def estimate_hbond_corr(formula):
"""
function to generate hydrogen bonding corrections given a formula and estimations
for various functional groups used in Peterson(2010) - valid mostly for Pt(111)
This is a very simplistic function. If you need more advanced descriptions of
hydrogen bonding, consider setting your own hbond_dict
"""
num_OH = formula.count('OH')
num_O = get_composition(formula.split('_s')[0]).setdefault('O', 0)
num_ketone = num_O - num_OH
if num_ketone < 0:
print "(number of O) - (number of OH) is negative??"
assert (False)
if formula in ["OH_s", "OH"]:
corr = -0.50
else:
corr = -0.25 * num_OH + -0.10 * num_ketone
print "estimated hbond correction for", formula, "is", corr
return corr
def estimate_hbond_corr(formula):
"""
Generate hydrogen bonding corrections given a formula and estimations
for various functional groups used in Peterson(2010) - valid mostly for Pt(111)
This is a very simplistic function. If you need more advanced descriptions of
hydrogen bonding, consider setting your own hbond_dict.
"""
num_OH = formula.count('OH')
num_O = get_composition(formula.split('_s')[0]).setdefault('O', 0)
num_ketone = num_O - num_OH
if num_ketone < 0:
print "(number of O) - (number of OH) is negative??"
assert(False)
if formula in ["OH_s", "OH"]:
corr = -0.50
else:
corr = -0.25 * num_OH + -0.10 * num_ketone
print "estimated hbond correction for", formula, "is", corr
return corr
def _baseparse(self):
# Make dictionary of useful information about species in model
if not self.species_definitions:
self.species_definitions = {}
for species in (self.gas_names + self.adsorbate_names +
self.transition_state_names + self.site_names + tuple(self._gas_sites)):
site_names = self.site_names + tuple(self._gas_sites)
ads_info = {}
if '_' in species:
name, site = species.rsplit('_', 1)
else:
name = species
site = self._default_site
ads_info['name'] = name
ads_info['site'] = site
if species in self.gas_names:
ads_info['type'] = 'gas'
ads_info['n_sites'] = 0
elif species in self.adsorbate_names:
ads_info['type'] = 'adsorbate'
ads_info['n_sites'] = 1
elif species in self.transition_state_names:
ads_info['type'] = 'transition_state'
ads_info['n_sites'] = 1
elif species in site_names:
ads_info['type'] = 'site'
ads_info['site'] = species
ads_info['formation_energy'] = 0
if species not in self._gas_sites:
ads_info['n_sites'] = 1
else:
ads_info['n_sites'] = 0
ads_info['site_names'] = ['gas']
ads_info['total'] = 0
ads_info['composition'] = {}
else:
ads_info['type'] = 'unknown'
if species not in site_names:
composition = get_composition(name)
ads_info['composition'] = composition
if species in self.species_definitions:
ads_info.update(self.species_definitions[species])
if ads_info['composition'] is None and species not in site_names:
raise ValueError('Could not determine composition for ' + species)
if species not in site_names:
self.species_definitions[species] = ads_info
else:
self.species_definitions[species] = \
self.species_definitions['*_' + species] = ads_info
for species in self.species_definitions.keys(): # set site definitions
# This entire block can probably be deleted since sites are now
# handled in the above section. Wait for a version or 2 to let
# the clauses deprecate...
site = self.species_definitions[species].get('site', None)
if site and site not in self.species_definitions:
ads_info = {}
ads_info['type'] = 'site'
ads_info['site'] = site
ads_info['formation_energy'] = 0
if site not in self._gas_sites:
ads_info['n_sites'] = 1
else:
ads_info['n_sites'] = 0
ads_info['site_names'] = ['gas']
ads_info['total'] = 0
ads_info['composition'] = {}
if self.site_definitions: # Deprecate later...
warnings.warn('Deprecation Warning: site_definitions will not be'
' supported in future versions. Please use new '
'species_definitions syntax.')
site_names = self.site_definitions[site]
if isinstance(site_names, basestring):
site_names = [site_names]
ads_info['site_names'] = site_names
if self.site_totals: # Deprecate later...
warnings.warn('Deprecation Warning: site_totals will not be'
' supported in future versions. Please use new '
'species_definitions syntax.')
ads_info['total'] = self.site_totals[site]
if site in self.species_definitions:
ads_info.update(self.species_definitions[site])
self.species_definitions[site] = self.species_definitions['*_' + site] \
= ads_info
if not self.atomic_reservoir_list:
# Make list of valid reference sets for e.g. boltzmann coverages
cart_product = []
all_atoms = []
composition_dict = {}
dummy_dict = {}
for sp in self.gas_names:
composition_dict[sp] = self.species_definitions[sp]['composition']
dummy_dict[sp] = 0 # dummy dict of energies
for key in composition_dict[sp].keys():
if key not in all_atoms:
all_atoms.append(key)
for key in all_atoms:
possibles = []
for sp in self.gas_names:
if composition_dict[sp].get(key, None):
possibles.append(sp)
cart_product.append(possibles)
ref_sets = []
for prod in catmap.functions.cartesian_product(*cart_product):
refdict = {}
for ai, pi in zip(all_atoms, prod):
refdict[ai] = pi
if (sorted(list(refdict.values())) ==
sorted(list(set(refdict.values()))) and
sorted(list(refdict.values())) not in
[sorted(list(rs.values())) for rs in ref_sets]):
if refdict and dummy_dict and composition_dict:
try:
self.convert_formation_energies(dummy_dict,
refdict, composition_dict)
ref_sets.append(refdict)
except ValueError:
pass
if ref_sets:
self.atomic_reservoir_list = ref_sets
else:
raise AttributeError('No valid reference sets from gas-phase species ' +
'in the system. Add gasses or specify atomic_reservoir_list')
def _baseparse(self):
#Make dictionary of useful information about species in model
if not self.species_definitions:
self.species_definitions = {}
for species in (self.gas_names + self.adsorbate_names +
self.transition_state_names + self.site_names +
tuple(self._gas_sites)):
site_names = self.site_names + tuple(self._gas_sites)
ads_info = {}
if '_' in species:
name, site = species.rsplit('_', 1)
else:
name = species
site = self._default_site
ads_info['name'] = name
ads_info['site'] = site
if species in self.gas_names:
ads_info['type'] = 'gas'
ads_info['n_sites'] = 0
elif species in self.adsorbate_names:
ads_info['type'] = 'adsorbate'
ads_info['n_sites'] = 1
elif species in self.transition_state_names:
ads_info['type'] = 'transition_state'
ads_info['n_sites'] = 1
elif species in site_names:
ads_info['type'] = 'site'
ads_info['site'] = species
ads_info['formation_energy'] = 0
if species not in self._gas_sites:
ads_info['n_sites'] = 1
else:
ads_info['n_sites'] = 0
ads_info['site_names'] = ['gas']
ads_info['total'] = 0
ads_info['composition'] = {}
else:
ads_info['type'] = 'unknown'
if species not in site_names:
composition = get_composition(name)
ads_info['composition'] = composition
if species in self.species_definitions:
ads_info.update(self.species_definitions[species])
if ads_info['composition'] is None and species not in site_names:
raise ValueError('Could not determine composition for ' +
species)
if species not in site_names:
self.species_definitions[species] = ads_info
else:
self.species_definitions[species] = \
self.species_definitions['*_'+species] = ads_info
for species in self.species_definitions.keys(): #set site definitions
##This entire block can probably be deleted since sites are now
#handled in the above section. Wait for a version or 2 to let
#the clauses deprecate...
site = self.species_definitions[species].get('site', None)
if site and site not in self.species_definitions:
ads_info = {}
ads_info['type'] = 'site'
ads_info['site'] = site
ads_info['formation_energy'] = 0
if site not in self._gas_sites:
ads_info['n_sites'] = 1
else:
ads_info['n_sites'] = 0
ads_info['site_names'] = ['gas']
ads_info['total'] = 0
ads_info['composition'] = {}
if self.site_definitions: #Deprecate later...
warnings.warn(
'Deprecation Warning: site_definitions will not be'
' supported in future versions. Please use new '
'species_definitions syntax.')
site_names = self.site_definitions[site]
if isinstance(site_names, basestring):
site_names = [site_names]
ads_info['site_names'] = site_names
if self.site_totals: #Deprecate later...
warnings.warn(
'Deprecation Warning: site_totals will not be'
' supported in future versions. Please use new '
'species_definitions syntax.')
ads_info['total'] = self.site_totals[site]
if site in self.species_definitions:
ads_info.update(self.species_definitions[site])
self.species_definitions[site] = self.species_definitions['*_'+site] \
= ads_info
if not self.atomic_reservoir_list:
#Make list of valid reference sets for e.g. boltzmann coverages
cart_product = []
all_atoms = []
composition_dict = {}
dummy_dict = {}
for sp in self.gas_names:
composition_dict[sp] = self.species_definitions[sp][
'composition']
dummy_dict[sp] = 0 #dummy dict of energies
for key in composition_dict[sp].keys():
if key not in all_atoms:
all_atoms.append(key)
for key in all_atoms:
possibles = []
for sp in self.gas_names:
if composition_dict[sp].get(key, None):
possibles.append(sp)
cart_product.append(possibles)
ref_sets = []
for prod in cartesian_product(*cart_product):
refdict = {}
for ai, pi in zip(all_atoms, prod):
refdict[ai] = pi
if (sorted(list(refdict.values())) == sorted(
list(set(refdict.values())))
and sorted(list(refdict.values()))
not in [sorted(list(rs.values())) for rs in ref_sets]):
if refdict and dummy_dict and composition_dict:
try:
self.convert_formation_energies(
dummy_dict, refdict, composition_dict)
ref_sets.append(refdict)
except ValueError:
pass
if ref_sets:
self.atomic_reservoir_list = ref_sets
else:
raise AttributeError('No valid reference sets from gas-phase species ' + \
'in the system. Add gasses or specify atomic_reservoir_list')