def cell_relax_lammps(indiv, Optimizer):
"""Move function to perform Lammps box/relax for cell. Intended for use in Crystal Optimization
Inputs:
indiv = Individual class object to be altered
Optimizer = Optimizer class object with needed parameters
Outputs:
indiv = Altered Individual class object
"""
if "MU" in Optimizer.debug:
debug = True
else:
debug = False
cwd1 = os.getcwd()
Optimizer.output.write("LAMMPS fix box/relax performed\n")
parameters = copy.deepcopy(Optimizer.calc.parameters)
passflag = True
try:
parameters["mass"][len(parameters["mass"]) - 1] += "\nfix 1 all box/relax iso 0.0 vmax 0.001"
except KeyError:
try:
parameters["pair_coeff"][0] += "\nfix 1 all box/relax iso 0.0 vmax 0.001"
except KeyError:
print "WARNING: LAMMPS Cell relax move trouble with potential. SKIPPING"
Optimizer.output.write(
"WARNING: Minimizer quit. LAMMPS Cell relax move trouble with potential - Box relaxation unsuccessful\n"
)
passflag = False
if passflag:
filesL = [Optimizer.pot_file]
if Optimizer.lammps_keep_files:
rank = 0
path = os.path.join(os.getcwd(), "{0}-rank{1}".format(Optimizer.filename, rank))
if not os.path.exists(os.path.join(path, "LAMMPSFiles")):
os.mkdir(os.path.join(path, "LAMMPSFiles"))
real_rank = MPI.COMM_WORLD.Get_rank()
tmpdir = os.path.join(os.path.join(path, "LAMMPSFiles"), "rank-{0}".format(real_rank))
# calc2 = LAMMPS(parameters=parameters, files=filesL,keep_tmp_files=True, tmp_dir=os.getcwd()+'/'+Optimizer.filename+'/Lammpsrun2/')
calc2 = LAMMPS(parameters=parameters, files=filesL, keep_tmp_files=True, tmp_dir=tmpdir)
else:
calc2 = LAMMPS(parameters=parameters, files=filesL)
atmsdup = indiv[0].copy()
atmsdup.set_calculator(calc2)
try:
OUT = atmsdup.calc.calculate(atmsdup)
indiv[0].set_cell(OUT["atoms"].get_cell())
indiv[0].set_positions(OUT["atoms"].get_positions())
Optimizer.output.write("Energy = " + repr(OUT["thermo"][-1]["pe"] / indiv[0].get_number_of_atoms()) + "\n")
except:
Optimizer.output.write("WARNING: Minimizer quit - Box relaxation unsuccessful\n")
# pdb.set_trace()
os.chdir(cwd1)
calc2.clean()
Optimizer.output.write(repr(indiv[0].get_cell()) + "\n")
muttype = "LBR"
if indiv.energy == 0:
indiv.history_index = indiv.history_index + "m" + muttype
else:
indiv.history_index = repr(indiv.index) + "m" + muttype
return indiv
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':
# logger.info('M:')
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()
#print 'rank, eval_energy.cell',rank,origcell
if Optimizer.forcing != 'RelaxBox':
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])
# logger.info('M: set cell')
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')
# logger.info('M:check dist')
totalsol, STR = check_min_dist(Optimizer, 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:
# logger.info('M:start calculator')
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, pea, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, Optimizer.fixed_region, Optimizer.fitness_scheme, STR, Optimizer.static_calc)
else:
# logger.info('M:start run_energy_eval')
totalsol, pea, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, False, Optimizer.fitness_scheme, STR)
logger.info('M:finish run_energy_eval, energy = {0} @ rank ={1}'.format(energy,rank))
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')
if Optimizer.forcing != 'RelaxBox':
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
#Add pealist to include atom index based on sorted PE.
logger.info('before sort{0}'.format(individ.energy))
sort_pealist(Optimizer,individ,pea)
energy = individ.energy
logger.info('after sort {0}'.format(individ.energy))
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 cell_relax_lammps(indiv, Optimizer):
"""Move function to perform Lammps box/relax for cell. Intended for use in Crystal Optimization
Inputs:
indiv = Individual class object to be altered
Optimizer = Optimizer class object with needed parameters
Outputs:
indiv = Altered Individual class object
"""
if 'MU' in Optimizer.debug:
debug = True
else:
debug = False
cwd1 = os.getcwd()
Optimizer.output.write('LAMMPS fix box/relax performed\n')
parameters = copy.deepcopy(Optimizer.calc.parameters)
passflag = True
try:
parameters['mass'][len(parameters['mass']) -
1] += '\nfix 1 all box/relax iso 0.0 vmax 0.001'
except KeyError:
try:
parameters['pair_coeff'][
0] += '\nfix 1 all box/relax iso 0.0 vmax 0.001'
except KeyError:
print 'WARNING: LAMMPS Cell relax move trouble with potential. SKIPPING'
Optimizer.output.write(
'WARNING: Minimizer quit. LAMMPS Cell relax move trouble with potential - Box relaxation unsuccessful\n'
)
passflag = False
if passflag:
filesL = [Optimizer.pot_file]
if Optimizer.lammps_keep_files:
rank = 0
path = os.path.join(os.getcwd(),
'{0}-rank{1}'.format(Optimizer.filename, rank))
if not os.path.exists(os.path.join(path, 'LAMMPSFiles')):
os.mkdir(os.path.join(path, 'LAMMPSFiles'))
real_rank = MPI.COMM_WORLD.Get_rank()
tmpdir = os.path.join(os.path.join(path, 'LAMMPSFiles'),
'rank-{0}'.format(real_rank))
# calc2 = LAMMPS(parameters=parameters, files=filesL,keep_tmp_files=True, tmp_dir=os.getcwd()+'/'+Optimizer.filename+'/Lammpsrun2/')
calc2 = LAMMPS(parameters=parameters,
files=filesL,
keep_tmp_files=True,
tmp_dir=tmpdir)
else:
calc2 = LAMMPS(parameters=parameters, files=filesL)
atmsdup = indiv[0].copy()
atmsdup.set_calculator(calc2)
try:
OUT = atmsdup.calc.calculate(atmsdup)
indiv[0].set_cell(OUT['atoms'].get_cell())
indiv[0].set_positions(OUT['atoms'].get_positions())
Optimizer.output.write('Energy = ' +
repr(OUT['thermo'][-1]['pe'] /
indiv[0].get_number_of_atoms()) + '\n')
except:
Optimizer.output.write(
'WARNING: Minimizer quit - Box relaxation unsuccessful\n')
#pdb.set_trace()
os.chdir(cwd1)
calc2.clean()
Optimizer.output.write(repr(indiv[0].get_cell()) + '\n')
muttype = 'LBR'
if indiv.energy == 0:
indiv.history_index = indiv.history_index + 'm' + muttype
else:
indiv.history_index = repr(indiv.index) + 'm' + muttype
return indiv
def cell_shape(indiv, Optimizer):
"""Move function to forcefully alter the unit cell shape
Inputs:
indiv = Individual class object to be altered
Optimizer = Optimizer class object with needed parameters
Outputs:
indiv = Altered Individual class object
"""
if 'MU' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write('Cell Shape change mutation\n')
Optimizer.output.write('Index = '+repr(indiv.index)+'\n')
structure=random.choice(Optimizer.cell_shape_options)
cello=indiv[0].get_cell()
if structure=='cubic':
#Set to cubic shape
an,bn,cn = [numpy.linalg.norm(v) for v in cello]
a=(an+bn+cn)/3.0
celln=numpy.array([[a,0,0],[0,a,0],[0,0,a]])
Optimizer.output.write('Mutating to cubic\n')
muttype='CSC'
elif structure=='hexagonal':
#Set to hexagonal shape
an,bn,cn = [numpy.linalg.norm(v) for v in cello]
a=(an+bn)/2.0
c=cn
if c<=a:
c=random.uniform(a+1,10)
trans=numpy.array([[1,0,0],[-0.5,(3.0**0.5)/2.0,0],[0,0,1]])
trans[0]=[a*i for i in trans[0]]
trans[1]=[a*i for i in trans[1]]
trans[2]=[c*i for i in trans[2]]
celln=trans
Optimizer.output.write('Mutating to Hexagonal\n')
muttype='CSH'
elif structure=='tetragonal':
#Set to tetragonal shape
an,bn,cn = [numpy.linalg.norm(v) for v in cello]
a=(an+bn)/2.0
c=cn
if c==a:
c=random.uniform(1,10)
celln=numpy.array([[a,0,0],[0,a,0],[0,0,c]])
Optimizer.output.write('Mutating to tetragonal\n')
muttype='CSTe'
elif structure=='orthorhombic':
#Set to orthorhombic
a=random.uniform(2,10)
b=random.uniform(2,10)
c=random.uniform(2,10)
celln=numpy.array([[a,0,0],[0,b,0],[0,0,c]])
Optimizer.output.write('Mutating to orthorhombic\n')
muttype='CSO'
elif structure=='monoclinic':
#Set to monoclinic
a,b,c = [numpy.linalg.norm(v) for v in cello]
if a==b:
b=random.uniform(1,10)
trans=numpy.array([(1+random.random())*c, 0, (1+random.random())*c])
celln=numpy.array([[a,0,0],[0,b,0],[0,0,0]])
celln[2]=trans
Optimizer.output.write('Mutating to monoclinic\n')
muttype='CSM'
elif structure=='triclinic':
#Set to triclinic
a,b,c = [numpy.linalg.norm(v) for v in cello]
celln=numpy.array([[a,0,0],[(1+random.random())*b,(1+random.random())*b,0],[(1+random.random())*c,0,(1+random.random())*c]])
Optimizer.output.write('Mutating to triclinic\n')
muttype='CSTr'
indiv[0].set_cell(celln)
#Relax new box shape with Lammps box/reax for cell
Optimizer.output.write('LAMMPS fix box/relax performed\n')
cwd1=os.getcwd()
parameters=copy.deepcopy(Optimizer.calc.parameters)
try:
parameters['mass'][len(parameters['mass'])-1] += '\nfix 1 all box/relax iso 0.0 vmax 0.001'
except KeyError:
parameters['pair_coeff'][0] += '\nfix 1 all box/relax iso 0.0 vmax 0.001'
filesL = [ Optimizer.pot_file ]
if Optimizer.lammps_keep_files:
calc2 = LAMMPS(parameters=parameters, files=filesL,keep_tmp_files=True, tmp_dir=os.getcwd()+'/'+Optimizer.filename+'/Lammpsrun2/')
else:
calc2 = LAMMPS(parameters=parameters, files=filesL)
atmsdup=indiv[0].copy()
atmsdup.set_calculator(calc2)
try:
OUT=atmsdup.calc.calculate(atmsdup)
indiv[0].set_cell(OUT['atoms'].get_cell())
indiv[0].set_positions(OUT['atoms'].get_positions())
Optimizer.output.write('Energy = '+repr(OUT['thermo'][-1]['pe']/indiv[0].get_number_of_atoms())+'\n')
except:
Optimizer.output.write('WARNING: Minimizer quit - Box relaxation unsuccessful\n')
#pdb.set_trace()
os.chdir(cwd1)
calc2.clean()
Optimizer.output.write(repr(indiv[0].get_cell())+'\n')
if indiv.energy==0:
indiv.history_index=indiv.history_index+'m'+muttype
else:
indiv.history_index=repr(indiv.index)+'m'+muttype
return indiv
