def change_masses(self, new_masses, mass_dictionary):
# Change the masses of the species stored, using the new_masses dictionary
# if any of the elements are in the mass_dictionary then use that mass instead
if not self.program_mass_dictionary:
# We only want to do this once - remember the program masses as a dictionary
if self.debug:
print("Setting program mass dictionary")
for symbol,mass in zip(self.species,self.masses_per_type):
element = cleanup_symbol(symbol)
self.program_mass_dictionary[element] = mass
if self.debug:
print("changing masses", self.program_mass_dictionary)
self.masses = []
self.masses_per_type = []
for symbol in self.species:
# the element name may be appended with a digit or an underscore
element = cleanup_symbol(symbol)
mass = new_masses[element]
if element in mass_dictionary:
mass = mass_dictionary[element]
self.masses_per_type.append(mass)
# end for symbol
self.masses = [ self.masses_per_type[atype] for atype in self.atom_type_list ]
if self.debug:
print("new masses", self.masses)
return
def mass_dictionary(self):
dictionary = {}
for symbol,mass in zip(self.species,self.masses_per_type):
# the element name may be appended with a digit or an underscore
element = cleanup_symbol(symbol)
dictionary[element] = mass
if self.debug:
print("new mass_dictionary", dictionary)
return dictionary
def set_element_names(self, element_names):
self.element_names = []
for el in element_names:
el = cleanup_symbol(el)
self.element_names.append(el)
return
def getSpecies(self):
return [ cleanup_symbol(el) for el in self.species ]