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figshare.py
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figshare.py
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"""
Downloads files from Figshare.
Main page: https://figshare.com/authors/Kamal_Choudhary/4445539
"""
import zipfile
import tempfile
import os
import numpy as np
import io
import json
import requests
from jarvis.db.jsonutils import loadjson
from jarvis.io.vasp.outputs import Vasprun
from jarvis.io.vasp.inputs import Poscar
from jarvis.io.wannier.outputs import WannierHam
from tqdm import tqdm
import matplotlib.image as mpimg
from jarvis.analysis.stm.tersoff_hamann import TersoffHamannSTM
# import matplotlib.pyplot as plt
# plt.switch_backend("agg")
def get_db_info():
"""Get DB info."""
db_info = {
# https://doi.org/10.6084/m9.figshare.6815705
"dft_2d": [
"https://ndownloader.figshare.com/files/38521268",
"d2-12-12-2022.json",
"Obtaining 2D dataset 1.1k ...",
"https://www.nature.com/articles/s41524-020-00440-1"
+ "\nOther versions:https://doi.org/10.6084/m9.figshare.6815705",
],
# https://doi.org/10.6084/m9.figshare.6815699
"dft_3d": [
"https://ndownloader.figshare.com/files/38521619",
"jdft_3d-12-12-2022.json",
"Obtaining 3D dataset 76k ...",
"https://www.nature.com/articles/s41524-020-00440-1"
+ "\nOther versions:https://doi.org/10.6084/m9.figshare.6815699",
],
# https://doi.org/10.6084/m9.figshare.6815705
"dft_2d_2021": [
"https://ndownloader.figshare.com/files/26808917",
"d2-3-12-2021.json",
"Obtaining 2D dataset 1.1k ...",
"https://www.nature.com/articles/s41524-020-00440-1",
],
# https://doi.org/10.6084/m9.figshare.6815699
"dft_3d_2021": [
"https://ndownloader.figshare.com/files/29204826",
"jdft_3d-8-18-2021.json",
"Obtaining 3D dataset 55k ...",
"https://www.nature.com/articles/s41524-020-00440-1",
],
# https://doi.org/10.6084/m9.figshare.6815699
"cfid_3d": [
"https://ndownloader.figshare.com/files/29205201",
"cfid_3d-8-18-2021.json",
"Obtaining 3D dataset 55k ...",
"https://www.nature.com/articles/s41524-020-00440-1"
+ "\nOther versions:https://doi.org/10.6084/m9.figshare.6815699",
],
# https://doi.org/10.6084/m9.figshare.14213522
"jff": [
"https://ndownloader.figshare.com/files/28937793",
# "https://ndownloader.figshare.com/files/26809760",
"jff-7-24-2021.json",
# "jff-3-12-2021.json",
"Obtaining JARVIS-FF 2k ...",
"https://www.nature.com/articles/s41524-020-00440-1",
],
# https://doi.org/10.6084/m9.figshare.21667874
"alignn_ff_db": [
"https://ndownloader.figshare.com/files/38522315",
# "https://ndownloader.figshare.com/files/26809760",
"id_prop.json",
"Obtaining ALIGNN-FF training DB 300k ...",
"https://arxiv.org/abs/2209.05554",
],
"mp_3d_2020": [
"https://ndownloader.figshare.com/files/26791259",
"all_mp.json",
"Obtaining Materials Project-3D CFID dataset 127k...",
"https://doi.org/10.1063/1.4812323",
],
# https://doi.org/10.6084/m9.figshare.14177630
"megnet": [
"https://ndownloader.figshare.com/files/26724977",
"megnet.json",
"Obtaining MEGNET-3D CFID dataset 69k...",
"https://pubs.acs.org/doi/10.1021/acs.chemmater.9b01294",
],
# https://doi.org/10.6084/m9.figshare.14745435
"megnet2": [
"https://ndownloader.figshare.com/files/28332741",
"megnet-mp-2019-04-01.json",
"Obtaining MEGNET-3D CFID dataset 133k...",
"https://pubs.acs.org/doi/10.1021/acs.chemmater.9b01294",
],
# https://doi.org/10.6084/m9.figshare.14745327
"edos_pdos": [
"https://ndownloader.figshare.com/files/29216859",
"edos-up_pdos-elast_interp-8-18-2021.json",
"Interpolated electronic total dos spin-up dataset 55k...",
"https://www.nature.com/articles/s41524-020-00440-1",
],
# https://doi.org/10.6084/m9.figshare.13054247
"mp_3d": [
"https://ndownloader.figshare.com/files/24979850",
"CFID_mp_desc_data_84k.json",
"Obtaining Materials Project-3D CFID dataset 84k...",
"https://doi.org/10.1063/1.4812323",
],
# https://doi.org/10.6084/m9.figshare.13055333
"oqmd_3d": [
"https://ndownloader.figshare.com/files/24981170",
"CFID_OQMD_460k.json",
"Obtaining OQMD-3D CFID dataset 460k...",
"https://www.nature.com/articles/npjcompumats201510",
],
# https://doi.org/10.6084/m9.figshare.14206169
"oqmd_3d_no_cfid": [
"https://ndownloader.figshare.com/files/26790182",
"all_oqmd.json",
"Obtaining OQMD-3D dataset 800k...",
"https://www.nature.com/articles/npjcompumats201510",
],
# https://doi.org/10.6084/m9.figshare.14205083
"twod_matpd": [
"https://ndownloader.figshare.com/files/26789006",
"twodmatpd.json",
"Obtaining 2DMatPedia dataset 6k...",
"https://www.nature.com/articles/s41597-019-0097-3",
],
# https://doi.org/10.6084/m9.figshare.14213603
"polymer_genome": [
"https://ndownloader.figshare.com/files/26809907",
"pgnome.json",
"Obtaining Polymer genome 1k...",
"https://www.nature.com/articles/sdata201612",
],
"qm9_std_jctc": [
"https://ndownloader.figshare.com/files/28715319",
"qm9_std_jctc.json",
"Obtaining QM9 standardized dataset 130k,"
+ "From https://doi.org/10.1021/acs.jctc.7b00577,+",
"https://www.nature.com/articles/sdata201422",
],
# https://doi.org/10.6084/m9.figshare.14827584
# Use qm9_std_jctc instaed
"qm9_dgl": [
"https://ndownloader.figshare.com/files/28541196",
"qm9_dgl.json",
"Obtaining QM9 dataset 130k, from DGL...",
"https://www.nature.com/articles/sdata201422",
],
# https://doi.org/10.6084/m9.figshare.14912820.v1
"cod": [
"https://ndownloader.figshare.com/files/28715301",
"cod_db.json",
"Obtaining COD dataset 431k",
"https://doi.org/10.1107/S1600576720016532",
],
# Use qm9_std_jctc instaed
"qm9": [
"https://ndownloader.figshare.com/files/27627596",
"qm9_data_cfid.json",
"Obtaining QM9 dataset 134k...",
"https://www.nature.com/articles/sdata201422",
],
# https://doi.org/10.6084/m9.figshare.15127788
"qe_tb": [
"https://ndownloader.figshare.com/files/29070555",
"jqe_tb_folder.json",
"Obtaining QETB dataset 860k...",
"https://arxiv.org/abs/2112.11585",
],
# https://doi.org/10.6084/m9.figshare.14812050
"omdb": [
"https://ndownloader.figshare.com/files/28501761",
"omdbv1.json",
"Obtaining OMDB dataset 12.5k...",
"https://doi.org/10.1002/qute.201900023",
],
# https://doi.org/10.6084/m9.figshare.14812044
"qmof": [
"https://figshare.com/ndownloader/files/30972640",
"qmof_db.json",
"Obtaining QMOF dataset 20k...",
"https://www.cell.com/matter/fulltext/S2590-2385(21)00070-9",
],
# https://doi.org/10.6084/m9.figshare.15127758
"hmof": [
"https://figshare.com/ndownloader/files/30972655",
"hmof_db_9_18_2021.json",
"Obtaining hMOF dataset 137k...",
"https://doi.org/10.1021/acs.jpcc.6b08729",
],
# https://figshare.com/account/projects/100325/articles/14960157
"c2db": [
"https://ndownloader.figshare.com/files/28682010",
"c2db_atoms.json",
"Obtaining C2DB dataset 3.5k...",
"https://iopscience.iop.org/article/10.1088/2053-1583/aacfc1",
],
# https://doi.org/10.6084/m9.figshare.25256236
"halide_peroskites": [
"https://figshare.com/ndownloader/files/44619562",
"halide_peroskites.json",
"Obtaining halide perovskite dataset229...",
"https://doi.org/10.1039/D1EE02971A",
],
# https://figshare.com/account/projects/100325/articles/14962356
"hopv": [
"https://ndownloader.figshare.com/files/28814184",
"hopv_15.json",
"Obtaining HOPV15 dataset 4.5k...",
"https://www.nature.com/articles/sdata201686",
],
# https://figshare.com/account/projects/100325/articles/14962356
"pdbbind_core": [
"https://ndownloader.figshare.com/files/28874802",
"pdbbind_2015_core.json",
"Obtaining PDBBind dataset 195...",
"https://doi.org/10.1093/bioinformatics/btu626",
],
# https://doi.org/10.6084/m9.figshare.14812038
"pdbbind": [
"https://ndownloader.figshare.com/files/28816368",
"pdbbind_2015.json",
"Obtaining PDBBind dataset 11k...",
"https://doi.org/10.1093/bioinformatics/btu626",
],
# https://doi.org/10.6084/m9.figshare.21713885
"snumat": [
"https://ndownloader.figshare.com/files/38521736",
"snumat.json",
"Obtaining SNUMAT Hybrid functional dataset 10k...",
"https://www.nature.com/articles/s41597-020-00723-8",
],
# https://doi.org/10.6084/m9.figshare.13215308
"aflow2": [
"https://ndownloader.figshare.com/files/25453265",
"CFID_AFLOW2.json",
"Obtaining AFLOW-2 CFID dataset 400k...",
"https://doi.org/10.1016/j.commatsci.2012.02.005",
],
# https://doi.org/10.6084/m9.figshare.14211860
"arXiv": [
"https://ndownloader.figshare.com/files/26804795",
"arXivdataset.json",
"Obtaining arXiv dataset 1.8 million...",
"https://www.kaggle.com/Cornell-University/arxiv",
],
# https://doi.org/10.6084/m9.figshare.14211857
"cord19": [
"https://ndownloader.figshare.com/files/26804798",
"cord19.json",
"Obtaining CORD19 dataset 223k...",
"https://github.com/usnistgov/cord19-cdcs-nist",
],
# https://doi.org/10.6084/m9.figshare.22583677
"ssub": [
"https://figshare.com/ndownloader/files/40084921",
"ssub.json",
"Obtaining SSUB dataset 1726...",
"https://github.com/wolverton-research-group/qmpy",
],
# https://doi.org/10.6084/m9.figshare.22721047
"mlearn": [
# "https://figshare.com/ndownloader/files/40424156",
"https://figshare.com/ndownloader/files/40357663",
"mlearn.json",
"Obtaining mlearn dataset 1730...",
"https://github.com/materialsvirtuallab/mlearn",
],
# https://doi.org/10.6084/m9.figshare.22814318
"foundry_ml_exp_bandgaps": [
"https://figshare.com/ndownloader/files/40557743",
"foundry_ml_exp_bandgaps.json",
"Obtaining foundry_ml_exp_bandgaps dataset 2069...",
"https://foundry-ml.org/#/datasets/10.18126/wg3u-g8vu",
],
# ToFix# https://doi.org/10.6084/m9.figshare.22815926
# "mat_scholar_ner": [
# "https://figshare.com/ndownloader/files/40563593",
# "mat_scholar_ner.json",
# "Obtaining mat_scholar_ner dataset XYZ...",
# "https://pubs.acs.org/doi/10.1021/acs.jcim.9b00470",
# ],
# https://doi.org/10.6084/m9.figshare.22817633
# Contains repeats
"ocp10k": [
"https://figshare.com/ndownloader/files/40566122",
"ocp10k.json",
"Obtaining OCP 10k train dataset, 59886...",
"https://github.com/Open-Catalyst-Project/ocp",
],
# https://doi.org/10.6084/m9.figshare.22817651
"arxiv_summary": [
"https://figshare.com/ndownloader/files/40566137",
"arxiv_summary.json",
"Obtaining arxiv summary cond.mat dataset 137927...",
"https://github.com/usnistgov/chemnlp",
],
# TODO:PubChem
# https://doi.org/10.6084/m9.figshare.22975787
"supercon_chem": [
"https://figshare.com/ndownloader/files/40719260",
"supercon_chem.json",
"Obtaining supercon chem dataset 16414...",
"https://www.nature.com/articles/s41524-018-0085-8",
],
# https://doi.org/10.6084/m9.figshare.22976285
"mag2d_chem": [
"https://figshare.com/ndownloader/files/40720004",
"mag2d_chem.json",
"Obtaining magnetic 2D chem dataset 226...",
"https://doi.org/10.24435/materialscloud:2019.0020/v1",
],
# https://doi.org/10.6084/m9.figshare.23000573
"vacancydb": [
"https://figshare.com/ndownloader/files/40750811",
"vacancydb.json",
"Obtaining vacancy dataset 464...",
"https://arxiv.org/abs/2205.08366",
],
# Contains repeats
# https://doi.org/10.6084/m9.figshare.23206193
"ocp100k": [
"https://figshare.com/ndownloader/files/40902845",
"ocp100k.json",
"Obtaining OCP100k dataset 149886...",
"https://github.com/Open-Catalyst-Project/ocp",
],
# https://doi.org/10.6084/m9.figshare.23250629
"ocp_all": [
"https://figshare.com/ndownloader/files/40974599",
"ocp_all.json",
"Obtaining OCPall dataset 510214...",
"https://github.com/Open-Catalyst-Project/ocp",
],
# https://doi.org/10.6084/m9.figshare.23225687
"tinnet_N": [
"https://figshare.com/ndownloader/files/40934285",
"tinnet_N.json",
"Obtaining TinNet Nitrogen dataset 329...",
"https://github.com/hlxin/tinnet",
],
# https://doi.org/10.6084/m9.figshare.23254151
"tinnet_O": [
"https://figshare.com/ndownloader/files/40978943",
"tinnet_O.json",
"Obtaining TinNet Oxygen dataset 747...",
"https://github.com/hlxin/tinnet",
],
# https://doi.org/10.6084/m9.figshare.23254154
"tinnet_OH": [
"https://figshare.com/ndownloader/files/40978949",
"tinnet_OH.json",
"Obtaining TinNet OH dataset 748...",
"https://github.com/hlxin/tinnet",
],
# https://doi.org/10.6084/m9.figshare.23909478
"AGRA_O": [
"https://figshare.com/ndownloader/files/41923284",
"AGRA_O.json",
"Obtaining AGRA Oxygen dataset 1000...",
"https://github.com/Feugmo-Group/AGRA",
],
# https://doi.org/10.6084/m9.figshare.23909478
"AGRA_OH": [
"https://figshare.com/ndownloader/files/41923287",
"AGRA_OH.json",
"Obtaining AGRA OH dataset 875...",
"https://github.com/Feugmo-Group/AGRA",
],
# https://doi.org/10.6084/m9.figshare.23909478
"AGRA_CO": [
"https://figshare.com/ndownloader/files/41923278",
"AGRA_CO.json",
"Obtaining AGRA CO dataset 193...",
"https://github.com/Feugmo-Group/AGRA",
],
# https://doi.org/10.6084/m9.figshare.23909478
"AGRA_CHO": [
"https://figshare.com/ndownloader/files/41923275",
"AGRA_CHO.json",
"Obtaining AGRA Oxygen dataset 214...",
"https://github.com/Feugmo-Group/AGRA",
],
# https://doi.org/10.6084/m9.figshare.23909478
"AGRA_COOH": [
"https://figshare.com/ndownloader/files/41923281",
"AGRA_COOH.json",
"Obtaining AGRA COOH dataset 280...",
"https://github.com/Feugmo-Group/AGRA",
],
# https://doi.org/10.6084/m9.figshare.21370572
"supercon_3d": [
"https://figshare.com/ndownloader/files/38307921",
"jarvis_epc_data_figshare_1058.json",
"Obtaining supercond. Tc dataset 1058...",
"https://www.nature.com/articles/s41524-022-00933-1",
],
# https://doi.org/10.6084/m9.figshare.21370572
"supercon_2d": [
"https://figshare.com/ndownloader/files/38950433",
"jarvis_epc_data_2d.json",
"Obtaining supercond. Tc dataset 161...",
"https://doi.org/10.1021/acs.nanolett.2c04420",
],
# https://doi.org/10.6084/m9.figshare.23267852
"m3gnet_mpf": [
"https://figshare.com/ndownloader/files/41009036",
"m3gnet_mpf.json",
"Obtaining m3gnet_mpf dataset 168917...",
"https://github.com/materialsvirtuallab/m3gnet",
],
# https://doi.org/10.6084/m9.figshare.13154159
"raw_files": [
"https://ndownloader.figshare.com/files/25295732",
"figshare_data-10-28-2020.json",
"Obtaining raw io files 145k...",
"https://www.nature.com/articles/s41524-020-00440-1",
],
}
return db_info
# Format: download_link, filename, message, reference
# Figshare link: https://figshare.com/account/home#/projects/100325
def get_stm_2d_dataset():
"""Get 2D STM image dataset."""
# Ref: https://www.nature.com/articles/s41597-021-00824-y
link_1 = "https://ndownloader.figshare.com/files/21884952"
r_jpg = requests.get(link_1)
z = zipfile.ZipFile(io.BytesIO(r_jpg.content))
link_2 = "https://ndownloader.figshare.com/files/21893379"
r_json = requests.get(link_2).content
latts = json.loads(r_json)
namelist = z.namelist()
pos_bias = []
neg_bias = []
print("Obtaining 2D STM dataset ...")
for i in namelist:
img_str = z.read(i)
values = mpimg.imread(io.BytesIO((img_str)), format="jpg")
# img=Image(values=values)
jid = i.split("/")[-1].split("_")[0]
bias = i.split("/")[-1].split("_")[1].split(".jpg")[0]
lat_system = latts[jid]
if bias == "pos":
info = {}
info["jid"] = jid
info["image_values"] = values
info["lat_type"] = lat_system
pos_bias.append(info)
if bias == "neg":
info = {}
info["jid"] = jid
info["image_values"] = values
info["lat_type"] = lat_system
neg_bias.append(info)
return pos_bias, neg_bias
def get_request_data(
js_tag="jdft_2d-4-26-2020.json",
url="https://ndownloader.figshare.com/files/22471019",
store_dir=None,
):
"""Get data with progress bar."""
zfile = js_tag + ".zip"
if store_dir is None:
path = str(os.path.join(os.path.dirname(__file__), zfile))
else:
path = str(os.path.join(store_dir, zfile))
# path = str(os.path.join(os.path.dirname(__file__), js_tag))
if not os.path.isfile(path):
# zfile = str(os.path.join(os.path.dirname(__file__), "tmp.zip"))
response = requests.get(url, stream=True)
total_size_in_bytes = int(response.headers.get("content-length", 0))
block_size = 1024 # 1 Kibibyte
progress_bar = tqdm(
total=total_size_in_bytes, unit="iB", unit_scale=True
)
with open(path, "wb") as file:
for data in response.iter_content(block_size):
progress_bar.update(len(data))
file.write(data)
progress_bar.close()
# f = open(zfile, "wb")
# f.write(r.content)
# f.close()
print("Loading the zipfile...")
data = json.loads(zipfile.ZipFile(path).read(js_tag))
print("Loading completed.")
# with zipfile.ZipFile(zfile, "r") as zipObj:
# # zipObj.extract(path)
# zipObj.extractall(os.path.join(os.path.dirname(__file__)))
# os.remove(zfile)
# data = loadjson(path)
return data
def data(dataset="dft_2d", store_dir=None):
"""Provide main function to download datasets."""
db_info = get_db_info()
if dataset not in list(db_info.keys()):
raise ValueError("Check DB name options.")
url = db_info[dataset][0]
js_tag = db_info[dataset][1]
message = db_info[dataset][2]
print(message)
message = "Reference:" + db_info[dataset][3]
print(message)
# r = requests.get(url)
# z = zipfile.ZipFile(io.BytesIO(r.content))
# data = json.loads(z.read(js_tag).decode("utf-8"))
# r = requests.get(url)
# z = zipfile.ZipFile(io.BytesIO(r.content))
# wdat = z.read(js_tag).decode("utf-8")
# fd, path = tempfile.mkstemp()
# with os.fdopen(fd, "w") as tmp:
# tmp.write(wdat)
# data = loadjson(path)
# path = str(os.path.join(os.path.dirname(__file__), js_tag))
# if not os.path.isfile(path):
# zfile = str(os.path.join(os.path.dirname(__file__), "tmp.zip"))
# r = requests.get(url)
# f = open(zfile, "wb")
# f.write(r.content)
# f.close()
# with zipfile.ZipFile(zfile, "r") as zipObj:
# # zipObj.extract(path)
# zipObj.extractall(os.path.join(os.path.dirname(__file__)))
# os.remove(zfile)
# data = loadjson(path)
dat = get_request_data(js_tag=js_tag, url=url, store_dir=store_dir)
return dat
def get_jid_data(jid="JVASP-667", dataset="dft_2d"):
"""Get info for a jid and dataset."""
d = data(dataset)
for i in d:
if i["jid"] == jid:
return i
def get_ff_eneleast():
"""Get JARVIS-FF related data."""
jff1 = str(os.path.join(os.path.dirname(__file__), "jff1.json"))
if not os.path.isfile(jff1):
r = requests.get("https://ndownloader.figshare.com/files/10307139")
f = open(jff1, "wb")
f.write(r.content)
f.close()
data_ff1 = loadjson(jff1)
return data_ff1
def make_stm_from_prev_parchg(
jid="JVASP-667", bias="Negative", filename="stm_image.png", min_size=10
):
"""Make STM images from previously calculated PARVHG files for 2D."""
fls = data("raw_files")
for i in fls["STM"]:
zip_name = jid + "_" + bias + ".zip"
if i["name"] == zip_name:
zip_file_url = i["download_url"]
r = requests.get(zip_file_url)
z = zipfile.ZipFile(io.BytesIO(r.content))
pchg = z.read("PARCHG").decode("utf-8")
fd, path = tempfile.mkstemp()
with os.fdopen(fd, "w") as tmp:
tmp.write(pchg)
TH_STM = TersoffHamannSTM(
chg_name=path, min_size=min_size, zcut=None
)
t_height = TH_STM.constant_height(filename=filename)
print("t_height", t_height)
return i
def get_wann_electron(jid="JVASP-816"):
"""Download electron WTBH if available."""
w = ""
ef = ""
fls = data("raw_files")
for i in fls["WANN"]:
if i["name"].split(".zip")[0] == jid:
r = requests.get(i["download_url"])
z = zipfile.ZipFile(io.BytesIO(r.content))
wdat = z.read("wannier90_hr.dat").decode("utf-8")
js_file = jid + ".json"
js = z.read(js_file).decode("utf-8")
fd, path = tempfile.mkstemp()
with os.fdopen(fd, "w") as tmp:
tmp.write(wdat)
w = WannierHam(path)
fd, path = tempfile.mkstemp()
with os.fdopen(fd, "w") as tmp:
tmp.write(js)
d = loadjson(path)
ef = d["info_mesh"]["efermi"]
fd, path = tempfile.mkstemp()
pos = z.read("POSCAR").decode("utf-8")
with os.fdopen(fd, "w") as tmp:
tmp.write(pos)
atoms = Poscar.from_file(path).atoms
return w, ef, atoms
def get_wann_phonon(jid="JVASP-1002", factor=15.633302):
"""Download phonon WTBH if available."""
# Requires phonopy
from jarvis.io.phonopy.outputs import get_phonon_tb
fls = data("raw_files")
for i in fls["FD-ELAST"]:
if isinstance(i, dict):
if i["name"].split(".zip")[0] == jid:
r = requests.get(i["download_url"])
z = zipfile.ZipFile(io.BytesIO(r.content))
vrun_path = z.read("vasprun.xml").decode("utf-8")
fd, path = tempfile.mkstemp()
with os.fdopen(fd, "w") as tmp:
tmp.write(vrun_path)
vrun = Vasprun(path)
fc = vrun.phonon_data()["force_constants"]
atoms = vrun.all_structures[0]
# print(atoms)
# atoms = Atoms.from_poscar(pos)
# print(atoms)
fd, path = tempfile.mkstemp()
get_phonon_tb(fc=fc, atoms=atoms, out_file=path, factor=factor)
# cvn = Spacegroup3D(atoms).conventional_standard_structure
w = WannierHam(path)
return w, atoms
def get_hk_tb(k=np.array([0, 0, 0]), w=[]):
"""Get Wannier TB Hamiltonian."""
nr = w.R.shape[0]
hk = np.zeros((w.nwan, w.nwan), dtype=complex)
kmat = np.tile(k, (nr, 1))
exp_ikr = np.exp(1.0j * 2 * np.pi * np.sum(kmat * w.R, 1))
temp = np.zeros(w.nwan**2, dtype=complex)
for i in range(nr):
temp += exp_ikr[i] * w.HR[i, :]
hk = np.reshape(temp, (w.nwan, w.nwan))
hk = (hk + hk.T.conj()) / 2.0
return hk
"""
QM9 xyz file
>>> def get_val(filename=''):
f=open(filename,'r')
lines=f.read().splitlines()
f.close()
info={}
for i in range(len(attr_index)):
info[attr_index[i]]=float(lines[1].split()[i+2])
return info
"""
"""
if __name__ == "__main__":
data_2d = data(dataset='dft_2d')
print('2d',len(data_2d))
data_3d = data(dataset='dft_3d')
print('3d',len(data_3d))
data_ml = data(dataset='cfid_3d')
print('cfid3d',len(data_ml))
data_ff = get_ff_eneleast()
print ('ff',len(data_ff))
"""