def eval_energy(Optimizer, individ):
"""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
"""
#logger = initialize_logger(Optimizer.loggername)
logger = logging.getLogger(Optimizer.loggername)
if 'MAST' in Optimizer.calc_method:
energy = individ.energy
bul = individ.bulki
signal = 'Received MAST structure\n'
logger.info(
'Received individual index = {0} from MAST with energy {1}. Returning with no evaluation'
.format(individ.index, individ.energy))
else:
if Optimizer.parallel:
rank = MPI.COMM_WORLD.Get_rank()
logger.info(
'Received individual HI = {0} with energy {1} for energy evaluation'
.format(individ.history_index, individ.energy))
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, 'Received by eval_energy')
Optimizer.debugfile.flush()
logger.debug('Writing recieved individual to debug file')
# Establish individual structure for evaluation. Piece together regions when necessary.
if Optimizer.structure == 'Defect':
indi = indiv.copy()
bulk = individ.bulki
nat = indi.get_number_of_atoms()
if debug:
logger.info(
'Extending defect structure to include bulk len(r1+r2)={0} len(bulk)={1}'
.format(nat, len(bulk)))
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)
if debug:
logger.info(
'Extending surface structure to include bulk len(r1+r2)={0} len(bulk)={1}'
.format(nat, len(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])
elif Optimizer.structure == 'Cluster':
totalsol = indiv.copy()
nat = len(totalsol)
if debug:
logger.info(
'Extending cluster with {0} atoms to center of evaluation box of size {1}'
.format(nat, Optimizer.large_box_size))
origcell = indiv.get_cell()
totalsol.set_cell([
Optimizer.large_box_size, Optimizer.large_box_size,
Optimizer.large_box_size
])
totalsol.translate([
Optimizer.large_box_size / 2.0, Optimizer.large_box_size / 2.0,
Optimizer.large_box_size / 2.0
])
elif Optimizer.structure == 'Crystal':
totalsol = indiv.copy()
nat = len(totalsol)
else:
print 'WARNING: In EvalEnergy. Optimizer.structure not recognized'
logger.warning('Optimizer.structure not recognized')
# Check for atoms that are too close or out of constrained location
if Optimizer.constrain_position:
if Optimizer.structure == 'Defect':
if debug:
logger.info('Constraining positions of defect')
totalsol, stro = constrain_positions(totalsol,
Optimizer.solidbulk,
Optimizer.sf)
if debug:
logger.info(stro)
STR += str0
min_len = 0.7
if not Optimizer.fixed_region:
if debug:
logger.info('Running check minimum distance')
totalsol, STR = check_min_dist(totalsol, Optimizer.structure, nat,
min_len, STR)
if debug:
write_xyz(Optimizer.debugfile, totalsol,
'After minlength check')
Optimizer.debugfile.flush()
logger.debug(
'Writing individual after checking minimum length')
# Set calculator to use to get forces/energies
if Optimizer.parallel:
calc = setup_calculator(Optimizer)
if Optimizer.fixed_region:
if debug:
logger.info('Setting up fixed region calculator')
pms = copy.deepcopy(calc.parameters)
try:
pms['mass'][
len(pms['mass']) -
1] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format(
nat)
except KeyError:
pms['pair_coeff'][
0] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format(
nat)
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)
if debug:
logger.info('Setting up no local minimization calculator')
Optimizer.lammps_min = None
Optimizer.static_calc = setup_calculator(Optimizer)
Optimizer.lammps_min = lmin
else:
calc = Optimizer.calc
totalsol.set_calculator(calc)
totalsol.set_pbc(True)
# Perform Energy Minimization
if not Optimizer.parallel:
if debug:
write_xyz(Optimizer.debugfile, totalsol,
'Individual sent to Energy Minimizer')
logger.debug('Writing structure sent to energy minimizer')
try:
cwd = os.getcwd()
if Optimizer.ase_min == True:
if debug:
logger.info('Running ASE minimizer')
if Optimizer.calc_method == 'LennardJones':
logger.warn('Must run ase LJ calculator with pbc=False')
totalsol.set_pbc(False)
totalsol, energy, pressure, volume, STR = run_ase_min(
totalsol, Optimizer.ase_min_fmax,
Optimizer.ase_min_maxsteps, Optimizer.fitness_scheme, STR)
else:
if debug:
logger.info('Running local energy calculator')
if Optimizer.fixed_region:
totalsol, energy, pressure, volume, STR = run_energy_eval(
totalsol, Optimizer.calc_method,
Optimizer.fixed_region, Optimizer.fitness_scheme, STR,
Optimizer.static_calc)
else:
totalsol, energy, pressure, volume, STR = run_energy_eval(
totalsol, Optimizer.calc_method, False,
Optimizer.fitness_scheme, STR)
except Exception, e:
logger.critical('Error in energy evaluation: {0}'.format(e),
exc_info=True)
path = os.path.join(cwd, 'TroubledLammps')
if not os.path.exists(path):
os.mkdir(path)
#Copy files over
shutil.copyfile(
calc.trajfile,
os.path.join(path, os.path.basename(calc.trajfile)))
shutil.copyfile(calc.infile,
os.path.join(path, os.path.basename(calc.infile)))
shutil.copyfile(calc.logfile,
os.path.join(path, os.path.basename(calc.logfile)))
shutil.copyfile(
calc.datafile,
os.path.join(path, os.path.basename(calc.datafile)))
raise RuntimeError('{0}:{1}'.format(Exception, e))
if not Optimizer.parallel:
if debug:
write_xyz(Optimizer.debugfile, totalsol,
'Individual after Energy Minimization')
Optimizer.debugfile.flush()
logger.debug(
'Writing structure recieved from energy minimizer')
# Separate structures into distinct pieces
if Optimizer.structure == 'Defect':
if Optimizer.fixed_region == True or Optimizer.finddefects == False:
if debug:
logger.info(
'Identifying atoms in defect structure based on ID')
individ[0] = totalsol[0:nat]
bul = totalsol[(nat):len(totalsol)]
individ[0].set_cell(csize)
else:
if debug:
logger.info(
'Applying find defects scheme to identify R1 and R2 for Defect'
)
if 'FD' 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]
elif Optimizer.structure == 'Surface':
if debug:
logger.info('Finding surface top layer')
top, bul = find_top_layer(totalsol, Optimizer.surftopthick)
indiv = top.copy()
individ[0] = top.copy()
bul = Atoms()
elif Optimizer.structure == 'Crystal':
if debug:
logger.info('Checking crystal cell type')
celltype = check_cell_type(totalsol)
STR += 'Cell structure = {0}\n'.format(celltype)
bul = Atoms()
individ[0] = totalsol.copy()
elif Optimizer.structure == 'Cluster':
volume = get_cluster_volume(totalsol)
bul = Atoms()
if debug:
logger.info(
'Translating cluster back to smaller box size location')
totalsol.translate([
-Optimizer.large_box_size / 2.0,
-Optimizer.large_box_size / 2.0,
-Optimizer.large_box_size / 2.0
])
totalsol.set_cell(origcell)
individ[0] = totalsol.copy()
# Add concentration energy dependence
if Optimizer.forcing == 'energy_bias':
if debug:
logger.info(
'Applying energy bias for atoms with different number of atoms of type than in atomlist'
)
n = [0] * len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
n[i] = len([
inds for inds in totalsol
if inds.symbol == Optimizer.atomlist[i][0]
])
n[i] = abs(n[i] - Optimizer.atomlist[i][1])
factor = sum(n)**3
energy = (energy + factor) / totalsol.get_number_of_atoms()
STR += 'Energy with Bias = {0}\n'.format(energy)
elif Optimizer.forcing == 'chem_pot':
if debug:
logger.info(
'Applying chemical potential bias for atoms with different number of atoms of type than in atomlist'
)
n = [0] * len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
n[i] = len([
inds for inds in totalsol
if inds.symbol == Optimizer.atomlist[i][0]
])
n[i] = n[i] * Optimizer.atomlist[i][3]
factor = sum(n)
energy = (energy + factor) / totalsol.get_number_of_atoms()
STR += 'Energy with Chemical Potential = {0}\n'.format(energy)
individ.energy = energy
individ.buli = bul
individ.pressure = pressure
individ.volume = volume
if Optimizer.fingerprinting:
if debug:
logger.info('Identifying fingerprint of new structure')
individ.fingerprint = get_fingerprint(Optimizer, individ,
Optimizer.fpbin,
Optimizer.fpcutoff)
if Optimizer.parallel:
calc.clean()
signal = 'Evaluated individual {0} on {1}\n'.format(
individ.index, rank)
signal += STR
else:
signal = STR
def eval_energy(Optimizer, individ):
"""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
"""
#logger = initialize_logger(Optimizer.loggername)
logger = logging.getLogger(Optimizer.loggername)
if 'MAST' in Optimizer.calc_method:
energy = individ.energy
bul = individ.bulki
signal = 'Received MAST structure\n'
logger.info('Received individual index = {0} from MAST with energy {1}. Returning with no evaluation'.format(
individ.index, individ.energy))
else:
if Optimizer.parallel:
rank = MPI.COMM_WORLD.Get_rank()
logger.info('Received individual HI = {0} with energy {1} for energy evaluation'.format(
individ.history_index, individ.energy))
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,'Received by eval_energy')
Optimizer.debugfile.flush()
logger.debug('Writing recieved individual to debug file')
# Establish individual structure for evaluation. Piece together regions when necessary.
if Optimizer.structure=='Defect':
indi=indiv.copy()
bulk=individ.bulki
nat=indi.get_number_of_atoms()
if debug:
logger.info('Extending defect structure to include bulk len(r1+r2)={0} len(bulk)={1}'.format(nat,len(bulk)))
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)
if debug:
logger.info('Extending surface structure to include bulk len(r1+r2)={0} len(bulk)={1}'.format(nat,len(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])
elif Optimizer.structure=='Cluster':
totalsol = indiv.copy()
nat = len(totalsol)
if debug:
logger.info('Extending cluster with {0} atoms to center of evaluation box of size {1}'.format(nat,Optimizer.large_box_size))
origcell = indiv.get_cell()
totalsol.set_cell([Optimizer.large_box_size,Optimizer.large_box_size,Optimizer.large_box_size])
totalsol.translate([Optimizer.large_box_size/2.0,Optimizer.large_box_size/2.0,Optimizer.large_box_size/2.0])
elif Optimizer.structure=='Crystal':
totalsol = indiv.copy()
nat = len(totalsol)
else:
print 'WARNING: In EvalEnergy. Optimizer.structure not recognized'
logger.warning('Optimizer.structure not recognized')
# Check for atoms that are too close or out of constrained location
if Optimizer.constrain_position:
if Optimizer.structure=='Defect':
if debug:
logger.info('Constraining positions of defect')
totalsol, stro = constrain_positions(totalsol, Optimizer.solidbulk, Optimizer.sf)
if debug:
logger.info(stro)
STR+=str0
min_len=0.7
if not Optimizer.fixed_region:
if debug:
logger.info('Running check minimum distance')
totalsol, STR = check_min_dist(totalsol, Optimizer.structure, nat, min_len, STR)
if debug:
write_xyz(Optimizer.debugfile,totalsol,'After minlength check')
Optimizer.debugfile.flush()
logger.debug('Writing individual after checking minimum length')
# Set calculator to use to get forces/energies
if Optimizer.parallel:
calc = setup_calculator(Optimizer)
if Optimizer.fixed_region:
if debug:
logger.info('Setting up fixed region calculator')
pms=copy.deepcopy(calc.parameters)
try:
pms['mass'][len(pms['mass'])-1] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format(nat)
except KeyError:
pms['pair_coeff'][0] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format(nat)
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)
if debug:
logger.info('Setting up no local minimization calculator')
Optimizer.lammps_min = None
Optimizer.static_calc = setup_calculator(Optimizer)
Optimizer.lammps_min = lmin
else:
calc=Optimizer.calc
totalsol.set_calculator(calc)
totalsol.set_pbc(True)
# Perform Energy Minimization
if not Optimizer.parallel:
if debug:
write_xyz(Optimizer.debugfile,totalsol,'Individual sent to Energy Minimizer')
logger.debug('Writing structure sent to energy minimizer')
try:
cwd = os.getcwd()
if Optimizer.ase_min == True:
if debug:
logger.info('Running ASE minimizer')
if Optimizer.calc_method=='LennardJones':
logger.warn('Must run ase LJ calculator with pbc=False')
totalsol.set_pbc(False)
totalsol, energy, pressure, volume, STR = run_ase_min(totalsol, Optimizer.ase_min_fmax, Optimizer.ase_min_maxsteps, Optimizer.fitness_scheme, STR)
else:
if debug:
logger.info('Running local energy calculator')
if Optimizer.fixed_region:
totalsol, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, Optimizer.fixed_region, Optimizer.fitness_scheme, STR, Optimizer.static_calc)
else:
totalsol, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, False, Optimizer.fitness_scheme, STR)
except Exception, e:
logger.critical('Error in energy evaluation: {0}'.format(e), exc_info=True)
path = os.path.join(cwd,'TroubledLammps')
if not os.path.exists(path):
os.mkdir(path)
#Copy files over
shutil.copyfile(calc.trajfile,os.path.join(path,os.path.basename(calc.trajfile)))
shutil.copyfile(calc.infile,os.path.join(path,os.path.basename(calc.infile)))
shutil.copyfile(calc.logfile,os.path.join(path,os.path.basename(calc.logfile)))
shutil.copyfile(calc.datafile,os.path.join(path,os.path.basename(calc.datafile)))
raise RuntimeError('{0}:{1}'.format(Exception,e))
if not Optimizer.parallel:
if debug:
write_xyz(Optimizer.debugfile,totalsol,'Individual after Energy Minimization')
Optimizer.debugfile.flush()
logger.debug('Writing structure recieved from energy minimizer')
# Separate structures into distinct pieces
if Optimizer.structure=='Defect':
if Optimizer.fixed_region==True or Optimizer.finddefects==False:
if debug:
logger.info('Identifying atoms in defect structure based on ID')
individ[0]=totalsol[0:nat]
bul=totalsol[(nat):len(totalsol)]
individ[0].set_cell(csize)
else:
if debug:
logger.info('Applying find defects scheme to identify R1 and R2 for Defect')
if 'FD' 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]
elif Optimizer.structure=='Surface':
if debug:
logger.info('Finding surface top layer')
top,bul=find_top_layer(totalsol,Optimizer.surftopthick)
indiv=top.copy()
individ[0]=top.copy()
bul = Atoms()
elif Optimizer.structure=='Crystal':
if debug:
logger.info('Checking crystal cell type')
celltype = check_cell_type(totalsol)
STR+='Cell structure = {0}\n'.format(celltype)
bul = Atoms()
individ[0] = totalsol.copy()
elif Optimizer.structure=='Cluster':
volume = get_cluster_volume(totalsol)
bul = Atoms()
if debug:
logger.info('Translating cluster back to smaller box size location')
totalsol.translate([-Optimizer.large_box_size/2.0,-Optimizer.large_box_size/2.0,-Optimizer.large_box_size/2.0])
totalsol.set_cell(origcell)
individ[0] = totalsol.copy()
# Add concentration energy dependence
if Optimizer.forcing=='energy_bias':
if debug:
logger.info('Applying energy bias for atoms with different number of atoms of type than in atomlist')
n=[0]*len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
n[i]=len([inds for inds in totalsol if inds.symbol==Optimizer.atomlist[i][0]])
n[i]=abs(n[i]-Optimizer.atomlist[i][1])
factor=sum(n)**3
energy=(energy+factor)/totalsol.get_number_of_atoms()
STR+='Energy with Bias = {0}\n'.format(energy)
elif Optimizer.forcing=='chem_pot':
if debug:
logger.info('Applying chemical potential bias for atoms with different number of atoms of type than in atomlist')
n=[0]*len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
n[i]=len([inds for inds in totalsol if inds.symbol==Optimizer.atomlist[i][0]])
n[i]=n[i]*Optimizer.atomlist[i][3]
factor=sum(n)
energy=(energy+factor)/totalsol.get_number_of_atoms()
STR+='Energy with Chemical Potential = {0}\n'.format(energy)
individ.energy=energy
individ.buli=bul
individ.pressure=pressure
individ.volume=volume
if Optimizer.fingerprinting:
if debug:
logger.info('Identifying fingerprint of new structure')
individ.fingerprint=get_fingerprint(Optimizer,individ,Optimizer.fpbin,Optimizer.fpcutoff)
if Optimizer.parallel:
calc.clean()
signal = 'Evaluated individual {0} on {1}\n'.format(individ.index,rank)
signal +=STR
else:
signal=STR
pressure = indiv.get_isotropic_pressure(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 = indiv.get_isotropic_pressure(stress)
volume = 0
na = indiv.get_number_of_atoms()
ena = en / na
energy = en
individ[0] = indiv
bul = 0
STR += 'EnergypAtm = ' + repr(ena) + '\n'
if Optimizer.structure == 'Crystal':
STR += 'Cell structure = ' + repr(check_cell_type(indiv)) + '\n'
# Add concentration energy dependence
if Optimizer.forcing == 'Energy_bias':
n = [0] * len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
n[i] = len([
inds for inds in indiv
if inds.symbol == Optimizer.atomlist[i][0]
])
n[i] = abs(n[i] - Optimizer.atomlist[i][1])
factor = sum(n)**3
energy = (en + factor) / na
elif Optimizer.forcing == 'Chem_pot':
n = [0] * len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
pressure=indiv.get_isotropic_pressure(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=indiv.get_isotropic_pressure(stress)
volume=0
na=indiv.get_number_of_atoms()
ena=en/na
energy=en
individ[0]=indiv
bul=0
STR+='EnergypAtm = '+repr(ena)+'\n'
if Optimizer.structure=='Crystal':
STR+='Cell structure = '+repr(check_cell_type(indiv))+'\n'
# Add concentration energy dependence
if Optimizer.forcing=='Energy_bias':
n=[0]*len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
n[i]=len([inds for inds in indiv if inds.symbol==Optimizer.atomlist[i][0]])
n[i]=abs(n[i]-Optimizer.atomlist[i][1])
factor=sum(n)**3
energy=(en+factor)/na
elif Optimizer.forcing=='Chem_pot':
n=[0]*len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
if Optimizer.structure=='Defect':
n[i]=len([inds for inds in totalsol if inds.symbol==Optimizer.atomlist[i][0]])
else:
