def run(mpfile, **kwargs):
import pymatgen
import pandas as pd
from mpcontribs.users.swf.rest.rester import SwfRester
# load data from google sheet
google_sheet = mpfile.document[mp_level01_titles[0]].pop('google_sheet')
google_sheet += '/export?format=xlsx'
df_dct = pd.read_excel(google_sheet, sheet_name=None)
# rename sheet columns
elements = ['Fe', 'V', 'Co']
df_dct['IP Energy Product'].columns = ['IP_Energy_product'] + elements
df_dct['total'].columns = elements
df_dct['MOKE'].columns = elements + ['thickness', 'MOKE_IP_Hc']
df_dct['VSM'].columns = elements + ['thickness', 'VSM_IP_Hc']
df_dct['formula'].columns = elements
df_dct['Kondorsky'].columns = ['angle', 'Kondorsky_Model', 'Experiment']
# round all compositions to 100%
for sheet, df in df_dct.items():
if sheet != 'Kondorsky':
for idx, row in df.iterrows():
df.loc[idx:idx, elements] = round_to_100_percent(row[elements])
row5 = df_dct['formula'].iloc[0]
formula5 = get_composition_from_string(
pymatgen.Composition(10 * row5).formula.replace(' ', ''))
dct = dict((k, clean_value(v, '%')) for k, v in row5.to_dict().items())
mpfile.add_hierarchical_data({'data': dct}, identifier=formula5)
mpfile.add_data_table(formula5,
df_dct['Kondorsky'],
name='Angular Dependence of Switching Field')
for sheet, df in df_dct.items():
if sheet == 'formula' or sheet == 'Kondorsky' or sheet == 'total':
continue
for idx, row in df.iterrows():
composition = pymatgen.Composition(row[elements] * 10)
formula = get_composition_from_string(
composition.formula.replace(' ', ''))
dct = dict((k, clean_value(v, '%'))
for k, v in row[elements].to_dict().items())
mpfile.add_hierarchical_data({'data': dct}, identifier=formula)
columns = [x for x in row.index if x not in elements]
if columns:
data = row[columns].round(decimals=1)
dct = dict(
(k, clean_value(v)) for k, v in data.to_dict().items())
mpfile.add_hierarchical_data({'data': dct}, identifier=formula)
def run(mpfile, **kwargs):
import pymatgen
import pandas as pd
from mpcontribs.users.swf.rest.rester import SwfRester
# load data from google sheet
google_sheet = mpfile.document[mp_level01_titles[0]].pop("google_sheet")
google_sheet += "/export?format=xlsx"
df_dct = pd.read_excel(google_sheet, sheet_name=None)
# rename sheet columns
elements = ["Fe", "V", "Co"]
df_dct["IP Energy Product"].columns = ["IP_Energy_product"] + elements
df_dct["total"].columns = elements
df_dct["MOKE"].columns = elements + ["thickness", "MOKE_IP_Hc"]
df_dct["VSM"].columns = elements + ["thickness", "VSM_IP_Hc"]
df_dct["formula"].columns = elements
df_dct["Kondorsky"].columns = ["angle", "Kondorsky_Model", "Experiment"]
# round all compositions to 100%
for sheet, df in df_dct.items():
if sheet != "Kondorsky":
for idx, row in df.iterrows():
df.loc[idx:idx, elements] = round_to_100_percent(row[elements])
row5 = df_dct["formula"].iloc[0]
formula5 = get_composition_from_string(
pymatgen.Composition(10 * row5).formula.replace(" ", ""))
dct = dict((k, clean_value(v, "%")) for k, v in row5.to_dict().items())
mpfile.add_hierarchical_data({"data": dct}, identifier=formula5)
mpfile.add_data_table(formula5,
df_dct["Kondorsky"],
name="Angular Dependence of Switching Field")
for sheet, df in df_dct.items():
if sheet == "formula" or sheet == "Kondorsky" or sheet == "total":
continue
for idx, row in df.iterrows():
composition = pymatgen.Composition(row[elements] * 10)
formula = get_composition_from_string(
composition.formula.replace(" ", ""))
dct = dict((k, clean_value(v, "%"))
for k, v in row[elements].to_dict().items())
mpfile.add_hierarchical_data({"data": dct}, identifier=formula)
columns = [x for x in row.index if x not in elements]
if columns:
data = row[columns].round(decimals=1)
dct = dict(
(k, clean_value(v)) for k, v in data.to_dict().items())
mpfile.add_hierarchical_data({"data": dct}, identifier=formula)
def run(mpfile, **kwargs):
import pymatgen
import pandas as pd
from mpcontribs.users.swf.rest.rester import SwfRester
# load data from google sheet
google_sheet = mpfile.document[mp_level01_titles[0]].pop('google_sheet')
google_sheet += '/export?format=xlsx'
df_dct = pd.read_excel(google_sheet, sheet_name=None)
# rename sheet columns
elements = ['Fe', 'V', 'Co']
df_dct['IP Energy Product'].columns = ['IP_Energy_product'] + elements
df_dct['total'].columns = elements
df_dct['MOKE'].columns = elements + ['thickness', 'MOKE_IP_Hc']
df_dct['VSM'].columns = elements + ['thickness', 'VSM_IP_Hc']
df_dct['formula'].columns = elements
df_dct['Kondorsky'].columns = ['angle', 'Kondorsky_Model', 'Experiment']
# round all compositions to 100%
for sheet, df in df_dct.items():
if sheet != 'Kondorsky':
for idx, row in df.iterrows():
df.loc[idx:idx, elements] = round_to_100_percent(row[elements])
row5 = df_dct['formula'].iloc[0]
formula5 = get_composition_from_string(
pymatgen.Composition(10*row5).formula.replace(' ', '')
)
dct = dict((k, clean_value(v, '%')) for k,v in row5.to_dict().items())
mpfile.add_hierarchical_data({'data': dct}, identifier=formula5)
mpfile.add_data_table(
formula5, df_dct['Kondorsky'], name='Angular Dependence of Switching Field'
)
for sheet, df in df_dct.items():
if sheet == 'formula' or sheet == 'Kondorsky' or sheet == 'total':
continue
for idx, row in df.iterrows():
composition = pymatgen.Composition(row[elements]*10)
formula = get_composition_from_string(composition.formula.replace(' ', ''))
dct = dict((k, clean_value(v, '%')) for k,v in row[elements].to_dict().items())
mpfile.add_hierarchical_data({'data': dct}, identifier=formula)
columns = [x for x in row.index if x not in elements]
if columns:
data = row[columns].round(decimals=1)
dct = dict((k, clean_value(v)) for k,v in data.to_dict().items())
mpfile.add_hierarchical_data({'data': dct}, identifier=formula)
def add_structure(self, source, name=None, identifier=None, fmt=None):
"""add a structure to the mpfile"""
from pymatgen import Structure, MPRester
if isinstance(source, Structure):
structure = source
elif isinstance(source, dict):
structure = Structure.from_dict(source)
elif os.path.exists(source):
structure = Structure.from_file(source, sort=True)
elif isinstance(source, six.string_types):
if fmt is None:
raise ValueError("Need fmt to get structure from string!")
structure = Structure.from_str(source, fmt, sort=True)
else:
raise ValueError(source, "not supported!")
if name is not None:
if not isinstance(name, six.string_types):
raise ValueError("structure name needs to be a string")
elif "." in name:
raise ValueError("structure name cannot contain dots (.)")
mpr = MPRester()
if not mpr.api_key:
raise ValueError(
"API key not set. Run `pmg config --add PMG_MAPI_KEY <USER_API_KEY>`."
)
matched_mpids = mpr.find_structure(structure)
formula = get_composition_from_string(structure.composition.formula)
if not matched_mpids:
if identifier is None:
identifier = formula
print(
"Structure not found in MP! Please submit via MPComplete to "
"obtain mp-id or manually choose an anchor mp-id! Continuing "
"with {} as identifier!".format(identifier))
else:
print("Structure not found in MP! Forcing {} as identifier!".
format(identifier))
elif identifier is None:
identifier = matched_mpids[0]
if len(matched_mpids) > 1:
print("Multiple matching structures found in MP. Using",
identifier)
elif identifier not in matched_mpids:
msg = "Structure does not match {} but instead {}!".format(
identifier, matched_mpids)
raise ValueError(msg)
idx = len(
self.document.get(identifier, {}).get(mp_level01_titles[3], {}))
sub_key = formula if name is None else name
if sub_key in self.document.get(identifier,
{}).get(mp_level01_titles[3], {}):
sub_key += "_{}".format(idx)
self.document.rec_update(
nest_dict(structure.as_dict(),
[identifier, mp_level01_titles[3], sub_key]))
return identifier
def run(mpfile, **kwargs):
input_dir = mpfile.hdata['_hdata']['input_dir']
identifier = get_composition_from_string('PbZr20Ti80O3')
print identifier
# 'SP128_NSO_LPFM0000.ibw' too big to display in notebook
files = ['BR_60016 (1).ibw', 'SP128_NSO_VPFM0000.ibw']
for f in files:
file_name = os.path.join(input_dir, f)
df = load_data(file_name)
name = f.split('.')[0]
mpfile.add_data_table(identifier, df, name)
print 'imported', f
xrd_file = os.path.join(input_dir, 'Program6_JA_6_2th0m Near SRO (002)_2.xrdml.xml')
data = read_xrdml(xrd_file)
df = DataFrame(np.stack((data['2Theta'],data['data']),1), columns=['2Theta','Intensity'])
opts = {'yaxis': {'type': 'log'}} # see plotly docs
mpfile.add_data_table(identifier, df, 'NearSRO', plot_options=opts)
print 'imported', os.path.basename(xrd_file)
rsm_file = os.path.join(input_dir, 'JA 42 RSM 103 STO 001.xrdml.xml')
rvals, df = load_RSM(rsm_file)
mpfile.add_hierarchical_data({'rsm_range': {
'x': '{} {}'.format(rvals[0], rvals[1]),
'y': '{} {}'.format(rvals[2], rvals[3]),
}}, identifier=identifier)
mpfile.add_data_table(identifier, df, 'RSM')
print 'imported', os.path.basename(rsm_file)
def run(mpfile, **kwargs):
input_file = mpfile.document['_hdata'].pop('input_file')
zip_path = os.path.join(os.environ['HOME'], 'work', input_file)
if not os.path.exists(zip_path):
return 'Please upload', zip_path
zip_file = ZipFile(zip_path, 'r')
composition_table_dict = mpfile.document['_hdata']['composition_table']
conc_funcs = get_concentration_functions(composition_table_dict)
for info in zip_file.infolist():
print info.filename
d = RecursiveDict()
# positions.x/y from filename, <scan-id>_<meas-element>_<X>_<Y>.csv
element, x, y = os.path.splitext(info.filename)[0].rsplit('_', 4)
d['position'] = RecursiveDict(
(k, clean_value(v, 'mm'))
for k, v in zip(['x', 'y'], [x, y])
)
# composition
d['composition'] = RecursiveDict(
(el, clean_value(f(x, y), convert_to_percent=True))
for el, f in conc_funcs.items()
)
# identifier
identifier = get_composition_from_string(''.join([
'{}{}'.format(el, int(round(Decimal(comp.split()[0]))))
for el, comp in d['composition'].items()
]))
# load csv file
try:
csv = zip_file.read(info.filename)
except KeyError:
print 'ERROR: Did not find %s in zip file' % info.filename
# read csv to pandas DataFrame and add to MPFile
df = read_csv(csv)
df = df[['Energy', 'XAS', 'XMCD']]
# min and max
d.rec_update(RecursiveDict(
(y, RecursiveDict([
('min', df[y].min()), ('max', df[y].max())
])) for y in ['XAS', 'XMCD']
))
# add data to MPFile
mpfile.add_hierarchical_data(nest_dict(d, ['data']), identifier=identifier)
mpfile.add_data_table(identifier, df, name=element)
def run(mpfile, **kwargs):
input_file = mpfile.document["_hdata"].pop("input_file")
zip_path = os.path.join(os.environ["HOME"], "work", input_file)
if not os.path.exists(zip_path):
return "Please upload", zip_path
zip_file = ZipFile(zip_path, "r")
composition_table_dict = mpfile.document["_hdata"]["composition_table"]
conc_funcs = get_concentration_functions(composition_table_dict)
for info in zip_file.infolist():
print info.filename
d = RecursiveDict()
# positions.x/y from filename, <scan-id>_<meas-element>_<X>_<Y>.csv
element, x, y = os.path.splitext(info.filename)[0].rsplit("_", 4)
d["position"] = RecursiveDict(
(k, clean_value(v, "mm")) for k, v in zip(["x", "y"], [x, y]))
# composition
d["composition"] = RecursiveDict(
(el, clean_value(f(x, y), convert_to_percent=True))
for el, f in conc_funcs.items())
# identifier
identifier = get_composition_from_string("".join([
"{}{}".format(el, int(round(Decimal(comp.split()[0]))))
for el, comp in d["composition"].items()
]))
# load csv file
try:
csv = zip_file.read(info.filename)
except KeyError:
print "ERROR: Did not find %s in zip file" % info.filename
# read csv to pandas DataFrame and add to MPFile
df = read_csv(csv)
df = df[["Energy", "XAS", "XMCD"]]
# min and max
d.rec_update(
RecursiveDict(
(y, RecursiveDict([("min", df[y].min()), ("max",
df[y].max())]))
for y in ["XAS", "XMCD"]))
# add data to MPFile
mpfile.add_hierarchical_data(nest_dict(d, ["data"]),
identifier=identifier)
mpfile.add_data_table(identifier, df, name=element)
def run(mpfile, **kwargs):
input_file = mpfile.document['_hdata'].pop('input_file')
zip_path = os.path.join(os.environ['HOME'], 'work', input_file)
if not os.path.exists(zip_path):
return 'Please upload', zip_path
zip_file = ZipFile(zip_path, 'r')
composition_table_dict = mpfile.document['_hdata']['composition_table']
conc_funcs = get_concentration_functions(composition_table_dict)
for info in zip_file.infolist():
print info.filename
d = RecursiveDict()
# positions.x/y from filename, <scan-id>_<meas-element>_<X>_<Y>.csv
element, x, y = os.path.splitext(info.filename)[0].rsplit('_', 4)
d['position'] = RecursiveDict(
(k, clean_value(v, 'mm')) for k, v in zip(['x', 'y'], [x, y]))
# composition
d['composition'] = RecursiveDict(
(el, clean_value(f(x, y), convert_to_percent=True))
for el, f in conc_funcs.items())
# identifier
identifier = get_composition_from_string(''.join([
'{}{}'.format(el, int(round(Decimal(comp.split()[0]))))
for el, comp in d['composition'].items()
]))
# load csv file
try:
csv = zip_file.read(info.filename)
except KeyError:
print 'ERROR: Did not find %s in zip file' % info.filename
# read csv to pandas DataFrame and add to MPFile
df = read_csv(csv)
df = df[['Energy', 'XAS', 'XMCD']]
# min and max
d.rec_update(
RecursiveDict(
(y, RecursiveDict([('min', df[y].min()), ('max',
df[y].max())]))
for y in ['XAS', 'XMCD']))
# add data to MPFile
mpfile.add_hierarchical_data(nest_dict(d, ['data']),
identifier=identifier)
mpfile.add_data_table(identifier, df, name=element)
def run(mpfile, dup_check_test_site=True):
from pymatgen import MPRester
existing_identifiers = {}
#for b in [False, True]:
# with DlrVietenRester(test_site=b) as mpr:
# for doc in mpr.query_contributions():
# existing_identifiers[doc['mp_cat_id']] = doc['_id']
# if not dup_check_test_site:
# break
google_sheet = mpfile.document[mp_level01_titles[0]].pop('google_sheet')
google_sheet += '/export?format=xlsx'
df_dct = pd.read_excel(google_sheet, sheetname=None)
mpr = MPRester()
update = 0
for sheet in df_dct.keys():
print(sheet)
df = df_dct[sheet]
sheet_split = sheet.split()
composition = sheet_split[0]
identifier = get_composition_from_string(composition)
if len(sheet_split) > 1 and mp_id_pattern.match(sheet_split[1]):
identifier = sheet_split[1]
print('identifier = {}'.format(identifier))
if 'CIF' in sheet_split:
print('adding CIF ...')
df.columns = [df.columns[0]] + [''] * (df.shape[1] - 1)
cif = df.to_csv(na_rep='',
index=False,
sep='\t',
quoting=csv.QUOTE_NONE)
mpfile.add_structure(cif, identifier=identifier, fmt='cif')
else:
print('adding data ...')
mpfile.add_hierarchical_data({'composition': composition},
identifier=identifier)
mpfile.add_data_table(identifier, df, name='dH_dS')
if identifier in existing_identifiers:
cid = existing_identifiers[identifier]
mpfile.insert_id(identifier, cid)
update += 1
print len(mpfile.ids), 'contributions to submit.'
if update > 0:
print update, 'contributions to update.'
def run(mpfile, **kwargs):
input_dir = mpfile.hdata["_hdata"]["input_dir"]
identifier = get_composition_from_string("PbZr20Ti80O3")
print identifier
# 'SP128_NSO_LPFM0000.ibw' too big to display in notebook
files = ["BR_60016 (1).ibw", "SP128_NSO_VPFM0000.ibw"]
for f in files:
file_name = os.path.join(input_dir, f)
df = load_data(file_name)
name = f.split(".")[0]
mpfile.add_data_table(identifier, df, name)
print "imported", f
xrd_file = os.path.join(input_dir, "Program6_JA_6_2th0m Near SRO (002)_2.xrdml.xml")
data = read_xrdml(xrd_file)
df = DataFrame(
np.stack((data["2Theta"], data["data"]), 1), columns=["2Theta", "Intensity"]
)
opts = {"yaxis": {"type": "log"}} # see plotly docs
mpfile.add_data_table(identifier, df, "NearSRO", plot_options=opts)
print "imported", os.path.basename(xrd_file)
rsm_file = os.path.join(input_dir, "JA 42 RSM 103 STO 001.xrdml.xml")
rvals, df = load_RSM(rsm_file)
mpfile.add_hierarchical_data(
{
"rsm_range": {
"x": "{} {}".format(rvals[0], rvals[1]),
"y": "{} {}".format(rvals[2], rvals[3]),
}
},
identifier=identifier,
)
mpfile.add_data_table(identifier, df, "RSM")
print "imported", os.path.basename(rsm_file)
def run(mpfile, **kwargs):
input_dir = mpfile.hdata['_hdata']['input_dir']
identifier = get_composition_from_string('PbZr20Ti80O3')
print identifier
# 'SP128_NSO_LPFM0000.ibw' too big to display in notebook
files = ['BR_60016 (1).ibw', 'SP128_NSO_VPFM0000.ibw']
for f in files:
file_name = os.path.join(input_dir, f)
df = load_data(file_name)
name = f.split('.')[0]
mpfile.add_data_table(identifier, df, name)
print 'imported', f
xrd_file = os.path.join(input_dir,
'Program6_JA_6_2th0m Near SRO (002)_2.xrdml.xml')
data = read_xrdml(xrd_file)
df = DataFrame(np.stack((data['2Theta'], data['data']), 1),
columns=['2Theta', 'Intensity'])
opts = {'yaxis': {'type': 'log'}} # see plotly docs
mpfile.add_data_table(identifier, df, 'NearSRO', plot_options=opts)
print 'imported', os.path.basename(xrd_file)
rsm_file = os.path.join(input_dir, 'JA 42 RSM 103 STO 001.xrdml.xml')
rvals, df = load_RSM(rsm_file)
mpfile.add_hierarchical_data(
{
'rsm_range': {
'x': '{} {}'.format(rvals[0], rvals[1]),
'y': '{} {}'.format(rvals[2], rvals[3]),
}
},
identifier=identifier)
mpfile.add_data_table(identifier, df, 'RSM')
print 'imported', os.path.basename(rsm_file)
def run(mpfile, **kwargs):
from pymatgen import Structure
reference_project = None
input_data, input_keys, extra = RecursiveDict(), RecursiveDict(
), RecursiveDict()
#input_urls = mpfile.document['_hdata'].pop('input_urls')
input_urls = {
'NUS': {
"file": "http://www.2dmatpedia.org/static/db.json.gz",
"detail": "http://www.2dmatpedia.org/2dmaterials/doc/{}"
},
'JARVIS': {
"file": "https://www.ctcms.nist.gov/~knc6/jdft_{}.json.tgz",
"detail": "https://www.ctcms.nist.gov/~knc6/jsmol/{}.html"
}
}
for project in input_urls:
input_url = input_urls[project]['file']
if '{}' in input_url:
input_url = input_url.format('2d') # TODO 3d for Jarvis
#dbfile = os.path.join(os.environ['HOME'], 'work', input_url.rsplit('/')[-1])
dbfile = input_url.rsplit('/')[-1]
if not os.path.exists(dbfile):
print('downloading', dbfile, '...')
urllib.request.urlretrieve(input_url, dbfile)
ext = os.path.splitext(dbfile)[1]
is_nus = bool(ext == '.gz')
id_key = 'source_id' if is_nus else 'mpid'
if not is_nus:
with tarfile.open(dbfile, "r:gz") as tar:
member = tar.getmembers()[0]
raw_data = json.load(tar.extractfile(member), cls=MontyDecoder)
else:
reference_project = project
raw_data = []
with gzip.open(dbfile, 'rb') as f:
for line in f:
raw_data.append(json.loads(line, cls=MontyDecoder))
input_data[project] = RecursiveDict((d[id_key], d) for d in raw_data)
input_keys[project] = [
'material_id', 'exfoliation_energy_per_atom', 'structure'
] if is_nus else ['jid', 'exfoliation_en', 'final_str']
extra[project] = [
('fin_en', ('E', 'meV/atom')),
('op_gap', ('ΔE|optB88vdW', 'meV/atom')),
('mbj_gap', ('ΔE|mbj', 'meV/atom')),
#('kv', ('Kᵥ', 'GPa')),
#('gv', ('Gᵥ', 'GPa'))
] if not is_nus else []
print(len(input_data[project]), 'materials loaded for', project)
projects = input_data.keys()
identifiers = []
for d in input_data.values():
identifiers += list(d.keys())
for identifier in set(identifiers):
print(identifier)
data, structures = RecursiveDict(), RecursiveDict()
for project in projects:
if project not in data:
data[project] = RecursiveDict()
if identifier in input_data[project]:
d = input_data[project][identifier]
structures[project] = d[input_keys[project][-1]]
if data.get('formula') is None:
data['formula'] = get_composition_from_string(
structures[project].composition.reduced_formula)
data[project]['id'] = input_urls[project]['detail'].format(
d[input_keys[project][0]])
if input_keys[project][1] in d:
Ex = d[input_keys[project][1]]
if project == reference_project:
Ex *= 1000.
data[project]['Eₓ'] = clean_value(Ex, 'eV')
for k, (sym, unit) in extra[project]:
if d[k] != 'na':
data[project][sym] = clean_value(d[k], unit)
mpfile.add_hierarchical_data(nest_dict(data, ['data']),
identifier=identifier)
#r = db.contributions.update_one(
# {'identifier': identifier, 'project': 'jarvis_dft'},
# {'$set': {'content.data': mpfile.document[identifier]['data']}},
# upsert=True
#)
#print(r.matched_count, r.modified_count, r.upserted_id)
doc = db.contributions.find_one(
{
'identifier': identifier,
'project': 'jarvis_dft'
}, {
'_id': 1,
'content.structures': 1
})
if 'structures' in doc['content']:
print('structures already added for', identifier)
continue
print(doc['_id'])
inserted_ids = []
for project, structure in structures.items():
try:
mpfile.add_structure(structure,
name=project,
identifier=identifier)
sdct = mpfile.document[identifier]['structures'][project]
sdct.pop('@module')
sdct.pop('@class')
if sdct['charge'] is None:
sdct.pop('charge')
sdct['identifier'] = identifier
sdct['project'] = 'jarvis_dft'
sdct['name'] = project
sdct['cid'] = doc['_id']
r = db.structures.insert_one(sdct)
inserted_ids.append(r.inserted_id)
except Exception as ex:
print(str(ex))
print(inserted_ids)
r = db.contributions.update_one(
{'_id': doc['_id']},
{'$set': {
'content.structures': inserted_ids
}})
print(r.matched_count, r.modified_count)
def run(mpfile, **kwargs):
from pymatgen import Structure
reference_project = None
input_data, input_keys, extra = RecursiveDict(), RecursiveDict(), RecursiveDict()
input_urls = mpfile.document['_hdata'].pop('input_urls')
for project in input_urls:
input_url = input_urls[project]['file']
if '{}' in input_url:
input_url = input_url.format('2d') # TODO 3d for Jarvis
dbfile = os.path.join(os.environ['HOME'], 'work', input_url.rsplit('/')[-1])
if not os.path.exists(dbfile):
print 'downloading', dbfile, '...'
urllib.urlretrieve(input_url, dbfile)
ext = os.path.splitext(dbfile)[1]
is_nus = bool(ext == '.gz')
id_key = 'parent_id' if is_nus else 'mpid'
if not is_nus:
with tarfile.open(dbfile, "r:gz") as tar:
member = tar.getmembers()[0]
raw_data = json.load(tar.extractfile(member), cls=MontyDecoder)
else:
reference_project = project
raw_data = []
with gzip.open(dbfile, 'rb') as f:
for line in f:
raw_data.append(json.loads(line, cls=MontyDecoder))
input_data[project] = RecursiveDict((d[id_key], d) for d in raw_data)
input_keys[project] = [
'material_id', 'exfoliation_energy_per_atom', 'structure'
] if is_nus else ['jid', 'exfoliation_en', 'final_str']
extra[project] = [
('fin_en', ('E', 'eV')),
('op_gap', ('ΔE|optB88vdW', 'eV')),
('mbj_gap', ('ΔE|mbj', 'eV')),
#('kv', ('Kᵥ', 'GPa')),
#('gv', ('Gᵥ', 'GPa'))
] if not is_nus else []
print len(input_data[project]), 'materials loaded for', project
projects = input_data.keys()
identifiers = []
for d in input_data.values():
identifiers += list(d.keys())
for identifier in identifiers:
data, structures = RecursiveDict(), RecursiveDict()
for project in projects:
if project not in data:
data[project] = RecursiveDict()
if identifier in input_data[project]:
d = input_data[project][identifier]
structures[project] = d[input_keys[project][-1]]
if data.get('formula') is None:
data['formula'] = get_composition_from_string(
structures[project].composition.reduced_formula
)
data[project]['id'] = input_urls[project]['detail'].format(d[input_keys[project][0]])
Ex = d[input_keys[project][1]]
if project == reference_project:
Ex *= 1000.
data[project]['Eₓ'] = clean_value(Ex, 'eV')
for k, (sym, unit) in extra[project]:
if d[k] != 'na':
data[project][sym] = clean_value(d[k], unit)
mpfile.add_hierarchical_data(nest_dict(data, ['data']), identifier=identifier)
for project, structure in structures.items():
name = '{}_{}'.format(data['formula'], project)
try:
mpfile.add_structure(structure, name=name, identifier=identifier)
except Exception as ex:
print str(ex)
def run(mpfile, **kwargs):
from pymatgen import Structure
reference_project = None
input_data, input_keys, extra = RecursiveDict(), RecursiveDict(
), RecursiveDict()
input_urls = mpfile.document['_hdata'].pop('input_urls')
for project in input_urls:
input_url = input_urls[project]['file']
if '{}' in input_url:
input_url = input_url.format('2d') # TODO 3d for Jarvis
dbfile = os.path.join(os.environ['HOME'], 'work',
input_url.rsplit('/')[-1])
if not os.path.exists(dbfile):
print 'downloading', dbfile, '...'
urllib.urlretrieve(input_url, dbfile)
ext = os.path.splitext(dbfile)[1]
is_nus = bool(ext == '.gz')
id_key = 'parent_id' if is_nus else 'mpid'
if not is_nus:
with tarfile.open(dbfile, "r:gz") as tar:
member = tar.getmembers()[0]
raw_data = json.load(tar.extractfile(member), cls=MontyDecoder)
else:
reference_project = project
raw_data = []
with gzip.open(dbfile, 'rb') as f:
for line in f:
raw_data.append(json.loads(line, cls=MontyDecoder))
input_data[project] = RecursiveDict((d[id_key], d) for d in raw_data)
input_keys[project] = [
'material_id', 'exfoliation_energy_per_atom', 'structure'
] if is_nus else ['jid', 'exfoliation_en', 'final_str']
extra[project] = [
('fin_en', ('E', 'meV/atom')),
('op_gap', ('ΔE|optB88vdW', 'meV/atom')),
('mbj_gap', ('ΔE|mbj', 'meV/atom')),
#('kv', ('Kᵥ', 'GPa')),
#('gv', ('Gᵥ', 'GPa'))
] if not is_nus else []
print len(input_data[project]), 'materials loaded for', project
projects = input_data.keys()
identifiers = []
for d in input_data.values():
identifiers += list(d.keys())
for identifier in identifiers:
data, structures = RecursiveDict(), RecursiveDict()
for project in projects:
if project not in data:
data[project] = RecursiveDict()
if identifier in input_data[project]:
d = input_data[project][identifier]
structures[project] = d[input_keys[project][-1]]
if data.get('formula') is None:
data['formula'] = get_composition_from_string(
structures[project].composition.reduced_formula)
data[project]['id'] = input_urls[project]['detail'].format(
d[input_keys[project][0]])
Ex = d[input_keys[project][1]]
if project == reference_project:
Ex *= 1000.
data[project]['Eₓ'] = clean_value(Ex, 'eV')
for k, (sym, unit) in extra[project]:
if d[k] != 'na':
data[project][sym] = clean_value(d[k], unit)
mpfile.add_hierarchical_data(nest_dict(data, ['data']),
identifier=identifier)
for project, structure in structures.items():
name = '{}_{}'.format(data['formula'], project)
try:
mpfile.add_structure(structure,
name=name,
identifier=identifier)
except Exception as ex:
print str(ex)
def run(mpfile, **kwargs):
# TODO clone solar_perovskite if needed, abort if insufficient permissions
import solar_perovskite
from solar_perovskite.core import GetExpThermo
from solar_perovskite.init.find_structures import FindStructures
from solar_perovskite.init.import_data import Importdata
from solar_perovskite.modelling.from_theo import EnthTheo
input_file = mpfile.hdata.general['input_file']
input_file = os.path.join(os.path.dirname(solar_perovskite.__file__), input_file)
table = read_csv(open(input_file, 'r').read().replace(';', ','))
dct = super(Table, table).to_dict(orient='records', into=RecursiveDict)
shomate = pd.read_csv(os.path.abspath(os.path.join(
os.path.dirname(solar_perovskite.__file__), "datafiles", "shomate.csv"
)), index_col=0)
shomate_dct = RecursiveDict()
for col in shomate.columns:
key = col.split('.')[0]
if key not in shomate_dct:
shomate_dct[key] = RecursiveDict()
d = shomate[col].to_dict(into=RecursiveDict)
subkey = '{}-{}'.format(int(d.pop('low')), int(d.pop('high')))
shomate_dct[key][subkey] = RecursiveDict(
(k, clean_value(v, max_dgts=6)) for k, v in d.items()
)
mpfile.add_hierarchical_data(nest_dict(shomate_dct, ['shomate']))
for row in dct:
sample_number = int(row['sample_number'])
identifier = row['closest phase MP (oxidized)'].replace('n.a.', '')
if not identifier.startswith('mp-'):
continue
if not identifier:
identifier = get_composition_from_string(row['composition oxidized phase'])
print identifier
print 'add hdata ...'
d = RecursiveDict()
d['tolerance_factor'] = row['tolerance_factor']
d['solid_solution'] = row['type of solid solution']
d['oxidized_phase'] = RecursiveDict()
d['oxidized_phase']['composition'] = row['composition oxidized phase']
d['oxidized_phase']['crystal-structure'] = row['crystal structure (fully oxidized)']
d['reduced_phase'] = RecursiveDict()
d['reduced_phase']['composition'] = row['composition reduced phase']
d['reduced_phase']['closest-MP'] = row['closest phase MP (reduced)'].replace('n.a.', '')
d = nest_dict(d, ['data'])
d['pars'] = get_fit_pars(sample_number)
d['pars']['theo_compstr'] = row['theo_compstr']
try:
fs = FindStructures(compstr=row['theo_compstr'])
theo_redenth = fs.find_theo_redenth()
imp = Importdata()
splitcomp = imp.split_comp(row['theo_compstr'])
conc_act = imp.find_active(mat_comp=splitcomp)[1]
et = EnthTheo(comp=row['theo_compstr'])
dh_max, dh_min = et.calc_dh_endm()
red_enth_mean_endm = (conc_act * dh_min) + ((1 - conc_act) * dh_max)
difference = theo_redenth - red_enth_mean_endm
d['pars']['dh_min'] = clean_value(dh_min + difference, max_dgts=8)
d['pars']['dh_max'] = clean_value(dh_max + difference, max_dgts=8)
except Exception as ex:
print('error in dh_min/max!')
print(str(ex))
pass
mpfile.add_hierarchical_data(d, identifier=identifier)
print 'add ΔH ...'
exp_thermo = GetExpThermo(sample_number, plotting=False)
enthalpy = exp_thermo.exp_dh()
table = get_table(enthalpy, 'H')
mpfile.add_data_table(identifier, table, name='enthalpy')
print 'add ΔS ...'
entropy = exp_thermo.exp_ds()
table = get_table(entropy, 'S')
mpfile.add_data_table(identifier, table, name='entropy')
print 'add raw data ...'
tga_results = os.path.join(os.path.dirname(solar_perovskite.__file__), 'tga_results')
for path in glob(os.path.join(tga_results, 'ExpDat_JV_P_{}_*.csv'.format(sample_number))):
print path.split('_{}_'.format(sample_number))[-1].split('.')[0], '...'
body = open(path, 'r').read()
cols = ['Time [min]', 'Temperature [C]', 'dm [%]', 'pO2']
table = read_csv(body, lineterminator=os.linesep, usecols=cols, skiprows=5)
table = table[cols].iloc[::100, :]
# scale/shift for better graphs
T, dm, p = [pd.to_numeric(table[col]) for col in cols[1:]]
T_min, T_max, dm_min, dm_max, p_max = T.min(), T.max(), dm.min(), dm.max(), p.max()
rT, rdm = abs(T_max - T_min), abs(dm_max - dm_min)
table[cols[2]] = (dm - dm_min) * rT/rdm
table[cols[3]] = p * rT/p_max
table.rename(columns={
'dm [%]': '(dm [%] + {:.4g}) * {:.4g}'.format(-dm_min, rT/rdm),
'pO2': 'pO₂ * {:.4g}'.format(rT/p_max)
}, inplace=True)
mpfile.add_data_table(identifier, table, name='raw')
def to_backgrid_dict(self):
"""Backgrid-conform dict from DataFrame"""
# shorten global import times by importing django here
import numpy as np
from mpcontribs.io.core.utils import get_composition_from_string
from pandas import MultiIndex
import pymatgen.util as pmg_util
from pymatgen.core.composition import CompositionError
table = dict()
nrows_max = 260
nrows = self.shape[0]
df = Table(self.head(n=nrows_max)) if nrows > nrows_max else self
numeric_columns = df.select_dtypes(
include=[np.number]).columns.tolist()
if isinstance(df.index, MultiIndex):
df.reset_index(inplace=True)
table['columns'] = []
table['rows'] = super(Table, df).to_dict(orient='records')
for col_index, col in enumerate(list(df.columns)):
cell_type = 'number'
# avoid looping rows to minimize use of `df.iat` (time-consuming in 3d)
if not col.startswith('level_') and col not in numeric_columns:
is_url_column, prev_unit, old_col = True, None, col
for row_index in range(df.shape[0]):
cell = str(df.iat[row_index, col_index])
cell_split = cell.split(' ', 1)
if not cell or len(
cell_split) == 1: # empty cell or no space
is_url_column = bool(
is_url_column
and (not cell or mp_id_pattern.match(cell)))
if is_url_column:
if cell:
value = 'https://materialsproject.org/materials/{}'.format(
cell)
table['rows'][row_index][col] = value
elif cell:
try:
composition = get_composition_from_string(cell)
composition = pmg_util.string.unicodeify(
composition)
table['rows'][row_index][col] = composition
except (CompositionError, ValueError,
OverflowError):
try:
# https://stackoverflow.com/a/38020041
result = urlparse(cell)
if not all([
result.scheme, result.netloc,
result.path
]):
break
is_url_column = True
except:
break
else:
value, unit = cell_split # TODO convert cell_split[0] to float?
is_url_column = False
try:
float(value
) # unit is only a unit if value is number
except ValueError:
continue
table['rows'][row_index].pop(old_col)
if prev_unit is None:
prev_unit = unit
col = '{} [{}]'.format(col, unit)
table['rows'][row_index][
col] = cell if prev_unit != unit else value
cell_type = 'uri' if is_url_column else 'string'
col_split = col.split('##')
nesting = [col_split[0]] if len(col_split) > 1 else []
table['columns'].append({
'name': col,
'cell': cell_type,
'nesting': nesting,
'editable': 0
})
if len(col_split) > 1:
table['columns'][-1].update(
{'label': '##'.join(col_split[1:])})
if len(table['columns']) > 12:
table['columns'][-1]['renderable'] = 0
header = RecursiveDict()
for idx, col in enumerate(table['columns']):
if 'label' in col:
k, sk = col['name'].split('##')
sk_split = sk.split()
if len(sk_split) == 2:
d = {'name': sk_split[0], 'unit': sk_split[1], 'idx': idx}
if k not in header:
header[k] = [d]
else:
header[k].append(d)
elif k in header:
header.pop(k)
for k, skl in header.items():
units = [sk['unit'] for sk in skl]
if units.count(units[0]) == len(units):
for sk in skl:
table['columns'][sk['idx']]['label'] = sk['name']
table['columns'][sk['idx']]['nesting'][0] = '{} {}'.format(
k, sk['unit'])
return table
def to_backgrid_dict(self):
"""Backgrid-conform dict from DataFrame"""
# shorten global import times by importing django here
from mpcontribs.io.core.utils import get_composition_from_string
from pandas import MultiIndex
import pymatgen.util as pmg_util
from pymatgen.core.composition import CompositionError
table = dict()
nrows_max = 260
nrows = self.shape[0]
df = Table(self.head(n=nrows_max)) if nrows > nrows_max else self
if isinstance(df.index, MultiIndex):
df.reset_index(inplace=True)
table["columns"] = []
table["rows"] = super(Table, df).to_dict(orient="records")
for col_index, col in enumerate(list(df.columns)):
cell_type = "number"
# avoid looping rows to minimize use of `df.iat` (time-consuming in 3d)
if not col.startswith("level_") and col[-1] != "]":
is_url_column = True
for row_index in range(df.shape[0]):
cell = str(df.iat[row_index, col_index])
is_url_column = bool(
is_url_column
and (not cell or mp_id_pattern.match(cell)))
if is_url_column:
if cell:
value = "https://materialsproject.org/materials/{}".format(
cell)
table["rows"][row_index][col] = value
elif cell:
try:
composition = get_composition_from_string(cell)
composition = pmg_util.string.unicodeify(
composition)
table["rows"][row_index][col] = composition
except (CompositionError, ValueError, OverflowError):
try:
# https://stackoverflow.com/a/38020041
result = urlparse(cell)
if not all([
result.scheme, result.netloc,
result.path
]):
break
is_url_column = True
except Exception:
break
cell_type = "uri" if is_url_column else "string"
col_split = col.split(".")
nesting = [col_split[0]] if len(col_split) > 1 else []
table["columns"].append({
"name": col,
"cell": cell_type,
"nesting": nesting,
"editable": 0
})
if len(col_split) > 1:
table["columns"][-1].update({"label": ".".join(col_split[1:])})
return table
