasprun = BSVasprun(bsvasprun_file, parse_projected_eigen=True)
bs = bsvasprun.get_band_structure(kpoints_filename=kpoint_file, line_mode=True)
plotter = BSPlotter(bs)
plotter.get_plot(vbm_cbm_marker=True)
plotter.show()
# banddos_fig = BSDOSPlotter()
# banddos_fig = BSDOSPlotter(bs_projection=None, dos_projection=None)
banddos_fig = BSDOSPlotter(bs_projection='elements', dos_projection='elements')
banddos_fig.get_plot(bs=bs, dos=completeDos)
import matplotlib.pyplot as plt
plt.show()
def Get_gap_degeneracy(self, filepath):
vaspband = BSVasprun(filepath + "/vasprun.xml")
bandstru = vaspband.get_band_structure(kpoints_filename=filepath+"/KPOINTS",line_mode=True)
self.bandgap = bandstru.get_band_gap()['energy']
self.degeneracy = bandstru.get_kpoint_degeneracy(bandstru.kpoints[self.pos['kptindex']].frac_coords)
magm_list.append(outcar.magnetization[atom]['tot'])
df_bulk.Magm[idx + 1] = magm_list
if tot_mag >= 0.5: # not a physical definition
df_bulk.Mag_O[idx+1] = 'FM'
elif tot_mag < 0.5:
df_bulk.Mag_O[idx+1] = 'NM'
except FileNotFoundError:
# print('%03d_%s/2nd files are not found' % (idx + 1.0, formula))
f.writelines('%03d_%s/2nd files are not found\n' % (idx + 1.0, formula))
continue
try:
bsv = BSVasprun('%03d_%s/2nd/DOS/vasprun.xml' % (idx+1.0, formula), parse_projected_eigen = True)
bs = bsv.get_band_structure(kpoints_filename = '%03d_%s/2nd/DOS/KPOINTS' % (idx + 1.0, formula), line_mode = True)
vbm = bs.as_dict()['vbm']['energy']
e_fermi = bs.as_dict()['efermi']
cbm = bs.as_dict()['cbm']['energy']
df_bulk.VBM[idx+1] = vbm
df_bulk.E_fermi[idx+1] = e_fermi
df_bulk.CBM[idx+1] = cbm
if bs.get_band_gap()['direct'] == True:
bgtype = 'Direct'
elif bs.get_band_gap()['direct'] == False:
bgtype = 'Indirect'
df_bulk.bgtype[idx+1] = bgtype
@Month2 : 五月
"""
import plotly
from pymatgen.io.vasp import BSVasprun, Vasprun
from pymatgen.electronic_structure.core import Spin
import plotly.graph_objs as go
import chart_studio.plotly as pltly
import chart_studio.tools as tls
dosrun = Vasprun('AlEuO3_Perovskite_BS/vasprun.xml')
run = BSVasprun("AlEuO3_Perovskite_BS/vasprun.xml",
parse_projected_eigen=True) # 读取vasprun.xml
bands = run.get_band_structure(kpoints_filename="AlEuO3_Perovskite_BS/KPOINTS",
line_mode=True,
efermi=dosrun.efermi)
emin = 1e100
emax = -1e100
for spin in bands.bands.keys():
for band in range(bands.nb_bands):
emin = min(emin, min(bands.bands[spin][band]))
emax = max(emax, max(bands.bands[spin][band]))
emin = emin - bands.efermi - 1
emax = emax - bands.efermi + 1
kptslist = [k for k in range(len(bands.kpoints))]
bandTraces = list()
for band in range(bands.nb_bands):
bandTraces.append(
#!/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')
"""
@Project : plotDosBS
@Author : Xu-Shan Zhao
@Filename: bsToMongoDB202005121111.py
@IDE : PyCharm
@Time1 : 2020-05-12 11:11:38
@Time2 : 2020/5/12 11:11
@Month1 : 5月
@Month2 : 五月
"""
from pymatgen.io.vasp import BSVasprun
import pymongo
import hashlib
bsvasprun = BSVasprun('AlEuO3_Perovskite_BS/vasprun.xml', parse_projected_eigen=True)
bs = bsvasprun.get_band_structure(kpoints_filename='AlEuO3_Perovskite_BS/KPOINTS', line_mode=True)
bs = bs.as_dict()
hashvalue = hashlib.sha256(str(bs).encode('utf-8')).hexdigest()
print(hashvalue)
bs.update(hashvalue=hashvalue)
client = pymongo.MongoClient(host='localhost', port=27017)
db = client['pymatgenFormatDBs']
collection = db['band_structure']
count = collection.count_documents({"hashvalue": hashvalue})
if count == 0:
collection.insert_one(bs)
else:
# -*- coding: utf-8 -*-
"""
Created on Wed May 15 10:33:43 2019
@author: nwpuf
"""
from pymatgen.io.vasp import Vasprun, BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotter, DosPlotter
import matplotlib.pyplot as plt
bsv = BSVasprun("vasprun.xml")
bs = bsv.get_band_structure(kpoints_filename="KPOINTS", line_mode=True)
print(bs.get_band_gap())
bsplot = BSPlotter(bs)
bsplot.get_plot(vbm_cbm_marker=True).show()
#dosrun = Vasprun("DOS/vasprun.xml", parse_dos=True)
#dos = dosrun.complete_dos
#dosplot = DosPlotter(sigma=0.1)
#dosplot.add_dos("Total DOS", dos)
#dosplot.add_dos_dict(dos.get_element_dos())
#ax = plt.gca()
#print(type(dosplot.get_plot()))
#dosplot.get_plot().show()
#解析晶体结构部分，输出三部分主要信息。
input_spacegroup, input_sites, input_lattice, input_structure = ParsePOSCAR(
POSCAR)
print(input_spacegroup, input_sites, input_lattice)
print("------------------------------------------------------------")
# POSCAR 晶体结构可视化 , 可视化需要软件VTK
input_poscarVis = StructureVis()
input_poscarVis.set_structure(input_structure)
input_poscarVis.show()
# 画能代结构图 ,
from pymatgen.io.vasp import Vasprun, BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotter
vasprun = BSVasprun(vasprun_path)
bankStructure = vasprun.get_band_structure(kpoints_filename=KPOINTS,
line_mode=True)
plt = BSPlotter(bankStructure)
# print(plt.get_ticks()) #Get all ticks and labels for a band structure plot. return A dictionary with ‘distance’
plt.show(ylim=(-36, 5)) # 这一行有问题。就是这个范围参数该如何得到。
# 解析INCAR部分,应该直接打印 INCAR 中所有参数信息也是没问题的。
incar = ParseINCAR(INCAR)
print("------------------------------------------------------------")
print(incar.as_dict())
# 解析KPOINTS 部分， 需要的参数有 kpoints， nkpoints, label,
kpoints = ParseKPOINTS(KPOINTS)
kPoints = kpoints['kpoints']
nkpoints = kpoints['nkpoints']
label = kpoints['label']
def process_vasprun(self, dir_name, taskname, filename):
"""
Adapted from matgendb.creator
Process a vasprun.xml file.
"""
vasprun_file = os.path.join(dir_name, filename)
vrun = Vasprun(vasprun_file)
d = vrun.as_dict()
# rename formula keys
for k, v in {"formula_pretty": "pretty_formula",
"composition_reduced": "reduced_cell_formula",
"composition_unit_cell": "unit_cell_formula"}.items():
d[k] = d.pop(v)
for k in ["eigenvalues", "projected_eigenvalues"]: # large storage space breaks some docs
if k in d["output"]:
del d["output"][k]
comp = Composition(d["composition_unit_cell"])
d["formula_anonymous"] = comp.anonymized_formula
d["formula_reduced_abc"] = comp.reduced_composition.alphabetical_formula
d["dir_name"] = os.path.abspath(dir_name)
d["completed_at"] = str(datetime.datetime.fromtimestamp(os.path.getmtime(vasprun_file)))
d["density"] = vrun.final_structure.density
# replace 'crystal' with 'structure'
d["input"]["structure"] = d["input"].pop("crystal")
d["output"]["structure"] = d["output"].pop("crystal")
for k, v in {"energy": "final_energy", "energy_per_atom": "final_energy_per_atom"}.items():
d["output"][k] = d["output"].pop(v)
if self.parse_dos == True or (str(self.parse_dos).lower() == "auto" and vrun.incar.get("NSW", 1) == 0):
try:
d["dos"] = vrun.complete_dos.as_dict()
except:
raise ValueError("No valid dos data exist in {}.".format(dir_name))
# Band structure parsing logic
if str(self.bandstructure_mode).lower() == "auto":
# if line mode nscf
if vrun.incar.get("ICHARG", 0) > 10 and vrun.kpoints.num_kpts > 0:
bs_vrun = BSVasprun(vasprun_file, parse_projected_eigen=True)
bs = bs_vrun.get_band_structure(line_mode=True)
# else if nscf
elif vrun.incar.get("ICHARG", 0) > 10:
bs_vrun = BSVasprun(vasprun_file, parse_projected_eigen=True)
bs = bs_vrun.get_band_structure()
# else just regular calculation
else:
bs = vrun.get_band_structure()
# only save the bandstructure if not moving ions
if vrun.incar["NSW"] == 0:
d["bandstructure"] = bs.as_dict()
# legacy line/True behavior for bandstructure_mode
elif self.bandstructure_mode:
bs_vrun = BSVasprun(vasprun_file, parse_projected_eigen=True)
bs = bs_vrun.get_band_structure(line_mode=(str(self.bandstructure_mode).lower() == "line"))
d["bandstructure"] = bs.as_dict()
# parse bandstructure for vbm/cbm/bandgap but don't save
else:
bs = vrun.get_band_structure()
# Parse electronic information if possible.
# For certain optimizers this is broken and we don't get an efermi resulting in the bandstructure
try:
bs_gap = bs.get_band_gap()
d["output"]["vbm"] = bs.get_vbm()["energy"]
d["output"]["cbm"] = bs.get_cbm()["energy"]
d["output"]["bandgap"] = bs_gap["energy"]
d["output"]["is_gap_direct"] = bs_gap["direct"]
d["output"]["is_metal"] = bs.is_metal()
if not bs_gap["direct"]:
d["output"]["direct_gap"] = bs.get_direct_band_gap()
if isinstance(bs, BandStructureSymmLine):
d["output"]["transition"] = bs_gap["transition"]
except Exception:
if self.bandstructure_mode is True:
import traceback
logger.error(traceback.format_exc())
logger.error("Error in " + os.path.abspath(dir_name) + ".\n" + traceback.format_exc())
raise
logger.warning("Error in parsing bandstructure")
if vrun.incar["IBRION"] == 1:
logger.warning("Vasp doesn't properly output efermi for IBRION == 1")
d["task"] = {"type": taskname, "name": taskname}
d["output_file_paths"] = self.process_raw_data(dir_name, taskname=taskname)
if "locpot" in d["output_file_paths"] and self.parse_locpot:
locpot = Locpot.from_file(os.path.join(dir_name, d["output_file_paths"]["locpot"]))
d["output"]["locpot"] = {i: locpot.get_average_along_axis(i) for i in range(3)}
if hasattr(vrun, "force_constants"):
# phonon-dfpt
d["output"]["force_constants"] = vrun.force_constants.tolist()
d["output"]["normalmode_eigenvals"] = vrun.normalmode_eigenvals.tolist()
d["output"]["normalmode_eigenvecs"] = vrun.normalmode_eigenvecs.tolist()
return d
complete_dos.update(hashvalue=hashvalue)
client = pymongo.MongoClient(host='localhost',
port=27017)
db = client['pymatgenFormatDBs']
collection = db['complete_dos']
count = collection.count_documents({"hashvalue":hashvalue})
if count == 0:
collection.insert_one(complete_dos)
else:
print("Same data is exist in DB.")
# Then band_structures
bsvasprun = BSVasprun('AlEuO3_Perovskite_BS/vasprun.xml')
bs = bsvasprun.get_band_structure().as_dict()
client = pymongo.MongoClient(host='localhost',
port=27017)
db = client['pymatgenFormatDBs']
collection = db['band_structures']
hashvalue = hashlib.sha256(str(bs).encode('utf-8')).hexdigest()
print(hashvalue)
bs.update(hashvalue=hashvalue)
count = collection.count_documents({"hashvalue":hashvalue})
if count == 0:
collection.insert_one(bs)
else: