def get_surface_restart_indiv(Optimizer, indiv):
"""
Function to generate an structopt Individual class object containing
a surface structure from a previously existing structure
Inputs:
Optimizer = structopt Optimizer class
indiv = ASE Atoms object containing the previously existing structure
Outputs:
individ = structopt Individual class object containing surface structure data
"""
#Load surface structure
surfs = read_xyz(Optimizer.surfacefile)
cells = Optimizer.surfacecell
surfs.set_cell(cells)
surf.set_pbc([True,True,False])
top,bulks=find_top_layer(indiv,Optimizer.surftopthick)
individ=Individual(top)
individ.bulki=bulks.copy()
individ.bulko=bulks.copy()
return individ
def get_surface_indiv(Optimizer):
"""
Function to generate an structopt Individual class object containing as surface structure.
Inputs:
Optimizer = structopt Optimizer class
Outputs:
individ = structopt Individual class object containing surface structure data
"""
#Load surface structure
surfs = read_xyz(Optimizer.surfacefile)
cells = Optimizer.surfacecell
surfs.set_cell(cells)
surf.set_pbc([True, True, False])
#Find top layer
top, bulks = find_top_layer(surfs, Optimizer.surftopthick)
mutopto = Optimizer.mutation_options
Optimizer.mutation_options = ['lattice_alteration_rdrd']
topind = top.copy()
ind = moves_switch(topind, Optimizer)
Optimizer.mutation_options = mutopto
individ = Individual(ind)
individ.bulki = bulks.copy()
individ.bulko = bulks.copy()
return individ
def get_surface_indiv(Optimizer):
"""
Function to generate an structopt Individual class object containing as surface structure.
Inputs:
Optimizer = structopt Optimizer class
Outputs:
individ = structopt Individual class object containing surface structure data
"""
#Load surface structure
surfs = read_xyz(Optimizer.surfacefile)
cells = Optimizer.surfacecell
surfs.set_cell(cells)
surf.set_pbc([True,True,False])
#Find top layer
top,bulks=find_top_layer(surfs,Optimizer.surftopthick)
mutopto = Optimizer.mutation_options
Optimizer.mutation_options = ['lattice_alteration_rdrd']
topind = top.copy()
ind = moves_switch(topind,Optimizer)
Optimizer.mutation_options = mutopto
individ = Individual(ind)
individ.bulki = bulks.copy()
individ.bulko = bulks.copy()
return individ