def test_almost_equals(self):
c1 = Composition({"Fe": 2.0, "O": 3.0, "Mn": 0})
c2 = Composition({"O": 3.2, "Fe": 1.9, "Zn": 0})
c3 = Composition({"Ag": 2.0, "O": 3.0})
c4 = Composition({"Fe": 2.0, "O": 3.0, "Ag": 2.0})
self.assertTrue(c1.almost_equals(c2, rtol=0.1))
self.assertFalse(c1.almost_equals(c2, rtol=0.01))
self.assertFalse(c1.almost_equals(c3, rtol=0.1))
self.assertFalse(c1.almost_equals(c4, rtol=0.1))
def test_almost_equals(self):
c1 = Composition({'Fe': 2.0, 'O': 3.0, 'Mn': 0})
c2 = Composition({'O': 3.2, 'Fe': 1.9, 'Zn': 0})
c3 = Composition({'Ag': 2.0, 'O': 3.0})
c4 = Composition({'Fe': 2.0, 'O': 3.0, 'Ag': 2.0})
self.assertTrue(c1.almost_equals(c2, rtol=0.1))
self.assertFalse(c1.almost_equals(c2, rtol=0.01))
self.assertFalse(c1.almost_equals(c3, rtol=0.1))
self.assertFalse(c1.almost_equals(c4, rtol=0.1))
def test_almost_equals(self):
c1 = Composition({"Fe": 2.0, "O": 3.0, "Mn": 0})
c2 = Composition({"O": 3.2, "Fe": 1.9, "Zn": 0})
c3 = Composition({"Ag": 2.0, "O": 3.0})
c4 = Composition({"Fe": 2.0, "O": 3.0, "Ag": 2.0})
self.assertTrue(c1.almost_equals(c2, rtol=0.1))
self.assertFalse(c1.almost_equals(c2, rtol=0.01))
self.assertFalse(c1.almost_equals(c3, rtol=0.1))
self.assertFalse(c1.almost_equals(c4, rtol=0.1))
def test_almost_equals(self):
c1 = Composition({'Fe': 2.0, 'O': 3.0, 'Mn': 0})
c2 = Composition({'O': 3.2, 'Fe': 1.9, 'Zn': 0})
c3 = Composition({'Ag': 2.0, 'O': 3.0})
c4 = Composition({'Fe': 2.0, 'O': 3.0, 'Ag': 2.0})
self.assertTrue(c1.almost_equals(c2, rtol=0.1))
self.assertFalse(c1.almost_equals(c2, rtol=0.01))
self.assertFalse(c1.almost_equals(c3, rtol=0.1))
self.assertFalse(c1.almost_equals(c4, rtol=0.1))
def run(mpfile, include_cifs=True, nmax=None, dup_check_test_site=True):
from pymatgen.core.composition import Composition
from pymatgen.core.structure import Structure
data_input = mpfile.document[mp_level01_titles[0]].pop('input')
phase_names = mpfile.hdata.general['info']['phase_names']
dir_path = os.path.dirname(os.path.realpath(__file__))
for k in data_input.keys():
data_input[k] = os.path.join(dir_path, data_input[k])
doi = mpfile.hdata.general['doi']
existing_mpids = {}
for b in [False, True]:
with Mno2PhaseSelectionRester(test_site=b) as mpr:
for doc in mpr.query_contributions(criteria={'content.doi': doi}):
existing_mpids[doc['mp_cat_id']] = doc['_id']
if not dup_check_test_site:
break
with open(data_input['formatted_entries'], "r") as fin:
mp_contrib_phases = json.loads(fin.read())
with open(data_input['hull_entries'], "r") as fin:
hull_states = json.loads(fin.read())
with open(data_input['mpid_existing'], 'r') as fin:
mp_dup = json.loads(fin.read())
with open(data_input['mpid_new'], 'r') as fin:
mp_cmp = json.loads(fin.read())
################################################################################################################
# add unique structures first (special cases)
################################################################################################################
if include_cifs:
for hstate in hull_states:
if 'other' == hstate['phase']:
c = Composition.from_dict(hstate['c'])
s = Structure.from_dict(hstate['s'])
for mpid in mpfile.ids:
formula = mpfile.hdata[mpid]['data']['Formula']
if c.almost_equals(Composition(formula)):
if nmax is not None and mpid in existing_mpids:
mpfile.document.pop(mpid) # skip duplicates
break
try:
mpfile.add_structure(s, identifier=mpid)
print formula, 'added to', mpid
except Exception as ex:
print 'tried to add structure to', mpid, 'but', str(ex)
if mpid in existing_mpids:
cid = existing_mpids[mpid]
mpfile.insert_id(mpid, cid)
print cid, 'inserted to update', mpid
break
# "phase": 'postspinel-NaMn2O4', "Formula": 'Na0.5MnO2',
# "dHf (eV/mol)": -1.415, "dHh (eV/mol)": '--', "Ground state?": 'Y',
################################################################################################################
# Get mp-ids for all entries based on matching the VASP directory path names
# Paths are different in the existing and new mp-id dictionary, so processing has to be independent
################################################################################################################
print 'get all mp-ids based on VASP directory paths ...'
for framework, fdat in mp_contrib_phases.items():
for i, phase in enumerate(fdat):
c = Composition(phase[0])
for hstate in hull_states:
if phase_names[framework] == hstate['phase'] and \
c.almost_equals(Composition.from_dict(hstate['c'])) and \
len(mp_contrib_phases[framework][i]) < 6:
mp_contrib_phases[framework][i].append(hstate['path'])
mp_contrib_phases[framework][i].append(hstate['s'])
for framework, fdat in mp_contrib_phases.items():
for i, phase in enumerate(fdat):
match_path = phase[4].replace('all_states/', '')
mp_ids = []
for path, ids in mp_dup.items():
mp_path = path.replace('/Users/patrick/Downloads/20160710_MPContrib_MnO2_DK/', '').replace(
'/3.double_relax/CONTCAR', '')
if match_path == mp_path:
mp_ids.extend(ids)
for path, id_dat in mp_cmp.items():
mp_path = path.replace('20160725_MnO2_DK_Cifs/20160710_MPContrib_MnO2_DK-', '').replace(
'-3.double_relax-CONTCAR.cif', '').replace('-', '/')
if match_path == mp_path:
if 'mp_id' in id_dat.keys():
mp_ids.append(id_dat['mp_id'])
mp_contrib_phases[framework][i].append(mp_ids)
################################################################################################################
# For structures that have mp-ids, add them to the contribution dictionary.
# For those that don't, run a separate dictionary to keep track of them
################################################################################################################
print 'add structures with mp-ids to contribution ...'
no_id_dict = {}
errors_file = os.path.join(os.path.dirname(__file__), 'errors.json')
with open(errors_file, 'r') as f:
errors = json.load(f)
for framework, fdat in mp_contrib_phases.items():
for phase in fdat:
d = RecursiveDict()
d["Phase"] = framework
d["Formula"] = phase[0]
try:
float(phase[1])
d["dHf"] = '{} eV/mol'.format(phase[1])
except:
d["dHf"] = '--'
try:
float(phase[3])
d["dHh"] = '{} eV/mol'.format(phase[3])
except:
d["dHh"] = '--'
d["GS"] = phase[2]
if len(phase[6]) == 0:
no_id_dict[phase[4].replace('all_states/', '')] = d
for mpid in phase[6]:
if nmax is not None:
if len(mpfile.ids) >= nmax-1:
break
elif mpid in existing_mpids:
continue # skip duplicates
mpfile.add_hierarchical_data(RecursiveDict({'data': d}), identifier=mpid)
print 'added', mpid
if mpid in existing_mpids:
cid = existing_mpids[mpid]
mpfile.insert_id(mpid, cid)
print cid, 'inserted to update', mpid
if include_cifs:
try:
mpfile.add_structure(phase[5], identifier=mpid)
print framework, phase[0], 'added to', mpid
except ValueError as ex:
print 'tried to add structure to', mpid, 'but', str(ex)
errors[mpid] = str(ex)
with open(errors_file, 'w') as f:
json.dump(errors, f)
print """
DONE.
{} structures to submit.
{} structures do not have mp-ids.
{} structures with mp-ids have errors.
""".format(len(mpfile.ids), len(no_id_dict), len(errors))
def run(mpfile, include_cifs=True):
data = mpfile.hdata.general['data']
phase_names = data['phase_names']
data_input = data.pop('input')
dir_path = os.path.dirname(os.path.realpath(__file__))
for k in data_input.keys():
data_input[k] = os.path.join(dir_path, data_input[k])
with open(data_input['formatted_entries'], "r") as fin:
mp_contrib_phases = json.loads(fin.read())
with open(data_input['hull_entries'], "r") as fin:
hull_states = json.loads(fin.read())
with open(data_input['mpid_existing'], 'r') as fin:
mp_dup = json.loads(fin.read())
with open(data_input['mpid_new'], 'r') as fin:
mp_cmp = json.loads(fin.read())
################################################################################################################
# add unique structures first (special cases)
################################################################################################################
if include_cifs:
for hstate in hull_states:
if 'other' == hstate['phase']:
c = Composition.from_dict(hstate['c'])
s = Structure.from_dict(hstate['s'])
for mpid in mpfile.ids:
formula = mpfile.hdata[mpid]['Formula']
if c.almost_equals(Composition(formula)):
try:
mpfile.add_structure(s, identifier=mpid)
print formula, 'added to', mpid
except Exception as ex:
print 'tried to add structure to', mpid, 'but', str(
ex)
break
# "phase": 'postspinel-NaMn2O4', "Formula": 'Na0.5MnO2',
# "dHf (eV/mol)": -1.415, "dHh (eV/mol)": '--', "Ground state?": 'Y',
################################################################################################################
# Get mp-ids for all entries based on matching the VASP directory path names
# Paths are different in the existing and new mp-id dictionary, so processing has to be independent
################################################################################################################
for framework, fdat in mp_contrib_phases.items():
for i, phase in enumerate(fdat):
c = Composition(phase[0])
for hstate in hull_states:
if phase_names[framework] == hstate['phase'] and \
c.almost_equals(Composition.from_dict(hstate['c'])) and \
len(mp_contrib_phases[framework][i]) < 6:
mp_contrib_phases[framework][i].append(hstate['path'])
mp_contrib_phases[framework][i].append(hstate['s'])
for framework, fdat in mp_contrib_phases.items():
for i, phase in enumerate(fdat):
match_path = phase[4].replace('all_states/', '')
mp_ids = []
for path, ids in mp_dup.items():
mp_path = path.replace(
'/Users/patrick/Downloads/20160710_MPContrib_MnO2_DK/',
'').replace('/3.double_relax/CONTCAR', '')
if match_path == mp_path:
mp_ids.extend(ids)
for path, id_dat in mp_cmp.items():
mp_path = path.replace(
'20160725_MnO2_DK_Cifs/20160710_MPContrib_MnO2_DK-',
'').replace('-3.double_relax-CONTCAR.cif',
'').replace('-', '/')
if match_path == mp_path:
if 'mp_id' in id_dat.keys():
mp_ids.append(id_dat['mp_id'])
mp_contrib_phases[framework][i].append(mp_ids)
################################################################################################################
# For structures that have mp-ids, add them to the contribution dictionary.
# For those that don't, run a separate dictionary to keep track of them
################################################################################################################
no_id_dict = {}
for framework, fdat in mp_contrib_phases.items():
for phase in fdat:
d = {
"Phase": framework,
"Formula": phase[0],
"dHf": '{} eV/mol'.format(phase[1]),
"dHh": '{} eV/mol'.format(phase[3]),
"GS": phase[2]
}
if len(phase[6]) == 0:
no_id_dict[phase[4].replace('all_states/', '')] = d
for mpid in phase[6]:
mpfile.add_hierarchical_data(mpid, d)
if include_cifs:
try:
mpfile.add_structure(phase[5], identifier=mpid)
print framework, phase[0], 'added to', mpid
except ValueError as ex:
print 'tried to add structure to', mpid, 'but', str(ex)
return 'DONE. {} do not have mp-ids!'.format(len(no_id_dict))
def run(mpfile, include_cifs=True, **kwargs):
from pymatgen.core.composition import Composition
from pymatgen.core.structure import Structure
data_input = mpfile.document[mp_level01_titles[0]].pop('input')
phase_names = mpfile.hdata.general['phase_names']
dir_path = os.path.dirname(os.path.realpath(__file__))
for k in data_input.keys():
data_input[k] = os.path.join(dir_path, data_input[k])
with open(data_input['formatted_entries'], "r") as fin:
mp_contrib_phases = json.loads(fin.read())
with open(data_input['hull_entries'], "r") as fin:
hull_states = json.loads(fin.read())
with open(data_input['mpid_existing'], 'r') as fin:
mp_dup = json.loads(fin.read())
with open(data_input['mpid_new'], 'r') as fin:
mp_cmp = json.loads(fin.read())
################################################################################################################
# add unique structures first (special cases)
################################################################################################################
if include_cifs:
for hstate in hull_states:
if 'other' == hstate['phase']:
c = Composition.from_dict(hstate['c'])
s = Structure.from_dict(hstate['s'])
for mpid in mpfile.ids:
formula = mpfile.hdata[mpid]['data']['Formula']
if c.almost_equals(Composition(formula)):
try:
mpfile.add_structure(s, identifier=mpid)
print formula, 'added to', mpid
except Exception as ex:
print 'tried to add structure to', mpid, 'but', str(
ex)
break
# "phase": 'postspinel-NaMn2O4', "Formula": 'Na0.5MnO2',
# "ΔH (eV/mol)": -1.415, "ΔHₕ (eV/mol)": '', "Ground state?": 'Y',
################################################################################################################
# Get mp-ids for all entries based on matching the VASP directory path names
# Paths are different in the existing and new mp-id dictionary, so processing has to be independent
################################################################################################################
print 'get all mp-ids based on VASP directory paths ...'
for framework, fdat in mp_contrib_phases.items():
for i, phase in enumerate(fdat):
c = Composition(phase[0])
for hstate in hull_states:
if phase_names[framework] == hstate['phase'] and \
c.almost_equals(Composition.from_dict(hstate['c'])) and \
len(mp_contrib_phases[framework][i]) < 6:
mp_contrib_phases[framework][i].append(hstate['path'])
mp_contrib_phases[framework][i].append(hstate['s'])
for framework, fdat in mp_contrib_phases.items():
for i, phase in enumerate(fdat):
match_path = phase[4].replace('all_states/', '')
mp_ids = []
for path, ids in mp_dup.items():
mp_path = path.replace(
'/Users/patrick/Downloads/20160710_MPContrib_MnO2_DK/',
'').replace('/3.double_relax/CONTCAR', '')
if match_path == mp_path:
mp_ids.extend(ids)
for path, id_dat in mp_cmp.items():
mp_path = path.replace(
'20160725_MnO2_DK_Cifs/20160710_MPContrib_MnO2_DK-',
'').replace('-3.double_relax-CONTCAR.cif',
'').replace('-', '/')
if match_path == mp_path:
if 'mp_id' in id_dat.keys():
mp_ids.append(id_dat['mp_id'])
mp_contrib_phases[framework][i].append(mp_ids)
################################################################################################################
# For structures that have mp-ids, add them to the contribution dictionary.
# For those that don't, run a separate dictionary to keep track of them
################################################################################################################
print 'add structures with mp-ids to contribution ...'
no_id_dict = {}
for framework, fdat in mp_contrib_phases.items():
for phase in fdat:
d = RecursiveDict()
d["Phase"] = framework
d["Formula"] = phase[0]
try:
float(phase[1])
d["ΔH"] = clean_value(phase[1], 'eV/mol')
except:
d["ΔH"] = 'N/A eV/mol'
try:
float(phase[3])
d["ΔHₕ"] = clean_value(phase[3], 'eV/mol')
except:
d["ΔHₕ"] = 'N/A eV/mol'
d["GS"] = 'Yes' if phase[2] == 'Y' else 'No'
if len(phase[6]) == 0:
print 'no id for', d['Formula'], d['Phase']
no_id_dict[phase[4].replace('all_states/', '')] = d
for mpid in phase[6]:
if include_cifs:
try:
mpfile.add_structure(phase[5], identifier=mpid)
print framework, phase[0], 'added to', mpid
except ValueError as ex:
print 'tried to add structure to', mpid, 'but', str(ex)
mpfile.add_hierarchical_data(RecursiveDict({'data': d}),
identifier=mpid)
print 'added', mpid
