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format source code with black -l 120 -t py38
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@robertrueger
robertrueger committed Mar 12, 2024
1 parent 5df7066 commit 5150b0c
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Showing 69 changed files with 4,734 additions and 4,080 deletions.
28 changes: 15 additions & 13 deletions __init__.py
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Expand Up @@ -3,57 +3,59 @@

from .__version__ import __version__


def __autoimport(path, folders):
import os
from os.path import join as opj
is_module = lambda x: x.endswith('.py') and not x.startswith('__init__')

is_module = lambda x: x.endswith(".py") and not x.startswith("__init__")

ret = []
for folder in folders:
for dirpath, dirnames, filenames in os.walk(opj(path,folder)):
for dirpath, dirnames, filenames in os.walk(opj(path, folder)):
modules = [os.path.splitext(f)[0] for f in filter(is_module, filenames)]
relpath = os.path.relpath(dirpath, path).split(os.sep)
for module in modules:
imp = '.'.join(relpath + [module])
tmp = __import__(imp, globals=globals(), fromlist=['*'], level=1)
if hasattr(tmp, '__all__'):
imp = ".".join(relpath + [module])
tmp = __import__(imp, globals=globals(), fromlist=["*"], level=1)
if hasattr(tmp, "__all__"):
ret += tmp.__all__
for name in tmp.__all__:
globals()[name] = vars(tmp)[name]
return ret


__all__ = __autoimport(__path__[0], ['core'])
__all__ = __autoimport(__path__[0], ["core"])


def init(path=None, folder=None, config_settings:Dict=None):
def init(path=None, folder=None, config_settings: Dict = None):
"""Initializes pyZacros and PLAMS environment. It internally calls the scm.plams.init() method."""
scm.plams.init( path=path, folder=folder, config_settings=config_settings )
scm.plams.init(path=path, folder=folder, config_settings=config_settings)


def finish(otherJM=None):
"""Wait for all threads to finish and clean the environment. It internally calls the scm.plams.finish() method."""
scm.plams.finish( otherJM=otherJM )
scm.plams.finish(otherJM=otherJM)


def load(filename):
"""Load previously saved job from ``.dill`` file. It internally calls the scm.plams.load() method."""
return scm.plams.load( filename )
return scm.plams.load(filename)


def load_all(path, jobmanager=None):
"""Load all jobs from *path*. It internally calls the scm.plams.load_all() method."""
return scm.plams.load_all( path=path, jobmanager=jobmanager )
return scm.plams.load_all(path=path, jobmanager=jobmanager)


def delete_job(job):
"""Remove *job* from its corresponding |JobManager| and delete the job folder from the disk. Mark *job* as 'deleted'. It internally calls the scm.plams.delete_job() method."""
scm.plams.load_all( job=job )
scm.plams.load_all(job=job)


def log(message, level=0):
"""Log *message* with verbosity *level*. It internally calls the scm.plams.log() method."""
scm.plams.load_all( message=message, level=level )
scm.plams.load_all(message=message, level=level)


def workdir():
Expand Down
2 changes: 1 addition & 1 deletion __version__.py
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@@ -1 +1 @@
__version__ = '1.2.0'
__version__ = "1.2.0"
142 changes: 68 additions & 74 deletions core/Cluster.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
from .Species import *
from .SpeciesList import SpeciesList

__all__ = ['Cluster']
__all__ = ["Cluster"]


class Cluster:
"""
Expand All @@ -16,41 +17,38 @@ class Cluster:
* ``label`` -- If None, a unique label is generated based on its composition.
"""

def __init__(self, species,
site_types = None,
entity_number = None,
neighboring = None,
multiplicity = 1,
energy = 0.000,
label = None):
def __init__(
self, species, site_types=None, entity_number=None, neighboring=None, multiplicity=1, energy=0.000, label=None
):
"""
Creates a new Cluster object
"""
self.species = species # e.g. [ Species("H*",1), Species("H*",1) ]
self.sites = len([ sp for sp in species if sp == Species.UNSPECIFIED or sp.is_adsorbed() ])
self.sites = len([sp for sp in species if sp == Species.UNSPECIFIED or sp.is_adsorbed()])

if( site_types is not None ):
if( not ( all([ type(st)==int for st in site_types ]) or all([ type(st)==str for st in site_types ]) ) ):
msg = "\n### ERROR ### ElementaryReaction.__init__.\n"
if site_types is not None:
if not (all([type(st) == int for st in site_types]) or all([type(st) == str for st in site_types])):
msg = "\n### ERROR ### ElementaryReaction.__init__.\n"
msg += " Inconsistent type for site_types. It should be a list of int or str\n"
raise NameError(msg)

self.site_types = site_types # e.g. [ "f", "f" ], [ 0, 0 ]
self.site_types = site_types # e.g. [ "f", "f" ], [ 0, 0 ]
else:
self.site_types = self.sites*[ 0 ]
self.site_types = self.sites * [0]

self.neighboring = neighboring # e.g. [ (0,1) ]
self.multiplicity = multiplicity # e.g. 2
self.energy = energy # Units eV
self.neighboring = neighboring # e.g. [ (0,1) ]
self.multiplicity = multiplicity # e.g. 2
self.energy = energy # Units eV

self.entity_number = entity_number
if( entity_number is None ): self.entity_number = SpeciesList.default_entity_numbers( self.sites, self.species )
if entity_number is None:
self.entity_number = SpeciesList.default_entity_numbers(self.sites, self.species)

#TODO Make a way to check denticity consistency
#if( sum([s.denticity for s in self.species]) != self.sites ):
#msg = "\n### ERROR ### Cluster.__init__.\n"
#msg += "Inconsistent dimensions for species or site_types\n"
#raise NameError(msg)
# TODO Make a way to check denticity consistency
# if( sum([s.denticity for s in self.species]) != self.sites ):
# msg = "\n### ERROR ### Cluster.__init__.\n"
# msg += "Inconsistent dimensions for species or site_types\n"
# raise NameError(msg)

self.__userLabel = label
self.__label = None
Expand All @@ -60,44 +58,40 @@ def __init__(self, species,
self.__composition = {}

for item in species:
if( item != Species.UNSPECIFIED ):
if item != Species.UNSPECIFIED:
self.__mass += item.mass()
else:
continue

for symbol,n in item.composition().items():
if( not symbol in self.__composition ):
for symbol, n in item.composition().items():
if not symbol in self.__composition:
self.__composition[symbol] = n
else:
self.__composition[symbol] += n


def __len__(self):
"""
Returns the number of species inside the cluster
"""
return len(self.species)


def __eq__(self, other):
"""
Returns True if both objects have the same label. Otherwise returns False
* ``other`` --
"""
if( self.__label == other.__label ):
if self.__label == other.__label:
return True
else:
return False


def __hash__(self):
"""
Returns a hash based on the label
"""
return hash(self.__label)


def __updateLabel(self):
"""
Updates the attribute 'label'
Expand All @@ -108,17 +102,17 @@ def __updateLabel(self):

self.__label = ""
for i in range(len(self.species)):
if( self.species[i] != Species.UNSPECIFIED ):
if self.species[i] != Species.UNSPECIFIED:
self.__label += self.species[i].symbol
else:
self.__label += "&"

if( len(self.entity_number)>1 ):
self.__label += str(self.entity_number[i]+1)
if len(self.entity_number) > 1:
self.__label += str(self.entity_number[i] + 1)
self.__label += str(self.site_types[i])

if self.neighboring is not None:
if(len(self.neighboring) > 0):
if len(self.neighboring) > 0:
self.__label += ":"

# For neighboring nodes are sorted
Expand All @@ -127,134 +121,134 @@ def __updateLabel(self):
lNeighboring = list(self.neighboring[i])
lNeighboring.sort()
self.__label += str(tuple(lNeighboring)).replace(" ", "")
if( i != len(self.neighboring)-1):
if i != len(self.neighboring) - 1:
self.__label += ","


def label(self):
"""
Returns the label of the cluster
"""
if( self.__label is None ):
if self.__label is None:
self.__updateLabel()

return self.__label


def __str__(self):
"""
Translates the object to a string
"""
output = "cluster " + self.__label +"\n"
output = "cluster " + self.__label + "\n"

if( self.sites != 0 ):
output += " sites " + str(self.sites)+"\n"
if self.sites != 0:
output += " sites " + str(self.sites) + "\n"

if self.neighboring is not None and len(self.neighboring) > 0:
output += " neighboring "
for i in range(len(self.neighboring)):
output += str(self.neighboring[i][0]+1)+"-"+str(self.neighboring[i][1]+1)
if( i != len(self.neighboring)-1 ):
output += str(self.neighboring[i][0] + 1) + "-" + str(self.neighboring[i][1] + 1)
if i != len(self.neighboring) - 1:
output += " "
output += "\n"

site_identate = {}
output += " lattice_state"+"\n"
output += " lattice_state" + "\n"
for i in range(self.sites):
if( self.entity_number[i] not in site_identate ):
site_identate[ self.entity_number[i] ] = 0
if self.entity_number[i] not in site_identate:
site_identate[self.entity_number[i]] = 0
else:
site_identate[ self.entity_number[i] ] = site_identate[ self.entity_number[i] ] + 1
site_identate[self.entity_number[i]] = site_identate[self.entity_number[i]] + 1

if( self.species[i] != Species.UNSPECIFIED ):
if( site_identate[ self.entity_number[i] ] >= self.species[i].denticity ):
msg = "\n### ERROR ### Cluster.__str__.\n"
msg += "Inconsistent of denticity value for "+self.species[i].symbol+"\n"
if self.species[i] != Species.UNSPECIFIED:
if site_identate[self.entity_number[i]] >= self.species[i].denticity:
msg = "\n### ERROR ### Cluster.__str__.\n"
msg += "Inconsistent of denticity value for " + self.species[i].symbol + "\n"
raise NameError(msg)

output += " "+str(self.entity_number[i]+1)+" "+self.species[i].symbol+" "+str(site_identate[self.entity_number[i]]+1)+"\n"
output += (
" "
+ str(self.entity_number[i] + 1)
+ " "
+ self.species[i].symbol
+ " "
+ str(site_identate[self.entity_number[i]] + 1)
+ "\n"
)
else:
output += " & & &\n"

output += " site_types "
for i in range(len(self.site_types)):

if( type(self.site_types[i]) == int ):
output += str(self.site_types[i]+1)
elif( type(self.site_types[i]) == str ):
if type(self.site_types[i]) == int:
output += str(self.site_types[i] + 1)
elif type(self.site_types[i]) == str:
output += self.site_types[i]

if( i != len(self.site_types)-1 ):
if i != len(self.site_types) - 1:
output += " "
output += "\n"

output += " graph_multiplicity "+str(self.multiplicity)+"\n"
output += " graph_multiplicity " + str(self.multiplicity) + "\n"

output += " cluster_eng "+("%12.5e"%self.energy)+"\n"
output += " cluster_eng " + ("%12.5e" % self.energy) + "\n"
output += "end_cluster"

return output


def composition(self):
"""
Returns a dictionary containing the number of atoms of each kind.
"""
return self.__composition


def mass(self):
"""
Returns the mass of the cluster in Da
"""
return self.__mass


def gas_species(self):
"""Returns the gas species."""
species = []

for sp in self.species:
if( sp != Species.UNSPECIFIED and sp.kind == Species.GAS ):
species.append( sp )
if sp != Species.UNSPECIFIED and sp.kind == Species.GAS:
species.append(sp)

species = SpeciesList( species )
species = SpeciesList(species)
species.remove_duplicates()
return species


def surface_species(self):
"""Returns the surface species."""
species = []

for sp in self.species:
if( sp != Species.UNSPECIFIED and sp.kind == Species.SURFACE ):
species.append( sp )
if sp != Species.UNSPECIFIED and sp.kind == Species.SURFACE:
species.append(sp)

species = SpeciesList( species )
species = SpeciesList(species)
species.remove_duplicates()
return species


def site_types_set(self):
"""
Returns the set of the sites types
"""
return set(self.site_types)


def replace_site_types( self, site_types_old, site_types_new ):
def replace_site_types(self, site_types_old, site_types_new):
"""
Replaces the site types names
* ``site_types_old`` -- List of strings containing the old site_types to be replaced
* ``site_types_new`` -- List of strings containing the new site_types which would replace old site_types_old.
"""
assert( len(site_types_old) == len(site_types_new) )
assert len(site_types_old) == len(site_types_new)

for i in range(len(site_types_old)):
for j in range(len(self.site_types)):
if( self.site_types[j] == site_types_old[i] ):
if self.site_types[j] == site_types_old[i]:
self.site_types[j] = site_types_new[i]

self.__updateLabel()
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