def setup(cls):
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
cls.snldb = SNLMongoAdapter.from_file(snl_f)
tasks_f = os.path.join(module_dir, 'materials.yaml')
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
cls.materials = db[task_creds['collection']]
def archive_deprecated_fws():
# find all snlgroups that are deprecated, and archive all WFs that have deprecated fw_ids so we don't run them
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
snldb = SNLMongoAdapter.from_file(snl_f)
snlgroups = snldb.snlgroups
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
for g in snlgroups.find({'canonical_snl.about.remarks':'DEPRECATED'}, {'snlgroup_id': 1}):
while lpdb.fireworks.find_one({'spec.snlgroup_id': g['snlgroup_id'], 'state': {'$ne': 'ARCHIVED'}}, {'fw_id': 1}):
fw = lpdb.fireworks.find_one({'spec.snlgroup_id': g['snlgroup_id'], 'state': {'$ne': 'ARCHIVED'}}, {'fw_id': 1})
print fw['fw_id']
lpdb.archive_wf(fw['fw_id'])
print 'DONE'
def find_alternate_canonical():
# see if we can replace a deprecated canonical SNL with a non-deprecated one
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
snldb = SNLMongoAdapter.from_file(snl_f)
snl = snldb.snl
snlgroups = snldb.snlgroups
for g in snlgroups.find({"canonical_snl.about.remarks":"DEPRECATED"}, {"snlgroup_id": 1, "all_snl_ids": 1}):
for s in snl.find({"snl_id": {"$in": g['all_snl_ids']}, "about.remarks": {"$ne": "DEPRECATED"}}):
canonical_mpsnl = MPStructureNL.from_dict(s)
snldb.switch_canonical_snl(g['snlgroup_id'], canonical_mpsnl)
print g['snlgroup_id']
break
print 'DONE'
def get_colls():
colls = namedtuple('Collections', ['snl', 'snlgroups'])
sma = SNLMongoAdapter.from_file(snl_f)
lp = LaunchPad.from_file(fw_f)
colls.snl = sma.snl
colls.snlgroups = sma.snlgroups
colls.fireworks = lp.fireworks
colls.launches = lp.launches
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
colls.tasks = db['tasks']
return colls
def detect():
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
snldb = SNLMongoAdapter.from_file(snl_f)
snl = snldb.snl
snlgroups = snldb.snlgroups
q = {"about._icsd.icsd_id":{"$exists":True}} # icsd strctures
q["about._icsd.coll_code"] = {"$exists":False} # old ICSD structure
q["about.history.description.fw_id"] = {"$exists":False} # non structure relaxations
for old_s in snl.find(q, {"snl_id": 1, 'about._icsd.icsd_id': 1, 'about._materialsproject.deprecated.crystal_id_deprecated': 1}):
icsd_id = old_s['about']['_icsd']['icsd_id']
crystal_id = old_s['about']['_materialsproject']['deprecated']['crystal_id_deprecated']
new_s = snl.find_one({"about._icsd.icsd_id":icsd_id, "about._icsd.coll_code":{"$exists":True}}, {"snl_id": 1})
if new_s:
n_groups = snlgroups.find({"all_snl_ids":{"$in":[old_s['snl_id'], new_s['snl_id']]}}).count()
if n_groups != 1:
# The crystal_id is bad
print crystal_id
def fix():
# initialize databases
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
snldb = SNLMongoAdapter.from_file(snl_f)
snl = snldb.snl
snlgroups = snldb.snlgroups
tasks_f = os.path.join(module_dir, 'tasks.yaml')
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
tasks = db['tasks']
tasks_f = os.path.join(module_dir, 'tasks.yaml')
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
tasks = db['tasks']
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
fws = lpdb.fireworks
launches = lpdb.launches
sb_f = os.path.join(module_dir, 'submission.yaml')
sbdb = SubmissionMongoAdapter.from_file(sb_f)
submissions = sbdb.jobs
bad_crystal_ids = []
crystals_file = os.path.join(module_dir, 'bad_crystals.txt')
with open(crystals_file) as f:
for line in f:
bad_crystal_ids.append(int(line.strip()))
for c_id in bad_crystal_ids:
if c_id == 100892 or c_id == 100202:
print 'SKIP'
else:
# FIX SNL
for s in snl.find({'about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'snl_id': 1}):
snl.update({'snl_id': s['snl_id']}, {'$pushAll': {"about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX SNLGROUPS
for s in snlgroups.find({'canonical_snl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'snlgroup_id': 1}):
snlgroups.update({'snlgroup_id': s['snlgroup_id']}, {'$pushAll': {"canonical_snl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX FWs pt 1
for s in fws.find({'spec.mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'fw_id': 1}):
fws.update({'fw_id': s['fw_id']}, {'$pushAll': {"spec.mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX FWs pt 2
for s in fws.find({'spec.force_mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'fw_id': 1}):
fws.update({'fw_id': s['fw_id']}, {'$pushAll': {"spec.force_mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX Launches
for s in launches.find({'action.update_spec.mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'launch_id': 1}):
launches.update({'launch_id': s['launch_id']}, {'$pushAll': {"action.update_spec.mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX TASKS
for s in tasks.find({'snl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'task_id': 1}):
tasks.update({'task_id': s['task_id']}, {'$pushAll': {"snl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
tasks.update({'task_id': s['task_id']}, {'$pushAll': {"snl_final.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX SUBMISSIONS
for s in submissions.find({'about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'submission_id': 1}):
submissions.update({'submission_id': s['submission_id']}, {'$pushAll': {"about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
print 'FIXED', c_id
from collections import Counter
from datetime import datetime
from fnmatch import fnmatch
from custodian.vasp.handlers import VaspErrorHandler
cwd = os.getcwd()
# DONE manually: "mp-987" -> fw_id: 119629
lpdb = LaunchPad.from_file(
'/global/homes/m/matcomp/mp_prod/config/config_Mendel/my_launchpad.yaml')
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': 100000
}
sma = SNLMongoAdapter.from_file(
'/global/homes/m/matcomp/mp_prod/config/dbs/snl_db.yaml')
with open('/global/homes/m/matcomp/mp_prod/materials_db_prod.yaml') as f:
creds = yaml.load(f)
client = MongoClient(creds['host'], creds['port'])
db = client[creds['db']]
db.authenticate(creds['username'], creds['password'])
materials = db['materials']
tasks = db['tasks']
print materials.count()
def append_wf(fw_id, parent_fw_id=None):
wf = lpdb.workflows.find_one({'nodes': fw_id}, {
'parent_links': 1,
'links': 1,
'name': 1
if __name__ == '__main__':
module_dir = os.path.dirname(os.path.abspath(__file__))
automation_f = os.path.join(module_dir, 'automation.yaml')
snl_f = os.path.join(module_dir, 'snl.yaml')
with open(automation_f) as f:
y = yaml.load(f)
mc = MongoClient(y['host'], y['port'])
db = mc[y['db']]
db.authenticate(y['username'], y['password'])
snldb = SNLMongoAdapter.from_file(snl_f)
prev_ids = [] # MPS ids that we already took care of
print 'INITIALIZING'
if RESET:
snldb._reset()
time.sleep(10) # makes me sleep better at night
else:
for mps in snldb.snl.find({}, {"about._materialsproject.deprecated.mps_ids": 1}):
prev_ids.extend(mps['about']['_materialsproject']['deprecated']['mps_ids'])
print 'PROCESSING'
for mps in db.mps.find(timeout=False):
try:
import time, yaml, sys
from fireworks.core.launchpad import LaunchPad
from fireworks.core.firework import Firework, Workflow
from mpworks.firetasks.controller_tasks import AddEStructureTask
from fireworks.utilities.fw_utilities import get_slug
from mpworks.snl_utils.snl_mongo import SNLMongoAdapter
from pymongo import MongoClient
from collections import Counter
from datetime import datetime
from fnmatch import fnmatch
# DONE manually: "mp-987" -> fw_id: 119629
lpdb = LaunchPad.from_file('/global/homes/m/matcomp/mp_prod/config/config_Mendel/my_launchpad.yaml')
spec = {'task_type': 'Controller: add Electronic Structure v2', '_priority': 100000}
sma = SNLMongoAdapter.from_file('/global/homes/m/matcomp/mp_prod/config/dbs/snl_db.yaml')
with open('/global/homes/m/matcomp/mp_prod/materials_db_prod.yaml') as f:
creds = yaml.load(f)
client = MongoClient(creds['host'], creds['port'])
db = client[creds['db']]
db.authenticate(creds['username'], creds['password'])
materials = db['materials']
tasks = db['tasks']
def append_wf(fw_id, parent_fw_id=None):
wf = lpdb.workflows.find_one({'nodes':fw_id}, {'parent_links':1,'links':1,'name':1})
try:
if parent_fw_id is None:
parent_fw_id = wf['parent_links'][str(fw_id)][-1]
# non-defused AddEStructureTask v2 already in children?
for child_fw_id in wf['links'][str(parent_fw_id)]:
def analyze(args):
"""analyze data at any point for a copy of the streaming figure"""
# NOTE: make copy online first with suffix _%Y-%m-%d and note figure id
fig = py.get_figure(creds['username'], args.fig_id)
if args.t:
if args.fig_id == 42:
label_entries = filter(
None, '<br>'.join(fig['data'][2]['text']).split('<br>'))
pairs = map(make_tuple, label_entries)
grps = set(chain.from_iterable(pairs))
snlgrp_cursor = sma.snlgroups.aggregate([{
'$match': {
'snlgroup_id': {
'$in': list(grps)
},
'canonical_snl.about.projects': {
'$ne': 'CederDahn Challenge'
}
}
}, {
'$project': {
'snlgroup_id': 1,
'canonical_snl.snlgroup_key': 1,
'_id': 0
}
}],
cursor={})
snlgroup_keys = {}
for d in snlgrp_cursor:
snlgroup_keys[
d['snlgroup_id']] = d['canonical_snl']['snlgroup_key']
print snlgroup_keys[40890]
sma2 = SNLMongoAdapter.from_file(
os.path.join(os.environ['DB_LOC'], 'materials_db.yaml'))
materials_cursor = sma2.database.materials.aggregate([{
'$match': {
'snlgroup_id_final': {
'$in': list(grps)
},
'snl_final.about.projects': {
'$ne': 'CederDahn Challenge'
}
}
}, {
'$project': {
'snlgroup_id_final': 1,
'_id': 0,
'task_id': 1,
'final_energy_per_atom': 1,
'band_gap.search_gap.band_gap': 1,
'volume': 1,
'nsites': 1
}
}],
cursor={})
snlgroup_data = {}
for material in materials_cursor:
snlgroup_id = material['snlgroup_id_final']
final_energy_per_atom = material['final_energy_per_atom']
band_gap = material['band_gap']['search_gap']['band_gap']
volume_per_atom = material['volume'] / material['nsites']
snlgroup_data[snlgroup_id] = {
'final_energy_per_atom': final_energy_per_atom,
'band_gap': band_gap,
'task_id': material['task_id'],
'volume_per_atom': volume_per_atom
}
print snlgroup_data[40890]
filestem = 'mpworks/check_snl/results/bad_snlgroups_2_'
with open(filestem+'in_matdb.csv', 'wb') as f, \
open(filestem+'notin_matdb.csv', 'wb') as g:
writer1, writer2 = csv.writer(f), csv.writer(g)
header = [
'category', 'composition', 'snlgroup_id 1', 'sg_num 1',
'task_id 1', 'snlgroup_id 2', 'sg_num 2', 'task_id 2',
'delta_energy', 'delta_bandgap', 'delta_volume_per_atom',
'rms_dist', 'scenario'
]
writer1.writerow(header)
writer2.writerow(header)
for primary_id, secondary_id in pairs:
if primary_id not in snlgroup_keys or \
secondary_id not in snlgroup_keys:
continue
composition, primary_sg_num = snlgroup_keys[
primary_id].split('--')
secondary_sg_num = snlgroup_keys[secondary_id].split(
'--')[1]
category = 'same SGs' if primary_sg_num == secondary_sg_num else 'diff. SGs'
if primary_id not in snlgroup_data or secondary_id not in snlgroup_data:
delta_energy, delta_bandgap, delta_volume_per_atom = '', '', ''
else:
delta_energy = "{0:.3g}".format(abs(
snlgroup_data[primary_id]['final_energy_per_atom'] - \
snlgroup_data[secondary_id]['final_energy_per_atom']
))
delta_bandgap = "{0:.3g}".format(abs(
snlgroup_data[primary_id]['band_gap'] - \
snlgroup_data[secondary_id]['band_gap']
))
delta_volume_per_atom = "{0:.3g}".format(abs(
snlgroup_data[primary_id]['volume_per_atom'] - \
snlgroup_data[secondary_id]['volume_per_atom']
))
scenario, rms_dist_str = '', ''
if category == 'diff. SGs' and delta_energy and delta_bandgap:
scenario = 'different' if (
float(delta_energy) > 0.01
or float(delta_bandgap) > 0.1) else 'similar'
snlgrp1_dict = sma.snlgroups.find_one(
{"snlgroup_id": primary_id})
snlgrp2_dict = sma.snlgroups.find_one(
{"snlgroup_id": secondary_id})
snlgrp1 = SNLGroup.from_dict(snlgrp1_dict)
snlgrp2 = SNLGroup.from_dict(snlgrp2_dict)
primary_structure = snlgrp1.canonical_structure
secondary_structure = snlgrp2.canonical_structure
rms_dist = matcher.get_rms_dist(
primary_structure, secondary_structure)
if rms_dist is not None:
rms_dist_str = "({0:.3g},{1:.3g})".format(
*rms_dist)
print rms_dist_str
row = [
category, composition,
primary_id, primary_sg_num,
snlgroup_data[primary_id]['task_id'] \
if primary_id in snlgroup_data else '',
secondary_id, secondary_sg_num,
snlgroup_data[secondary_id]['task_id'] \
if secondary_id in snlgroup_data else '',
delta_energy, delta_bandgap, delta_volume_per_atom,
rms_dist_str, scenario
]
if delta_energy and delta_bandgap: writer1.writerow(row)
else: writer2.writerow(row)
elif args.fig_id == 16:
out_fig = Figure()
badsnls_trace = Scatter(x=[],
y=[],
text=[],
mode='markers',
name='SG Changes')
bisectrix = Scatter(x=[0, 230],
y=[0, 230],
mode='lines',
name='bisectrix')
print 'pulling bad snls from plotly ...'
bad_snls = OrderedDict()
for category, text in zip(fig['data'][2]['y'],
fig['data'][2]['text']):
for snl_id in map(int, text.split('<br>')):
bad_snls[snl_id] = category
with open('mpworks/check_snl/results/bad_snls.csv', 'wb') as f:
print 'pulling bad snls from database ...'
mpsnl_cursor = sma.snl.find({
'snl_id': {
'$in': bad_snls.keys()
},
'about.projects': {
'$ne': 'CederDahn Challenge'
}
})
writer = csv.writer(f)
writer.writerow([
'snl_id', 'category', 'snlgroup_key', 'nsites', 'remarks',
'projects', 'authors'
])
print 'writing bad snls to file ...'
for mpsnl_dict in mpsnl_cursor:
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
row = [
mpsnl.snl_id, bad_snls[mpsnl.snl_id],
mpsnl.snlgroup_key
]
row += _get_snl_extra_info(mpsnl)
writer.writerow(row)
sg_num = mpsnl.snlgroup_key.split('--')[1]
if (bad_snls[mpsnl.snl_id] == 'SG default' and sg_num != '-1') or \
bad_snls[mpsnl.snl_id] == 'SG change':
mpsnl.structure.remove_oxidation_states()
sf = SpacegroupAnalyzer(mpsnl.structure, symprec=0.1)
badsnls_trace['x'].append(mpsnl.sg_num)
badsnls_trace['y'].append(sf.get_spacegroup_number())
badsnls_trace['text'].append(mpsnl.snl_id)
if bad_snls[mpsnl.snl_id] == 'SG default':
print sg_num, sf.get_spacegroup_number()
print 'plotting out-fig ...'
out_fig['data'] = Data([bisectrix, badsnls_trace])
out_fig['layout'] = Layout(
showlegend=False,
hovermode='closest',
title='Spacegroup Assignment Changes',
xaxis=XAxis(showgrid=False,
title='old SG number',
range=[0, 230]),
yaxis=YAxis(showgrid=False,
title='new SG number',
range=[0, 230]),
)
filename = 'spacegroup_changes_'
filename += datetime.datetime.now().strftime('%Y-%m-%d')
py.plot(out_fig, filename=filename, auto_open=False)
elif args.fig_id == 43: # SNLGroupMemberChecker
matcher2 = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=True,
comparator=ElementComparator())
print 'pulling data from plotly ...'
trace = Scatter(x=[],
y=[],
text=[],
mode='markers',
name='mismatches')
bad_snls = OrderedDict() # snlgroup_id : [ mismatching snl_ids ]
for category, text in zip(fig['data'][2]['y'],
fig['data'][2]['text']):
if category != 'mismatch': continue
for entry in text.split('<br>'):
fields = entry.split(':')
snlgroup_id = int(fields[0].split(',')[0])
print snlgroup_id
snlgrp_dict = sma.snlgroups.find_one(
{'snlgroup_id': snlgroup_id})
snlgrp = SNLGroup.from_dict(snlgrp_dict)
s1 = snlgrp.canonical_structure.get_primitive_structure()
bad_snls[snlgroup_id] = []
for i, snl_id in enumerate(fields[1].split(',')):
mpsnl_dict = sma.snl.find_one({'snl_id': int(snl_id)})
if 'CederDahn Challenge' in mpsnl_dict['about'][
'projects']:
print 'skip CederDahn: %s' % snl_id
continue
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
s2 = mpsnl.structure.get_primitive_structure()
is_match = matcher2.fit(s1, s2)
if is_match: continue
bad_snls[snlgroup_id].append(snl_id)
trace['x'].append(snlgroup_id)
trace['y'].append(i + 1)
trace['text'].append(snl_id)
if len(bad_snls[snlgroup_id]) < 1:
bad_snls.pop(snlgroup_id, None)
with open('mpworks/check_snl/results/bad_snlgroups.csv',
'wb') as f:
print 'pulling bad snlgroups from database ...'
snlgroup_cursor = sma.snlgroups.find({
'snlgroup_id': {
'$in': bad_snls.keys()
},
})
writer = csv.writer(f)
writer.writerow(
['snlgroup_id', 'snlgroup_key', 'mismatching snl_ids'])
print 'writing bad snlgroups to file ...'
for snlgroup_dict in snlgroup_cursor:
snlgroup = SNLGroup.from_dict(snlgroup_dict)
row = [
snlgroup.snlgroup_id,
snlgroup.canonical_snl.snlgroup_key,
' '.join(bad_snls[snlgroup.snlgroup_id])
]
writer.writerow(row)
print 'plotting out-fig ...'
out_fig = Figure()
out_fig['data'] = Data([trace])
out_fig['layout'] = Layout(
showlegend=False,
hovermode='closest',
title='Member Mismatches of SNLGroup Canonicals',
xaxis=XAxis(showgrid=False,
title='snlgroup_id',
showexponent='none'),
yaxis=YAxis(showgrid=False, title='# mismatching SNLs'),
)
filename = 'groupmember_mismatches_'
filename += datetime.datetime.now().strftime('%Y-%m-%d')
py.plot(out_fig, filename=filename, auto_open=False)
else:
errors = Counter()
bad_snls = OrderedDict()
bad_snlgroups = OrderedDict()
for i, d in enumerate(fig['data']):
if not isinstance(d, Scatter): continue
if not 'x' in d or not 'y' in d or not 'text' in d: continue
start_id = int(d['name'].split(' - ')[0][:-1]) * 1000
marker_colors = d['marker']['color']
if i < 2 * num_snl_streams: # spacegroups
errors += Counter(marker_colors)
for idx, color in enumerate(marker_colors):
snl_id = start_id + d['x'][idx]
color_index = category_colors.index(color)
category = categories[color_index]
bad_snls[snl_id] = category
else: # groupmembers
for idx, color in enumerate(marker_colors):
if color != category_colors[0]: continue
snlgroup_id = start_id + d['x'][idx]
mismatch_snl_id, canonical_snl_id = d['text'][idx].split(
' != ')
bad_snlgroups[snlgroup_id] = int(mismatch_snl_id)
print errors
fig_data = fig['data'][-1]
fig_data['x'] = [
errors[color] for color in fig_data['marker']['color']
]
filename = _get_filename()
print filename
#py.plot(fig, filename=filename)
with open('mpworks/check_snl/results/bad_snls.csv', 'wb') as f:
mpsnl_cursor = sma.snl.find({'snl_id': {'$in': bad_snls.keys()}})
writer = csv.writer(f)
writer.writerow([
'snl_id', 'category', 'snlgroup_key', 'nsites', 'remarks',
'projects', 'authors'
])
for mpsnl_dict in mpsnl_cursor:
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
row = [
mpsnl.snl_id, bad_snls[mpsnl.snl_id], mpsnl.snlgroup_key
]
row += _get_snl_extra_info(mpsnl)
writer.writerow(row)
with open('mpworks/check_snl/results/bad_snlgroups.csv', 'wb') as f:
snlgrp_cursor = sma.snlgroups.find(
{'snlgroup_id': {
'$in': bad_snlgroups.keys()
}})
first_mismatch_snls_cursor = sma.snl.find(
{'snl_id': {
'$in': bad_snlgroups.values()
}})
first_mismatch_snl_info = OrderedDict()
for mpsnl_dict in first_mismatch_snls_cursor:
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
first_mismatch_snl_info[mpsnl.snl_id] = _get_snl_extra_info(
mpsnl)
writer = csv.writer(f)
writer.writerow([
'snlgroup_id', 'snlgroup_key', 'canonical_snl_id',
'first_mismatching_snl_id', 'nsites', 'remarks', 'projects',
'authors'
])
for snlgrp_dict in snlgrp_cursor:
snlgrp = SNLGroup.from_dict(snlgrp_dict)
first_mismatch_snl_id = bad_snlgroups[snlgrp.snlgroup_id]
row = [
snlgrp.snlgroup_id, snlgrp.canonical_snl.snlgroup_key,
snlgrp.canonical_snl.snl_id, first_mismatch_snl_id
]
row += [
' & '.join(pair) if pair[0] != pair[1] else pair[0]
for pair in zip(
_get_snl_extra_info(snlgrp.canonical_snl),
first_mismatch_snl_info[int(first_mismatch_snl_id)])
]
writer.writerow(row)
import os
import plotly.plotly as py
from pandas import DataFrame
from mpworks.snl_utils.snl_mongo import SNLMongoAdapter
sma = SNLMongoAdapter.auto_load()
sma2 = SNLMongoAdapter.from_file(
os.path.join(os.environ['DB_LOC'], 'materials_db.yaml'))
def _get_snlgroup_id(snl_id):
return sma.snlgroups.find_one({'all_snl_ids': int(snl_id)}, {
'snlgroup_id': 1,
'_id': 0
})['snlgroup_id']
def _get_mp_id(snlgroup_id):
mat = sma2.database.materials.find_one({'snlgroup_id_final': snlgroup_id},
{
'_id': 0,
'task_id': 1
})
if mat is not None:
return mat['task_id']
return 'not found'
def _get_mp_link(mp_id):
if mp_id == 'not found': return mp_id
url = 'link:$$https://materialsproject.org/materials/'
def analyze(args):
"""analyze data at any point for a copy of the streaming figure"""
# NOTE: make copy online first with suffix _%Y-%m-%d and note figure id
fig = py.get_figure(creds['username'], args.fig_id)
if args.t:
if args.fig_id == 42:
label_entries = filter(None, '<br>'.join(fig['data'][2]['text']).split('<br>'))
pairs = map(make_tuple, label_entries)
grps = set(chain.from_iterable(pairs))
snlgrp_cursor = sma.snlgroups.aggregate([
{ '$match': {
'snlgroup_id': { '$in': list(grps) },
'canonical_snl.about.projects': {'$ne': 'CederDahn Challenge'}
} },
{ '$project': { 'snlgroup_id': 1, 'canonical_snl.snlgroup_key': 1, '_id': 0 } }
], cursor={})
snlgroup_keys = {}
for d in snlgrp_cursor:
snlgroup_keys[d['snlgroup_id']] = d['canonical_snl']['snlgroup_key']
print snlgroup_keys[40890]
sma2 = SNLMongoAdapter.from_file(
os.path.join(os.environ['DB_LOC'], 'materials_db.yaml')
)
materials_cursor = sma2.database.materials.aggregate([
{ '$match': {
'snlgroup_id_final': { '$in': list(grps) },
'snl_final.about.projects': {'$ne': 'CederDahn Challenge'}
} },
{ '$project': {
'snlgroup_id_final': 1, '_id': 0, 'task_id': 1,
'final_energy_per_atom': 1,
'band_gap.search_gap.band_gap': 1,
'volume': 1, 'nsites': 1
}}
], cursor={})
snlgroup_data = {}
for material in materials_cursor:
snlgroup_id = material['snlgroup_id_final']
final_energy_per_atom = material['final_energy_per_atom']
band_gap = material['band_gap']['search_gap']['band_gap']
volume_per_atom = material['volume'] / material['nsites']
snlgroup_data[snlgroup_id] = {
'final_energy_per_atom': final_energy_per_atom,
'band_gap': band_gap, 'task_id': material['task_id'],
'volume_per_atom': volume_per_atom
}
print snlgroup_data[40890]
filestem = 'mpworks/check_snl/results/bad_snlgroups_2_'
with open(filestem+'in_matdb.csv', 'wb') as f, \
open(filestem+'notin_matdb.csv', 'wb') as g:
writer1, writer2 = csv.writer(f), csv.writer(g)
header = [
'category', 'composition',
'snlgroup_id 1', 'sg_num 1', 'task_id 1',
'snlgroup_id 2', 'sg_num 2', 'task_id 2',
'delta_energy', 'delta_bandgap', 'delta_volume_per_atom',
'rms_dist', 'scenario'
]
writer1.writerow(header)
writer2.writerow(header)
for primary_id, secondary_id in pairs:
if primary_id not in snlgroup_keys or \
secondary_id not in snlgroup_keys: continue
composition, primary_sg_num = snlgroup_keys[primary_id].split('--')
secondary_sg_num = snlgroup_keys[secondary_id].split('--')[1]
category = 'same SGs' if primary_sg_num == secondary_sg_num else 'diff. SGs'
if primary_id not in snlgroup_data or secondary_id not in snlgroup_data:
delta_energy, delta_bandgap, delta_volume_per_atom = '', '', ''
else:
delta_energy = "{0:.3g}".format(abs(
snlgroup_data[primary_id]['final_energy_per_atom'] - \
snlgroup_data[secondary_id]['final_energy_per_atom']
))
delta_bandgap = "{0:.3g}".format(abs(
snlgroup_data[primary_id]['band_gap'] - \
snlgroup_data[secondary_id]['band_gap']
))
delta_volume_per_atom = "{0:.3g}".format(abs(
snlgroup_data[primary_id]['volume_per_atom'] - \
snlgroup_data[secondary_id]['volume_per_atom']
))
scenario, rms_dist_str = '', ''
if category == 'diff. SGs' and delta_energy and delta_bandgap:
scenario = 'different' if (
float(delta_energy) > 0.01 or float(delta_bandgap) > 0.1
) else 'similar'
snlgrp1_dict = sma.snlgroups.find_one({ "snlgroup_id": primary_id })
snlgrp2_dict = sma.snlgroups.find_one({ "snlgroup_id": secondary_id })
snlgrp1 = SNLGroup.from_dict(snlgrp1_dict)
snlgrp2 = SNLGroup.from_dict(snlgrp2_dict)
primary_structure = snlgrp1.canonical_structure
secondary_structure = snlgrp2.canonical_structure
rms_dist = matcher.get_rms_dist(primary_structure, secondary_structure)
if rms_dist is not None:
rms_dist_str = "({0:.3g},{1:.3g})".format(*rms_dist)
print rms_dist_str
row = [
category, composition,
primary_id, primary_sg_num,
snlgroup_data[primary_id]['task_id'] \
if primary_id in snlgroup_data else '',
secondary_id, secondary_sg_num,
snlgroup_data[secondary_id]['task_id'] \
if secondary_id in snlgroup_data else '',
delta_energy, delta_bandgap, delta_volume_per_atom,
rms_dist_str, scenario
]
if delta_energy and delta_bandgap: writer1.writerow(row)
else: writer2.writerow(row)
elif args.fig_id == 16:
out_fig = Figure()
badsnls_trace = Scatter(x=[], y=[], text=[], mode='markers', name='SG Changes')
bisectrix = Scatter(x=[0,230], y=[0,230], mode='lines', name='bisectrix')
print 'pulling bad snls from plotly ...'
bad_snls = OrderedDict()
for category, text in zip(fig['data'][2]['y'], fig['data'][2]['text']):
for snl_id in map(int, text.split('<br>')):
bad_snls[snl_id] = category
with open('mpworks/check_snl/results/bad_snls.csv', 'wb') as f:
print 'pulling bad snls from database ...'
mpsnl_cursor = sma.snl.find({
'snl_id': { '$in': bad_snls.keys() },
'about.projects': {'$ne': 'CederDahn Challenge'}
})
writer = csv.writer(f)
writer.writerow([
'snl_id', 'category', 'snlgroup_key', 'nsites', 'remarks', 'projects', 'authors'
])
print 'writing bad snls to file ...'
for mpsnl_dict in mpsnl_cursor:
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
row = [ mpsnl.snl_id, bad_snls[mpsnl.snl_id], mpsnl.snlgroup_key ]
row += _get_snl_extra_info(mpsnl)
writer.writerow(row)
sg_num = mpsnl.snlgroup_key.split('--')[1]
if (bad_snls[mpsnl.snl_id] == 'SG default' and sg_num != '-1') or \
bad_snls[mpsnl.snl_id] == 'SG change':
mpsnl.structure.remove_oxidation_states()
sf = SpacegroupAnalyzer(mpsnl.structure, symprec=0.1)
badsnls_trace['x'].append(mpsnl.sg_num)
badsnls_trace['y'].append(sf.get_spacegroup_number())
badsnls_trace['text'].append(mpsnl.snl_id)
if bad_snls[mpsnl.snl_id] == 'SG default':
print sg_num, sf.get_spacegroup_number()
print 'plotting out-fig ...'
out_fig['data'] = Data([bisectrix, badsnls_trace])
out_fig['layout'] = Layout(
showlegend=False, hovermode='closest',
title='Spacegroup Assignment Changes',
xaxis=XAxis(showgrid=False, title='old SG number', range=[0,230]),
yaxis=YAxis(showgrid=False, title='new SG number', range=[0,230]),
)
filename = 'spacegroup_changes_'
filename += datetime.datetime.now().strftime('%Y-%m-%d')
py.plot(out_fig, filename=filename, auto_open=False)
elif args.fig_id == 43: # SNLGroupMemberChecker
matcher2 = StructureMatcher(
ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=False, scale=True,
attempt_supercell=True, comparator=ElementComparator()
)
print 'pulling data from plotly ...'
trace = Scatter(x=[], y=[], text=[], mode='markers', name='mismatches')
bad_snls = OrderedDict() # snlgroup_id : [ mismatching snl_ids ]
for category, text in zip(fig['data'][2]['y'], fig['data'][2]['text']):
if category != 'mismatch': continue
for entry in text.split('<br>'):
fields = entry.split(':')
snlgroup_id = int(fields[0].split(',')[0])
print snlgroup_id
snlgrp_dict = sma.snlgroups.find_one({ 'snlgroup_id': snlgroup_id })
snlgrp = SNLGroup.from_dict(snlgrp_dict)
s1 = snlgrp.canonical_structure.get_primitive_structure()
bad_snls[snlgroup_id] = []
for i, snl_id in enumerate(fields[1].split(',')):
mpsnl_dict = sma.snl.find_one({ 'snl_id': int(snl_id) })
if 'CederDahn Challenge' in mpsnl_dict['about']['projects']:
print 'skip CederDahn: %s' % snl_id
continue
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
s2 = mpsnl.structure.get_primitive_structure()
is_match = matcher2.fit(s1, s2)
if is_match: continue
bad_snls[snlgroup_id].append(snl_id)
trace['x'].append(snlgroup_id)
trace['y'].append(i+1)
trace['text'].append(snl_id)
if len(bad_snls[snlgroup_id]) < 1:
bad_snls.pop(snlgroup_id, None)
with open('mpworks/check_snl/results/bad_snlgroups.csv', 'wb') as f:
print 'pulling bad snlgroups from database ...'
snlgroup_cursor = sma.snlgroups.find({
'snlgroup_id': { '$in': bad_snls.keys() },
})
writer = csv.writer(f)
writer.writerow(['snlgroup_id', 'snlgroup_key', 'mismatching snl_ids'])
print 'writing bad snlgroups to file ...'
for snlgroup_dict in snlgroup_cursor:
snlgroup = SNLGroup.from_dict(snlgroup_dict)
row = [
snlgroup.snlgroup_id, snlgroup.canonical_snl.snlgroup_key,
' '.join(bad_snls[snlgroup.snlgroup_id])
]
writer.writerow(row)
print 'plotting out-fig ...'
out_fig = Figure()
out_fig['data'] = Data([trace])
out_fig['layout'] = Layout(
showlegend=False, hovermode='closest',
title='Member Mismatches of SNLGroup Canonicals',
xaxis=XAxis(showgrid=False, title='snlgroup_id', showexponent='none'),
yaxis=YAxis(showgrid=False, title='# mismatching SNLs'),
)
filename = 'groupmember_mismatches_'
filename += datetime.datetime.now().strftime('%Y-%m-%d')
py.plot(out_fig, filename=filename, auto_open=False)
else:
errors = Counter()
bad_snls = OrderedDict()
bad_snlgroups = OrderedDict()
for i,d in enumerate(fig['data']):
if not isinstance(d, Scatter): continue
if not 'x' in d or not 'y' in d or not 'text' in d: continue
start_id = int(d['name'].split(' - ')[0][:-1])*1000
marker_colors = d['marker']['color']
if i < 2*num_snl_streams: # spacegroups
errors += Counter(marker_colors)
for idx,color in enumerate(marker_colors):
snl_id = start_id + d['x'][idx]
color_index = category_colors.index(color)
category = categories[color_index]
bad_snls[snl_id] = category
else: # groupmembers
for idx,color in enumerate(marker_colors):
if color != category_colors[0]: continue
snlgroup_id = start_id + d['x'][idx]
mismatch_snl_id, canonical_snl_id = d['text'][idx].split(' != ')
bad_snlgroups[snlgroup_id] = int(mismatch_snl_id)
print errors
fig_data = fig['data'][-1]
fig_data['x'] = [ errors[color] for color in fig_data['marker']['color'] ]
filename = _get_filename()
print filename
#py.plot(fig, filename=filename)
with open('mpworks/check_snl/results/bad_snls.csv', 'wb') as f:
mpsnl_cursor = sma.snl.find({ 'snl_id': { '$in': bad_snls.keys() } })
writer = csv.writer(f)
writer.writerow([
'snl_id', 'category', 'snlgroup_key', 'nsites', 'remarks', 'projects', 'authors'
])
for mpsnl_dict in mpsnl_cursor:
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
row = [ mpsnl.snl_id, bad_snls[mpsnl.snl_id], mpsnl.snlgroup_key ]
row += _get_snl_extra_info(mpsnl)
writer.writerow(row)
with open('mpworks/check_snl/results/bad_snlgroups.csv', 'wb') as f:
snlgrp_cursor = sma.snlgroups.find({ 'snlgroup_id': { '$in': bad_snlgroups.keys() } })
first_mismatch_snls_cursor = sma.snl.find({ 'snl_id': { '$in': bad_snlgroups.values() } })
first_mismatch_snl_info = OrderedDict()
for mpsnl_dict in first_mismatch_snls_cursor:
mpsnl = MPStructureNL.from_dict(mpsnl_dict)
first_mismatch_snl_info[mpsnl.snl_id] = _get_snl_extra_info(mpsnl)
writer = csv.writer(f)
writer.writerow([
'snlgroup_id', 'snlgroup_key',
'canonical_snl_id', 'first_mismatching_snl_id',
'nsites', 'remarks', 'projects', 'authors'
])
for snlgrp_dict in snlgrp_cursor:
snlgrp = SNLGroup.from_dict(snlgrp_dict)
first_mismatch_snl_id = bad_snlgroups[snlgrp.snlgroup_id]
row = [
snlgrp.snlgroup_id, snlgrp.canonical_snl.snlgroup_key,
snlgrp.canonical_snl.snl_id, first_mismatch_snl_id
]
row += [
' & '.join(pair) if pair[0] != pair[1] else pair[0]
for pair in zip(
_get_snl_extra_info(snlgrp.canonical_snl),
first_mismatch_snl_info[int(first_mismatch_snl_id)]
)
]
writer.writerow(row)
import os
import plotly.plotly as py
from pandas import DataFrame
from mpworks.snl_utils.snl_mongo import SNLMongoAdapter
sma = SNLMongoAdapter.auto_load()
sma2 = SNLMongoAdapter.from_file(
os.path.join(os.environ['DB_LOC'], 'materials_db.yaml')
)
def _get_snlgroup_id(snl_id):
return sma.snlgroups.find_one(
{'all_snl_ids': int(snl_id)},
{'snlgroup_id': 1, '_id': 0}
)['snlgroup_id']
def _get_mp_id(snlgroup_id):
mat = sma2.database.materials.find_one(
{'snlgroup_id_final': snlgroup_id},
{'_id': 0, 'task_id': 1}
)
if mat is not None:
return mat['task_id']
return 'not found'
def _get_mp_link(mp_id):
if mp_id == 'not found': return mp_id
url = 'link:$$https://materialsproject.org/materials/'
url += mp_id
url += '$$[%s]' % mp_id
