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 setup_fixed_region_calculator(Optimizer):
"""Function to set up a fixed region calculator for use with LAMMPS and ASE
"""
calc = self.calc
pms = copy.deepcopy(calc.parameters)
nat = sum([c for sym, c, m, mu in self.atomlist])
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'
ncalc = LAMMPS(parameters=pms,
files=calc.files,
keep_tmp_files=calc.keep_tmp_files,
tmp_dir=calc.tmp_dir)
return ncalc
from MAST.structopt_stem.io.read_xyz import read_xyz
from MAST.structopt_stem.io.write_xyz import write_xyz
from ase import Atom,Atoms
from MAST.structopt_stem.tools.lammps import LAMMPS
import os
# 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
def setup_calculator(Optimizer):
"""
Subprogram to set up the ASE style calculator for a system
Input:
Optimizer = Optimizer class object with parameters for setting up calculator
Output:
calc = ASE Calculator object for running a calculation
"""
if 'SetCalc' in Optimizer.debug:
debug = True
#logger = initialize_logger(Optimizer.loggername)
logger = logging.getLogger(Optimizer.loggername)
else:
debug = False
atomlist = Optimizer.atomlist
#atomlist=sorted(atomlist,key=lambda symbol: symbol[0])
if Optimizer.calc_method == 'VASP':
if debug:
logger.info('Setting up vasp calculator = {0}'.format(
Optimizer.vaspcalc))
calc = eval(Optimizer.vaspcalc)
elif 'MAST' in Optimizer.calc_method:
if debug:
logger.info('Setting up dummy calculator for MAST')
calc = LennardJones()
elif Optimizer.calc_method == 'LennardJones':
if debug:
logger.info('Setting up Lennard Jones calculator from ASE')
calc = LennardJones()
else:
if Optimizer.pair_style == 'tersoff':
if debug:
logger.info(
'Setting up LAMMPS calculator with Tersoff potential')
parcoff = '* * {0}'.format(Optimizer.pot_file)
for one in atomlist:
parcoff += ' {0}'.format(one[0])
pair_coeff = [parcoff]
mass = ['1 {0}'.format(atomlist[0][2])]
if len(atomlist) > 1:
for i in range(len(atomlist) - 1):
mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2]))
parameters = { 'pair_style' : Optimizer.pair_style, \
'pair_coeff' : pair_coeff , 'mass' : mass }
filesL = [Optimizer.pot_file]
elif Optimizer.pair_style == 'eam':
if debug:
logger.info('Setting up LAMMPS calculator with EAM potential')
pair_coeff = ['* * {0}'.format(Optimizer.pot_file)]
parameters = {
'pair_style': Optimizer.pair_style,
'pair_coeff': pair_coeff
}
filesL = [Optimizer.pot_file]
elif Optimizer.pair_style == 'eam/fs' or Optimizer.pair_style == 'eam/alloy':
if debug:
logger.info(
'Setting up LAMMPS calculator with EAM/FS , EAM/ALLOY potential'
)
parcoff = '* * {0}'.format(Optimizer.pot_file)
for one in atomlist:
parcoff += ' {0}'.format(one[0])
pair_coeff = [parcoff]
mass = ['1 {0}'.format(atomlist[0][2])]
if len(atomlist) > 1:
for i in range(len(atomlist) - 1):
mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2]))
parameters = {
'pair_style': Optimizer.pair_style,
'pair_coeff': pair_coeff,
'mass': mass
}
filesL = [Optimizer.pot_file]
elif Optimizer.pair_style == 'eam/cd':
if debug:
logger.info(
'Setting up LAMMPS calculator with EAM/CD potential')
parcoff = '* * {0}'.format(Optimizer.pot_file)
for one in atomlist:
parcoff += ' {0}'.format(one[0])
pair_coeff = [parcoff]
parameters = {
'pair_style': Optimizer.pair_style,
'pair_coeff': pair_coeff
}
filesL = [Optimizer.pot_file]
elif Optimizer.pair_style == 'edip':
if debug:
logger.info('Setting up LAMMPS calculator with EDIP potential')
parcoff = '* * {0}'.format(Optimizer.pot_file)
for one in atomlist:
parcoff += ' {0}'.format(one[0])
pair_coeff = [parcoff]
mass = ['1 {0}'.format(atomlist[0][2])]
if len(atomlist) > 1:
for i in range(len(atomlist) - 1):
mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2]))
parameters = { 'pair_style' : Optimizer.pair_style, \
'pair_coeff' : pair_coeff , 'mass' : mass, 'newton': 'on' }
filesL = [Optimizer.pot_file]
elif Optimizer.pair_style == 'bop':
if debug:
logger.info('Setting up LAMMPS calculator with BOP potential')
parcoff = '* * {0}'.format(Optimizer.pot_file)
for one in atomlist:
parcoff += ' {0}'.format(one[0])
parcoff += '\ncommunicate single cutoff {0}'.format(
Optimizer.bopcutoff)
pair_coeff = [parcoff]
mass = ['1 {0}'.format(atomlist[0][2])]
if len(atomlist) > 1:
for i in range(len(atomlist) - 1):
mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2]))
parameters = { 'pair_style' : Optimizer.pair_style, \
'pair_coeff' : pair_coeff, 'mass' : mass, 'newton': 'on' }
filesL = [Optimizer.pot_file]
elif Optimizer.pair_style == 'buck':
if debug:
logger.info(
'Setting up LAMMPS calculator with Buckingham potential')
pairstyle = '{0} {1}'.format(Optimizer.pair_style,
Optimizer.buckcutoff)
pair_coeff = Optimizer.buckparameters
mass = ['1 {0}'.format(atomlist[0][2])]
if len(atomlist) > 1:
for i in range(len(atomlist) - 1):
mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2]))
parameters = {'pair_style': pairstyle, 'pair_coeff': pair_coeff, \
'mass' : mass }
filesL = None
## ZS
elif 'lj' in Optimizer.pair_style:
if debug:
logger.info(
'Setting up LAMMPS calculator with Lennard Jones potential'
)
pairstyle = Optimizer.pair_style
pair_coeff = [Optimizer.pair_coeff]
mass = ['1 {0}'.format(atomlist[0][2])]
if len(atomlist) > 1:
for i in range(len(atomlist) - 1):
mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2]))
parameters = { 'pair_style' : Optimizer.pair_style, \
'pair_coeff' : pair_coeff, 'mass' : mass}
filesL = None
elif Optimizer.pair_style == 'other':
"""WARNING: This style still needs work. Intended to allow user flexibility with potential specification"""
if debug:
logger.info(
'Setting up LAMMPS calculator with user input potential')
mass = ['1 {0}'.format(atomlist[0][2])]
if len(atomlist) > 1:
for i in range(len(atomlist) - 1):
mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2]))
if Optimizer.ps_other != None:
logger.info(
'Setting up LAMMPS calculator with EAM/FS , EAM/ALLOY potential'
)
if 'newton' in Optimizer.ps_other:
parameters = {'pair_style' : Optimizer.ps_name, \
'pair_coeff': [Optimizer.pair_coeff], 'mass': mass,'newton':'on'}
else:
parameters = {'pair_style' : Optimizer.ps_name, \
'pair_coeff': [Optimizer.pair_coeff], 'mass': mass,'newton':'off'}
if 'charges' in Optimizer.ps_other:
cs = Optimizer.ps_other.split('charges:')
parameters['mass'][len(parameters['mass']) - 1] += cs[1]
parameters['newton'] += '\natom_style charge'
else:
parameters = {'pair_style' : Optimizer.ps_name, \
'pair_coeff': Optimizer.pair_coeff, 'mass': mass}
if Optimizer.pot_file != None:
filesL = Optimizer.pot_file
else:
filesL = None
else:
if debug:
logger.warn(
'No LAMMPS potential recognized. Setting up LAMMPS calculator with Lennard Jones potential'
)
parameters = {}
filesL = None
print 'WARNING: No LAMMPS potential recognized. Assuming Lennard Jones Potential'
if Optimizer.lammps_min != None:
if debug:
logger.info(
'Adding local energy minimizer to LAMMPS calculator')
try:
parameters['mass'][len(parameters['mass']) -
1] += '\nmin_style {0}'.format(
Optimizer.lammps_min_style)
except KeyError:
parameters['pair_coeff'][0] += '\nmin_style {0}'.format(
Optimizer.lammps_min_style)
parameters['minimize'] = Optimizer.lammps_min
parameters['thermosteps'] = Optimizer.lammps_thermo_steps
if Optimizer.lammps_command != None:
parameters['lammps_command'] = Optimizer.lammps_command
if Optimizer.lammps_keep_files:
if debug:
logger.info('Setting up directory for keeping LAMMPS files')
try:
rank = MPI.COMM_WORLD.Get_rank()
if Optimizer.parallel:
if 'Island_Method' not in Optimizer.algorithm_type:
real_rank = MPI.COMM_WORLD.Get_rank()
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'))
logger.info('Making directory: {0}'.format(
os.path.join(path, 'LAMMPSFiles')))
except:
rank = 0
if filesL != None:
path = os.path.join(
os.getcwd(), '{0}-rank{1}'.format(Optimizer.filename,
rank))
if Optimizer.parallel and ('Island_Method'
not in Optimizer.algorithm_type):
tmpdir = os.path.join(os.path.join(path, 'LAMMPSFiles'),
'rank-{0}'.format(real_rank))
calc = LAMMPS(parameters=parameters, files=filesL, \
keep_tmp_files=True, tmp_dir=tmpdir)
else:
calc = LAMMPS(parameters=parameters, files=filesL, \
keep_tmp_files=True, tmp_dir=os.path.join(path, 'LAMMPSFiles'))
else:
path = os.path.join(
os.getcwd(), '{0}-rank{1}'.format(Optimizer.filename,
rank))
# calc = LAMMPS(parameters=parameters, keep_tmp_files=True, \
# tmp_dir=os.path.join(path,'LAMMPSFiles'))
if Optimizer.parallel and ('Island_Method'
not in Optimizer.algorithm_type):
tmpdir = os.path.join(os.path.join(path, 'LAMMPSFiles'),
'rank-{0}'.format(real_rank))
calc = LAMMPS(parameters=parameters, \
keep_tmp_files=True, tmp_dir=tmpdir)
else:
calc = LAMMPS(parameters=parameters, \
keep_tmp_files=True, tmp_dir=os.path.join(path, 'LAMMPSFiles'))
else:
if filesL != None:
calc = LAMMPS(parameters=parameters, files=filesL)
else:
calc = LAMMPS(parameters=parameters)
return calc
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_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
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:
from MAST.structopt_stem.tools.lammps import LAMMPS
# Set up calculator
parcoff = '* * SiC.edip C Si'
pair_coeff = [parcoff]
mass = ['1 12.011', '2 28.0855']
parameters = {
'pair_style': 'edip',
'pair_coeff': pair_coeff,
'mass': mass,
'newton': 'on'
}
mincomd = '1e-8 1e-8 5000 10000'
parameters['minimize'] = mincomd
filesL = ['SiC.edip']
calc = LAMMPS(parameters=parameters, files=filesL)
# Read File
structure = read_xyz('indiv00.xyz', -1)
# Calculate Energy
structure.set_cell([13.092, 13.092, 13.092])
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('re-relaxed.xyz', totalsol, repr(en))
fe = en