parameters = {'pair_style': 'eam/cd', 'pair_coeff': pair_coeff}
mincomd = '1e-8 1e-8 5000 10000'
parameters['minimize'] = mincomd
filesL = ['FeCr.cdeam']
calc = LAMMPS(parameters=parameters,
files=filesL,
keep_tmp_files=True,
tmp_dir=os.path.join(os.getcwd(), 'LAMMPSFiles'))
files = os.listdir(os.getcwd())
files = [file for file in files if '.xyz' in file]
for file in flist:
# Read File
structure = read_xyz(file, -1)
# Calculate Energy
structure.set_cell([22.96, 22.96, 22.96])
structure.set_pbc(True)
structure.set_calculator(calc)
OUT = structure.calc.calculate(structure)
totalsol = OUT['atoms']
totalsol.set_pbc(True)
en = OUT['thermo'][-1]['pe']
#Write Relaxed Structure
write_xyz('r{0}'.format(file), totalsol, repr(en))
fe = en
for sym, u in [('Cr', -3.8363), ('Fe', -4.21224)]:
nc = len([atm for atm in structure if atm.symbol == sym])
fe -= float(nc) * float(u)
print 'FeCr Interstitial - ' + file
print ' Potential Energy = ' + repr(en)
print ' Formation Energy = ' + repr(fe)
# Set up calculator
parcoff = '* * FeCr.cdeam Cr Fe'
pair_coeff = [parcoff]
parameters = { 'pair_style' : 'eam/cd', 'pair_coeff' : pair_coeff }
mincomd = '1e-8 1e-8 5000 10000'
parameters['minimize'] = mincomd
filesL = [ 'FeCr.cdeam' ]
calc = LAMMPS(parameters=parameters, files=filesL, keep_tmp_files=True, tmp_dir=os.path.join(os.getcwd(), 'LAMMPSFiles'))
files = os.listdir(os.getcwd())
files = [file for file in files if '.xyz' in file]
for file in flist:
# Read File
structure = read_xyz(file,-1)
# Calculate Energy
structure.set_cell([22.96, 22.96, 22.96])
structure.set_pbc(True)
structure.set_calculator(calc)
OUT=structure.calc.calculate(structure)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
en=OUT['thermo'][-1]['pe']
#Write Relaxed Structure
write_xyz('r{0}'.format(file),totalsol,repr(en))
fe = en
for sym,u in [('Cr',-3.8363),('Fe',-4.21224)]:
nc=len([atm for atm in structure if atm.symbol==sym])
fe-= float(nc)*float(u)
print 'FeCr Interstitial - ' + file
print ' Potential Energy = '+repr(en)
print ' Formation Energy = '+repr(fe)
def eval_energy(input):
"""Function to evaluate energy of an individual
Inputs:
input = [Optimizer class object with parameters, Individual class structure to be evaluated]
Outputs:
energy, bul, individ, signal
energy = energy of Individual evaluated
bul = bulk structure of Individual if simulation structure is Defect
individ = Individual class structure evaluated
signal = string of information about evaluation
"""
if input[0] == None:
energy = 0
bul = 0
individ = 0
rank = MPI.COMM_WORLD.Get_rank()
signal = 'Evaluated none individual on ' + repr(rank) + '\n'
else:
[Optimizer, individ] = input
if Optimizer.calc_method == 'MAST':
energy = individ.energy
bul = individ.energy
signal = 'Recieved MAST structure\n'
else:
if Optimizer.parallel: rank = MPI.COMM_WORLD.Get_rank()
if not Optimizer.genealogy:
STR = '----Individual ' + str(
individ.index) + ' Optimization----\n'
else:
STR = '----Individual ' + str(
individ.history_index) + ' Optimization----\n'
indiv = individ[0]
if 'EE' in Optimizer.debug:
debug = True
else:
debug = False
if debug:
write_xyz(Optimizer.debugfile, indiv, 'Recieved by eval_energy')
Optimizer.debugfile.flush()
if Optimizer.structure == 'Defect':
indi = indiv.copy()
if Optimizer.alloy == True:
bulk = individ.bulki
else:
bulk = individ.bulko
nat = indi.get_number_of_atoms()
csize = bulk.get_cell()
totalsol = Atoms(cell=csize, pbc=True)
totalsol.extend(indi)
totalsol.extend(bulk)
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in totalsol if atm.symbol == sym])
STR += 'Defect configuration contains ' + repr(
nc) + ' ' + repr(sym) + ' atoms\n'
elif Optimizer.structure == 'Surface':
totalsol = Atoms()
totalsol.extend(indiv)
nat = indiv.get_number_of_atoms()
totalsol.extend(individ.bulki)
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in totalsol if atm.symbol == sym])
STR += 'Surface-Bulk configuration contains ' + repr(
nc) + ' ' + repr(sym) + ' atoms\n'
cell = numpy.maximum.reduce(indiv.get_cell())
totalsol.set_cell([cell[0], cell[1], 500])
totalsol.set_pbc([True, True, False])
if Optimizer.constrain_position:
ts = totalsol.copy()
indc, indb, vacant, swap, stro = find_defects(
ts, Optimizer.solidbulk, 0)
sbulk = Optimizer.solidbulk.copy()
bcom = sbulk.get_center_of_mass()
#totalsol.translate(-bulkcom)
#indc.translate(-bulkcom)
#totalsol.append(Atom(position=[0,0,0]))
# for one in indc:
# index = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0]
# if totalsol.get_distance(-1,index) > Optimizer.sf:
# r = random.random()
# totalsol.set_distance(-1,index,Optimizer.sf*r,fix=0)
# totalsol.pop()
# totalsol.translate(bulkcom)
com = indc.get_center_of_mass()
dist = (sum((bcom[i] - com[i])**2 for i in range(3)))**0.5
if dist > Optimizer.sf:
STR += 'Shifting structure to within region\n'
r = random.random() * Optimizer.sf
comv = numpy.linalg.norm(com)
ncom = [one * r / comv for one in com]
trans = [ncom[i] - com[i] for i in range(3)]
indices = []
for one in indc:
id = [
atm.index for atm in totalsol
if atm.position[0] == one.position[0]
and atm.position[1] == one.position[1]
and atm.position[2] == one.position[2]
][0]
totalsol[id].position += trans
# Check for atoms that are too close
min_len = 0.7
#pdb.set_trace()
if not Optimizer.fixed_region:
if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface':
cutoffs = [2.0 for one in totalsol]
nl = NeighborList(cutoffs,
bothways=True,
self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms = Atoms()
nbatoms.append(one)
indices, offsets = nl.get_neighbors(one.index)
for index, d in zip(indices, offsets):
index = int(index)
sym = totalsol[index].symbol
pos = totalsol[index].position + numpy.dot(
d, totalsol.get_cell())
at = Atom(symbol=sym, position=pos)
nbatoms.append(at)
while True:
dflag = False
for i in range(1, len(nbatoms)):
d = nbatoms.get_distance(0, i)
if d < min_len:
nbatoms.set_distance(0,
i,
min_len + .01,
fix=0.5)
STR += '--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag = True
if dflag == False:
break
for i in range(len(indices)):
totalsol[indices[i]].position = nbatoms[i + 1].position
totalsol[one.index].position = nbatoms[0].position
nl.update(totalsol)
if debug:
write_xyz(Optimizer.debugfile, totalsol,
'After minlength check')
Optimizer.debugfile.flush()
else:
for i in range(len(indiv)):
for j in range(len(indiv)):
if i != j:
d = indiv.get_distance(i, j)
if d < min_len:
indiv.set_distance(i, j, min_len, fix=0.5)
STR += '--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
if debug:
write_xyz(Optimizer.debugfile, indiv,
'After minlength check')
Optimizer.debugfile.flush()
# Set calculator to use to get forces/energies
if Optimizer.parallel:
calc = setup_calculator(Optimizer)
if Optimizer.fixed_region:
pms = copy.deepcopy(calc.parameters)
try:
pms['mass'][
len(pms['mass']) - 1] += '\ngroup RO id >= ' + repr(
nat) + '\nfix freeze RO setforce 0.0 0.0 0.0\n'
except KeyError:
pms['pair_coeff'][0] += '\ngroup RO id >= ' + repr(
nat) + '\nfix freeze RO setforce 0.0 0.0 0.0\n'
calc = LAMMPS(parameters=pms,
files=calc.files,
keep_tmp_files=calc.keep_tmp_files,
tmp_dir=calc.tmp_dir)
lmin = copy.copy(Optimizer.lammps_min)
Optimizer.lammps_min = None
Optimizer.static_calc = setup_calculator(Optimizer)
Optimizer.lammps_min = lmin
else:
calc = Optimizer.calc
if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface':
totalsol.set_calculator(calc)
totalsol.set_pbc(True)
else:
indiv.set_calculator(calc)
indiv.set_pbc(
True) #Current bug in ASE optimizer-Lammps prevents pbc=false
if Optimizer.structure == 'Cluster':
indiv.set_cell([500, 500, 500])
indiv.translate([250, 250, 250])
cwd = os.getcwd()
# Perform Energy Minimization
if not Optimizer.parallel:
Optimizer.output.flush()
if Optimizer.ase_min == True:
try:
if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface':
dyn = BFGS(totalsol)
else:
dyn = BFGS(indiv)
dyn.run(fmax=Optimizer.ase_min_fmax,
steps=Optimizer.ase_min_maxsteps)
except OverflowError:
STR += '--- Error: Infinite Energy Calculated - Implement Random ---\n'
box = Atoms()
indiv = gen_pop_box(Optimizer.natoms, Optimizer.atomlist,
Optimizer.size)
indiv.set_calculator(calc)
dyn = BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
except numpy.linalg.linalg.LinAlgError:
STR += '--- Error: Singular Matrix - Implement Random ---\n'
indiv = gen_pop_box(Optimizer.natoms, Optimizer.atomlist,
Optimizer.size)
indiv.set_calculator(calc)
dyn = BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
# Get Energy of Minimized Structure
if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface':
en = totalsol.get_potential_energy()
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure = totalsol.get_isotropic_pressure(
totalsol.get_stress())
cell_max = numpy.maximum.reduce(totalsol.get_positions())
cell_min = numpy.minimum.reduce(totalsol.get_positions())
cell = cell_max - cell_min
volume = cell[0] * cell[1] * cell[2]
else:
pressure = 0
volume = 0
na = totalsol.get_number_of_atoms()
ena = en / na
energy = en
individ[0] = totalsol[0:nat]
bul = totalsol[(nat):len(totalsol)]
STR += 'Number of positions = ' + repr(
len(bul) + len(individ[0])) + '\n'
individ[0].set_cell(csize)
indiv = individ[0]
else:
en = indiv.get_potential_energy()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure = indiv.get_isotropic_pressure(indiv.get_stress())
cell_max = numpy.maximum.reduce(indiv.get_positions())
cell_min = numpy.minimum.reduce(indiv.get_positions())
cell = cell_max - cell_min
volume = cell[0] * cell[1] * cell[2]
else:
pressure = 0
volume = 0
na = indiv.get_number_of_atoms()
ena = en / na
energy = ena
individ[0] = indiv
bul = 0
else:
if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface':
if Optimizer.calc_method == 'VASP':
en = totalsol.get_potential_energy()
calcb = Vasp(restart=True)
totalsol = calcb.get_atoms()
stress = calcb.read_stress()
else:
try:
totcop = totalsol.copy()
if debug:
write_xyz(Optimizer.debugfile, totcop,
'Individual sent to lammps')
OUT = totalsol.calc.calculate(totalsol)
totalsol = OUT['atoms']
totalsol.set_pbc(True)
if Optimizer.fixed_region:
if debug:
print 'Energy of fixed region calc = ', OUT[
'thermo'][-1]['pe']
totalsol.set_calculator(Optimizer.static_calc)
OUT = totalsol.calc.calculate(totalsol)
totalsol = OUT['atoms']
totalsol.set_pbc(True)
if debug:
print 'Energy of static calc = ', OUT[
'thermo'][-1]['pe']
en = OUT['thermo'][-1]['pe']
stress = numpy.array([
OUT['thermo'][-1][i]
for i in ('pxx', 'pyy', 'pzz', 'pyz', 'pxz', 'pxy')
]) * (-1e-4 * GPa)
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if debug:
write_xyz(Optimizer.debugfile, totalsol,
'After Lammps Minimization')
Optimizer.debugfile.flush()
except Exception, e:
os.chdir(cwd)
STR += 'WARNING: Exception during energy eval:\n' + repr(
e) + '\n'
f = open('problem-structures.xyz', 'a')
write_xyz(f,
totcop,
data='Starting structure hindex=' +
individ.history_index)
write_xyz(f, totalsol, data='Lammps Min structure')
en = 10
stress = 0
f.close()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure = totalsol.get_isotropic_pressure(stress)
cell_max = numpy.maximum.reduce(totalsol.get_positions())
cell_min = numpy.minimum.reduce(totalsol.get_positions())
cell = cell_max - cell_min
volume = cell[0] * cell[1] * cell[2]
else:
pressure = totalsol.get_isotropic_pressure(stress)
volume = 0
na = totalsol.get_number_of_atoms()
ena = en / na
energy = en
if Optimizer.structure == 'Defect':
if Optimizer.fixed_region == True or Optimizer.finddefects == False:
individ[0] = totalsol[0:nat]
bul = totalsol[(nat):len(totalsol)]
individ[0].set_cell(csize)
else:
if 'FI' in Optimizer.debug:
outt = find_defects(
totalsol,
Optimizer.solidbulk,
Optimizer.sf,
atomlistcheck=Optimizer.atomlist,
trackvacs=Optimizer.trackvacs,
trackswaps=Optimizer.trackswaps,
debug=Optimizer.debugfile)
else:
outt = find_defects(
totalsol,
Optimizer.solidbulk,
Optimizer.sf,
atomlistcheck=Optimizer.atomlist,
trackvacs=Optimizer.trackvacs,
trackswaps=Optimizer.trackswaps,
debug=False)
individ[0] = outt[0]
bul = outt[1]
individ.vacancies = outt[2]
individ.swaps = outt[3]
STR += outt[4]
indiv = individ[0]
else:
top, bul = find_top_layer(totalsol, Optimizer.surftopthick)
indiv = top.copy()
individ[0] = top.copy()
else:
def eval_energy(input):
"""Function to evaluate energy of an individual
Inputs:
input = [Optimizer class object with parameters, Individual class structure to be evaluated]
Outputs:
energy, bul, individ, signal
energy = energy of Individual evaluated
bul = bulk structure of Individual if simulation structure is Defect
individ = Individual class structure evaluated
signal = string of information about evaluation
"""
if input[0]==None:
energy=0
bul=0
individ=0
rank = MPI.COMM_WORLD.Get_rank()
signal='Evaluated none individual on '+repr(rank)+'\n'
else:
[Optimizer, individ]=input
if Optimizer.calc_method=='MAST':
energy = individ.energy
bul = individ.energy
signal = 'Recieved MAST structure\n'
else:
if Optimizer.parallel: rank = MPI.COMM_WORLD.Get_rank()
if not Optimizer.genealogy:
STR='----Individual ' + str(individ.index)+ ' Optimization----\n'
else:
STR='----Individual ' + str(individ.history_index)+ ' Optimization----\n'
indiv=individ[0]
if 'EE' in Optimizer.debug:
debug = True
else:
debug = False
if debug:
write_xyz(Optimizer.debugfile,indiv,'Recieved by eval_energy')
Optimizer.debugfile.flush()
if Optimizer.structure=='Defect':
indi=indiv.copy()
if Optimizer.alloy==True:
bulk=individ.bulki
else:
bulk=individ.bulko
nat=indi.get_number_of_atoms()
csize=bulk.get_cell()
totalsol=Atoms(cell=csize, pbc=True)
totalsol.extend(indi)
totalsol.extend(bulk)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in totalsol if atm.symbol==sym])
STR+='Defect configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n'
elif Optimizer.structure=='Surface':
totalsol=Atoms()
totalsol.extend(indiv)
nat=indiv.get_number_of_atoms()
totalsol.extend(individ.bulki)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in totalsol if atm.symbol==sym])
STR+='Surface-Bulk configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n'
cell=numpy.maximum.reduce(indiv.get_cell())
totalsol.set_cell([cell[0],cell[1],500])
totalsol.set_pbc([True,True,False])
if Optimizer.constrain_position:
ts = totalsol.copy()
indc,indb,vacant,swap,stro = find_defects(ts,Optimizer.solidbulk,0)
sbulk = Optimizer.solidbulk.copy()
bcom = sbulk.get_center_of_mass()
#totalsol.translate(-bulkcom)
#indc.translate(-bulkcom)
#totalsol.append(Atom(position=[0,0,0]))
# for one in indc:
# index = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0]
# if totalsol.get_distance(-1,index) > Optimizer.sf:
# r = random.random()
# totalsol.set_distance(-1,index,Optimizer.sf*r,fix=0)
# totalsol.pop()
# totalsol.translate(bulkcom)
com = indc.get_center_of_mass()
dist = (sum((bcom[i] - com[i])**2 for i in range(3)))**0.5
if dist > Optimizer.sf:
STR+='Shifting structure to within region\n'
r = random.random()*Optimizer.sf
comv = numpy.linalg.norm(com)
ncom = [one*r/comv for one in com]
trans = [ncom[i]-com[i] for i in range(3)]
indices = []
for one in indc:
id = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0]
totalsol[id].position += trans
# Check for atoms that are too close
min_len=0.7
#pdb.set_trace()
if not Optimizer.fixed_region:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
cutoffs=[2.0 for one in totalsol]
nl=NeighborList(cutoffs,bothways=True,self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms=Atoms()
nbatoms.append(one)
indices, offsets=nl.get_neighbors(one.index)
for index, d in zip(indices,offsets):
index = int(index)
sym=totalsol[index].symbol
pos=totalsol[index].position + numpy.dot(d,totalsol.get_cell())
at=Atom(symbol=sym,position=pos)
nbatoms.append(at)
while True:
dflag=False
for i in range(1,len(nbatoms)):
d=nbatoms.get_distance(0,i)
if d < min_len:
nbatoms.set_distance(0,i,min_len+.01,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag=True
if dflag==False:
break
for i in range(len(indices)):
totalsol[indices[i]].position=nbatoms[i+1].position
totalsol[one.index].position=nbatoms[0].position
nl.update(totalsol)
if debug:
write_xyz(Optimizer.debugfile,totalsol,'After minlength check')
Optimizer.debugfile.flush()
else:
for i in range(len(indiv)):
for j in range(len(indiv)):
if i != j:
d=indiv.get_distance(i,j)
if d < min_len:
indiv.set_distance(i,j,min_len,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
if debug:
write_xyz(Optimizer.debugfile,indiv,'After minlength check')
Optimizer.debugfile.flush()
# Set calculator to use to get forces/energies
if Optimizer.parallel:
calc = setup_calculator(Optimizer)
if Optimizer.fixed_region:
pms=copy.deepcopy(calc.parameters)
try:
pms['mass'][len(pms['mass'])-1] += '\ngroup RO id >= '+repr(nat)+'\nfix freeze RO setforce 0.0 0.0 0.0\n'
except KeyError:
pms['pair_coeff'][0] += '\ngroup RO id >= '+repr(nat)+'\nfix freeze RO setforce 0.0 0.0 0.0\n'
calc = LAMMPS(parameters=pms, files=calc.files, keep_tmp_files=calc.keep_tmp_files, tmp_dir=calc.tmp_dir)
lmin = copy.copy(Optimizer.lammps_min)
Optimizer.lammps_min = None
Optimizer.static_calc = setup_calculator(Optimizer)
Optimizer.lammps_min = lmin
else:
calc=Optimizer.calc
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
totalsol.set_calculator(calc)
totalsol.set_pbc(True)
else:
indiv.set_calculator(calc)
indiv.set_pbc(True) #Current bug in ASE optimizer-Lammps prevents pbc=false
if Optimizer.structure=='Cluster':
indiv.set_cell([500,500,500])
indiv.translate([250,250,250])
cwd=os.getcwd()
# Perform Energy Minimization
if not Optimizer.parallel:
Optimizer.output.flush()
if Optimizer.ase_min == True:
try:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
dyn=BFGS(totalsol)
else:
dyn=BFGS(indiv)
dyn.run(fmax=Optimizer.ase_min_fmax, steps=Optimizer.ase_min_maxsteps)
except OverflowError:
STR+='--- Error: Infinite Energy Calculated - Implement Random ---\n'
box=Atoms()
indiv=gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size)
indiv.set_calculator(calc)
dyn=BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
except numpy.linalg.linalg.LinAlgError:
STR+='--- Error: Singular Matrix - Implement Random ---\n'
indiv=gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size)
indiv.set_calculator(calc)
dyn=BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
# Get Energy of Minimized Structure
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
en=totalsol.get_potential_energy()
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=totalsol.get_isotropic_pressure(totalsol.get_stress())
cell_max=numpy.maximum.reduce(totalsol.get_positions())
cell_min=numpy.minimum.reduce(totalsol.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=0
volume=0
na=totalsol.get_number_of_atoms()
ena=en/na
energy=en
individ[0]=totalsol[0:nat]
bul=totalsol[(nat):len(totalsol)]
STR+='Number of positions = '+repr(len(bul)+len(individ[0]))+'\n'
individ[0].set_cell(csize)
indiv=individ[0]
else:
en=indiv.get_potential_energy()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=indiv.get_isotropic_pressure(indiv.get_stress())
cell_max=numpy.maximum.reduce(indiv.get_positions())
cell_min=numpy.minimum.reduce(indiv.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=0
volume=0
na=indiv.get_number_of_atoms()
ena=en/na
energy=ena
individ[0]=indiv
bul=0
else:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
if Optimizer.calc_method=='VASP':
en=totalsol.get_potential_energy()
calcb=Vasp(restart=True)
totalsol=calcb.get_atoms()
stress=calcb.read_stress()
else:
try:
totcop=totalsol.copy()
if debug: write_xyz(Optimizer.debugfile,totcop,'Individual sent to lammps')
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
if Optimizer.fixed_region:
if debug:
print 'Energy of fixed region calc = ', OUT['thermo'][-1]['pe']
totalsol.set_calculator(Optimizer.static_calc)
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
if debug:
print 'Energy of static calc = ', OUT['thermo'][-1]['pe']
en=OUT['thermo'][-1]['pe']
stress=numpy.array([OUT['thermo'][-1][i] for i in ('pxx','pyy','pzz','pyz','pxz','pxy')])*(-1e-4*GPa)
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if debug:
write_xyz(Optimizer.debugfile,totalsol,'After Lammps Minimization')
Optimizer.debugfile.flush()
except Exception, e:
os.chdir(cwd)
STR+='WARNING: Exception during energy eval:\n'+repr(e)+'\n'
f=open('problem-structures.xyz','a')
write_xyz(f,totcop,data='Starting structure hindex='+individ.history_index)
write_xyz(f,totalsol,data='Lammps Min structure')
en=10
stress=0
f.close()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=totalsol.get_isotropic_pressure(stress)
cell_max=numpy.maximum.reduce(totalsol.get_positions())
cell_min=numpy.minimum.reduce(totalsol.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=totalsol.get_isotropic_pressure(stress)
volume=0
na=totalsol.get_number_of_atoms()
ena=en/na
energy=en
if Optimizer.structure=='Defect':
if Optimizer.fixed_region==True or Optimizer.finddefects==False:
individ[0]=totalsol[0:nat]
bul=totalsol[(nat):len(totalsol)]
individ[0].set_cell(csize)
else:
if 'FI' in Optimizer.debug:
outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=Optimizer.debugfile)
else:
outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=False)
individ[0]=outt[0]
bul=outt[1]
individ.vacancies = outt[2]
individ.swaps = outt[3]
STR += outt[4]
indiv=individ[0]
else:
top,bul=find_top_layer(totalsol,Optimizer.surftopthick)
indiv=top.copy()
individ[0]=top.copy()
else:
