def create_hull(self):
""" Begin the hull creation routines and perform the
post-processing specified by initial arguments.
"""
if self.args.get('uniq'):
from matador.utils.cursor_utils import filter_unique_structures
if self.args.get('uniq') is True:
sim_tol = 0.1
else:
sim_tol = self.args.get('uniq')
print_notify('Filtering for unique structures...')
self.cursor = filter_unique_structures(self.cursor,
args=self.args,
quiet=True,
sim_tol=sim_tol,
hull=True,
energy_key=self.energy_key)
self.construct_phase_diagram()
if not self.hull_cursor:
print_warning(
'No structures on hull with chosen chemical potentials.')
else:
print_notify(
'{} structures found within {} eV of the hull, including chemical potentials.'
.format(len(self.hull_cursor), self.hull_cutoff))
display_results(self.hull_cursor,
hull=True,
energy_key=self.energy_key,
**self.args)
if self.compute_voltages:
print("Constructing electrode system with active ion: {}".format(
self.species[0]))
self.voltage_curve()
if self.compute_volumes:
self.volume_curve()
if not self.args.get('no_plot'):
if self.compute_voltages and self.voltage_data:
self.plot_voltage_curve(show=False)
if self.compute_volumes and self.volume_data:
self.plot_volume_curve(show=False)
self.plot_hull(**self.args['plot_kwargs'],
debug=self.args.get('debug'),
show=True)
def print_diff(self, **args):
""" Use the display_results function to print the diff. """
display_results(self.cursor,
hull=True,
additions=self.additions,
deletions=self.deletions)
if self.additions is not None:
if args.get('summary'):
print(
'{} additions and {} replacements as best at stoichiometry.'
.format(len(self.additions), len(self.deletions)))
else:
print('{} additions and {} deletions.'.format(
len(self.additions), len(self.deletions)))
def __str__(self):
""" Print underlying phase diagram. """
return display_results(self.cursor,
hull=True,
colour=False,
energy_key=self.formation_key,
sort=False,
return_str=True)
def perform_id_query(self):
""" Query the `text_id` field for the ID provided in the args for a calc_match
or hull/voltage query. Use the results of the text_id query to match to other
entries that have the same calculation parameters. Sets self.query_dict and
self.calc_dict.
Raises:
RuntimeError: if no structures are found.
"""
self.cursor = []
query_dict = dict()
query_dict['$and'] = []
query_dict['$and'].append(self._query_id())
if not self.args.get('ignore_warnings'):
query_dict['$and'].append(self._query_quality())
self.repo = self._collection
self.cursor = list(self._find_and_sort(query_dict))
if not self.cursor:
raise RuntimeError('Could not find a match with {} try widening your search.'.format(self.args.get('id')))
if len(self.cursor) >= 1:
display_results(list(self.cursor)[:self.top], **self.args)
if len(self.cursor) > 1:
print_warning('Matched multiple structures with same text_id. The first one will be used.')
# save special copy of calc_dict for hulls
self.calc_dict = dict()
self.calc_dict['$and'] = []
# to avoid deep recursion, and since this is always called first
# don't append, just set
self.query_dict = self._query_calc(self.cursor[0])
if self.args.get('composition'):
self.args['intersection'] = True
self.query_dict['$and'].append(self._query_composition())
self.calc_dict['$and'] = list(self.query_dict['$and'])
def perform_query(self):
""" Find results that match the query_dict
inside the MongoDB database.
"""
# if no query submitted, find all
if self._empty_query and self.args.get('id') is None:
self.repo = self._collection
self.cursor, cursor_count = self._perform_empty_query()
# if no special query has been made already, begin executing the query
if not self._empty_query:
self.repo = self._collection
if self.debug:
print('Query dict:')
print(dumps(self.query_dict, indent=1))
# execute query
self.cursor, cursor_count = self._find_and_sort(self.query_dict)
if self._non_elemental:
self.cursor = filter_cursor_by_chempots(self._chempots, self.cursor)
print('{} results found for query in {}.'.format(cursor_count, self.repo.name))
self._num_to_display = cursor_count
if self.args.get('subcmd') != 'swaps' and not self._create_hull:
self._set_filter_display_results(cursor_count)
# if a summary has been requested, cursor must be converted to list
if self.args.get('summary'):
self.cursor = list(self.cursor)
if self.args.get('subcmd') != 'swaps' and not self._create_hull:
if self._num_to_display >= 1 or self._num_to_display is None:
if self._num_to_display == cursor_count:
display_results(self.cursor, **self.args)
else:
display_results(self.cursor[:self._num_to_display], **self.args)
if isinstance(self.cursor, pm.cursor.Cursor):
self.cursor.rewind()
def query2files(cursor,
dirname=None,
max_files=10000,
top=None,
prefix=None,
cell=None,
param=None,
res=None,
pdb=None,
json=None,
xsf=None,
markdown=True,
latex=False,
subcmd=None,
argstr=None,
**kwargs):
""" Many-to-many convenience function for many structures being written to
many file types.
Parameters:
cursor (:obj:`list` of :obj:`dict`/:class:`AtomicSwapper`): list of matador dictionaries to write out.
Keyword arguments:
dirname (str): the folder to save the results into. Will be created if non-existent.
Will have integer appended to it if already existing.
max_files (int): if the number of files to be written exceeds this number, then raise RuntimeError.
**kwargs (dict): dictionary of {filetype: bool(whether to write)}. Accepted file types
are cell, param, res, pdb, json, xsf, markdown and latex.
"""
multiple_files = any((cell, param, res, pdb, xsf))
prefix = prefix + '-' if prefix is not None else ''
if isinstance(cursor, AtomicSwapper):
cursor = cursor.cursor
subcmd = "swaps"
if subcmd in ['polish', 'swaps']:
info = False
hash_dupe = False
else:
info = True
hash_dupe = False
if isinstance(cursor, list):
num = len(cursor)
else:
num = cursor.count()
if top is not None:
if top < num:
num = top
num_files = num * sum(1 for ext in [cell, param, res, pdb, xsf] if ext)
if multiple_files:
print('Intending to write', num, 'structures to file...')
if num_files > max_files:
raise RuntimeError(
"Not writing {} files as it exceeds argument `max_files` limit of {}"
.format(num_files, max_files))
if dirname is None:
dirname = generate_relevant_path(subcmd=subcmd, **kwargs)
_dir = False
dir_counter = 0
# postfix integer on end of directory name if it exists
while not _dir:
if dir_counter != 0:
directory = dirname + str(dir_counter)
else:
directory = dirname
if not os.path.isdir(directory):
os.makedirs(directory)
_dir = True
else:
dir_counter += 1
for _, doc in enumerate(cursor[:num]):
# generate an appropriate filename for the structure
root_source = get_root_source(doc)
if '_swapped_stoichiometry' in doc:
formula = get_formula_from_stoich(doc['_swapped_stoichiometry'])
else:
formula = get_formula_from_stoich(doc['stoichiometry'])
if subcmd == 'swaps':
root_source = root_source.replace('-swap-', '-')
name = root_source
if 'OQMD ' in root_source:
name = '{formula}-OQMD_{src}'.format(
formula=formula, src=root_source.split(' ')[-1])
elif 'mp-' in root_source:
name = '{formula}-MP_{src}'.format(formula=formula,
src=root_source.split('-')[-1])
if 'icsd' in doc and 'CollCode' not in name:
name += '-CollCode{}'.format(doc['icsd'])
else:
pf_id = None
for source in doc['source']:
if 'pf-' in source:
pf_id = source.split('-')[-1]
break
else:
if 'pf_ids' in doc:
pf_id = doc['pf_ids'][0]
if pf_id is not None:
name += '-PF-{}'.format(pf_id)
# if swaps, prepend new composition
if subcmd == 'swaps':
new_formula = get_formula_from_stoich(get_stoich(
doc['atom_types']))
name = '{}-swap-{}'.format(new_formula, name)
path = "{directory}/{prefix}{name}".format(directory=directory,
prefix=prefix,
name=name)
if param:
doc2param(doc, path, hash_dupe=hash_dupe)
if cell:
doc2cell(doc, path, hash_dupe=hash_dupe)
if res:
doc2res(doc, path, info=info, hash_dupe=hash_dupe)
if json:
doc2json(doc, path, hash_dupe=hash_dupe)
if pdb:
doc2pdb(doc, path, hash_dupe=hash_dupe)
if xsf:
doc2xsf(doc, path)
hull = subcmd in ['hull', 'voltage']
if isinstance(cursor, pm.cursor.Cursor):
cursor.rewind()
md_path = "{directory}/{directory}.md".format(directory=directory)
md_kwargs = {}
md_kwargs.update(kwargs)
md_kwargs.update({
'markdown': True,
'latex': False,
'argstr': argstr,
'hull': hull
})
md_string = display_results(cursor, **md_kwargs)
with open(md_path, 'w') as f:
f.write(md_string)
if latex:
if isinstance(cursor, pm.cursor.Cursor):
cursor.rewind()
tex_path = "{directory}/{directory}.tex".format(directory=directory)
print('Writing LaTeX file', tex_path + '...')
tex_kwargs = {}
tex_kwargs.update(kwargs)
tex_kwargs.update({
'latex': True,
'markdown': False,
'argstr': argstr,
'hull': hull
})
tex_string = display_results(cursor, **tex_kwargs)
with open(tex_path, 'w') as f:
f.write(tex_string)
print('Done!')
def __repr__(self):
return display_results(self.hull_cursor, args=self.args, hull=True, energy_key=self.energy_key, return_str=True)