def vasp_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA',
isif=7,
nsw=5,
ibrion=1,
ediffg=-1e-3,
lwave=False,
lcharg=False)
calc.calculate(Al)
# Explicitly parse atomic position output file from Vasp
CONTCAR_Al = io.read('CONTCAR', format='vasp')
print('Stress after relaxation:\n', calc.read_stress())
print('Al cell post relaxation from calc:\n',
calc.get_atoms().get_cell())
print('Al cell post relaxation from atoms:\n', Al.get_cell())
print('Al cell post relaxation from CONTCAR:\n', CONTCAR_Al.get_cell())
# All the cells should be the same.
assert (calc.get_atoms().get_cell() == CONTCAR_Al.get_cell()).all()
assert (Al.get_cell() == CONTCAR_Al.get_cell()).all()
return Al
def run_energy_eval(totalsol, calc_method='LAMMPS', fx_region=False, fit_scheme='totalenfit', STR='', static_calc=None):
if calc_method=='VASP':
en=totalsol.get_potential_energy()
calcb=Vasp(restart=True)
totalsol=calcb.get_atoms()
stress=calcb.read_stress()
else:
totcop = totalsol.copy()
OUT = totalsol.calc.calculate(totalsol)
totalsol = OUT['atoms']
pea = OUT['pea']
# M: test
# if MPI.COMM_WORLD.Get_rank() == 0:
# for i in range(len(totalsol)) :
# print i,totalsol[i].symbol,totalsol[i].position, pea[i]
totalsol.set_pbc(True)
if fx_region:
STR+='Energy of fixed region calc = {0}\n'.format(OUT['thermo'][-1]['pe'])
totalsol.set_calculator(static_calc)
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
STR+='Energy of static calc = {0}\n'.format(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)
if fit_scheme == 'enthalpyfit':
pressure = totalsol.get_isotropic_pressure(stress)
else:
pressure = 0
volume = totalsol.get_volume()
energy=en
STR+='Energy per atom = {0}\n'.format(energy/len(totalsol))
return totalsol, pea, energy, pressure, volume, STR
def run_energy_eval(totalsol, calc_method='LAMMPS', fx_region=False, fit_scheme='totalenfit', STR='', static_calc=None):
if calc_method=='VASP':
en=totalsol.get_potential_energy()
calcb=Vasp(restart=True)
totalsol=calcb.get_atoms()
stress=calcb.read_stress()
else:
totcop = totalsol.copy()
OUT = totalsol.calc.calculate(totalsol)
totalsol = OUT['atoms']
totalsol.set_pbc(True)
if fx_region:
STR+='Energy of fixed region calc = {0}\n'.format(OUT['thermo'][-1]['pe'])
totalsol.set_calculator(static_calc)
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
STR+='Energy of static calc = {0}\n'.format(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)
if fit_scheme == 'enthalpyfit':
pressure = totalsol.get_isotropic_pressure(stress)
else:
pressure = 0
volume = totalsol.get_volume()
energy=en
STR+='Energy per atom = {0}\n'.format(energy/len(totalsol))
return totalsol, energy, pressure, volume, STR
def defect_strain_matrices(label,conc,Latt):
from ase.calculators.vasp import Vasp
calc = Vasp(restart=1)
atoms = calc.get_atoms()
LattDef = numpy.array(atoms.get_cell())
# LattDef = correct_lattice_matrix(numpy.array(atoms.get_cell()))
dstrain = (1/conc)*numpy.dot(numpy.subtract(LattDef,Latt),numpy.linalg.inv(Latt))
dstrain_vec = asetools.tensorise(dstrain)
outfile = 'defect_strain.txt'
fout = open(outfile,'w')
print>>fout, label
print>>fout, "concentration {:^10}".format(conc)
print>>fout, "defect strain matrix"
for item in dstrain:
print>>fout, ' '.join(map(str, item))
print>>fout, "defect strain vector"
for item in dstrain_vec:
print>>fout, item
print>>fout, "Defect supercell lattice"
for item in LattDef:
print>>fout, ' '.join(map(str, item))
print>>fout, "Perfect supercell lattice"
for item in Latt:
print>>fout, ' '.join(map(str, item))
fout.close
def test_vasp_co():
"""
Run some VASP tests to ensure that the VASP calculator works. This
is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables
"""
from ase.test.vasp import installed
assert installed()
from ase import Atoms
from ase.io import write
from ase.calculators.vasp import Vasp
import numpy as np
def array_almost_equal(a1, a2, tol=np.finfo(type(1.0)).eps):
"""Replacement for old numpy.testing.utils.array_almost_equal."""
return (np.abs(a1 - a2) < tol).all()
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='PBE',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False)
co.calc = calc
en = co.get_potential_energy()
write('vasp_co.traj', co)
assert abs(en + 14.918933) < 5e-3
# Secondly, check that restart from the previously created VASP output works
calc2 = Vasp(restart=True)
co2 = calc2.get_atoms()
# Need tolerance of 1e-14 because VASP itself changes coordinates
# slightly between reading POSCAR and writing CONTCAR even if no ionic
# steps are made.
assert array_almost_equal(co.positions, co2.positions, 1e-14)
assert en - co2.get_potential_energy() == 0.
assert array_almost_equal(calc.get_stress(co), calc2.get_stress(co2))
assert array_almost_equal(calc.get_forces(co), calc2.get_forces(co2))
assert array_almost_equal(calc.get_eigenvalues(), calc2.get_eigenvalues())
assert calc.get_number_of_bands() == calc2.get_number_of_bands()
assert calc.get_xc_functional() == calc2.get_xc_functional()
# Cleanup
calc.clean()
def calc_defect_strain_matrix(Latt): from ase.calculators.vasp import Vasp # defect lattice calc = Vasp(restart=1) atoms = calc.get_atoms() LattDef = numpy.array(atoms.get_cell()) dstrain = conc*numpy.dot(numpy.subtract(LattDef,Latt.T),numpy.linalg.inv(Latt.T)) dstrain=asetools.symmetrize(dstrain) return dstrain
def get_locpot_array(file): """ Returns the charge densities on the fine FFT-grid in a numpy array.""" from ase.calculators.vasp import VaspChargeDensity from ase.calculators.vasp import Vasp calc = Vasp(restart=True) cell = calc.get_atoms() vol = cell.get_volume() pot_array = numpy.vstack((VaspChargeDensity(file)).chg) numpy.divide(pot_array,vol) return pot_array
def vasp_vol_relax():
Al = bulk("Al", "fcc", a=4.5, cubic=True)
calc = Vasp(xc="LDA", isif=7, nsw=5, ibrion=1, ediffg=-1e-3, lwave=False, lcharg=False)
calc.calculate(Al)
# Explicitly parse atomic position output file from Vasp
CONTCAR_Al = io.read("CONTCAR", format="vasp")
print("Stress after relaxation:\n", calc.read_stress())
print("Al cell post relaxation from calc:\n", calc.get_atoms().get_cell())
print("Al cell post relaxation from atoms:\n", Al.get_cell())
print("Al cell post relaxation from CONTCAR:\n", CONTCAR_Al.get_cell())
# All the cells should be the same.
assert (calc.get_atoms().get_cell() == CONTCAR_Al.get_cell()).all()
assert (Al.get_cell() == CONTCAR_Al.get_cell()).all()
return Al
def vasp_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA', isif=7, nsw=5,
ibrion=1, ediffg=-1e-3, lwave=False, lcharg=False)
calc.calculate(Al)
# Explicitly parse atomic position output file from Vasp
CONTCAR_Al = io.read('CONTCAR', format='vasp')
print 'Stress after relaxation:\n', calc.read_stress()
print 'Al cell post relaxation from calc:\n', calc.get_atoms().get_cell()
print 'Al cell post relaxation from atoms:\n', Al.get_cell()
print 'Al cell post relaxation from CONTCAR:\n', CONTCAR_Al.get_cell()
# All the cells should be the same.
assert (calc.get_atoms().get_cell() == CONTCAR_Al.get_cell()).all()
assert (Al.get_cell() == CONTCAR_Al.get_cell()).all()
return Al
def ase_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA')
Al.set_calculator(calc)
from ase.constraints import StrainFilter
sf = StrainFilter(Al)
qn = QuasiNewton(sf, logfile='relaxation.log')
qn.run(fmax=0.1, steps=5)
print 'Stress:\n', calc.read_stress()
print 'Al post ASE volume relaxation\n', calc.get_atoms().get_cell()
return Al
def ase_vol_relax():
Al = bulk('Al', 'fcc', a=4.5, cubic=True)
calc = Vasp(xc='LDA')
Al.calc = calc
from ase.constraints import StrainFilter
sf = StrainFilter(Al)
qn = QuasiNewton(sf, logfile='relaxation.log')
qn.run(fmax=0.1, steps=5)
print('Stress:\n', calc.read_stress())
print('Al post ASE volume relaxation\n', calc.get_atoms().get_cell())
return Al
def ase_vol_relax():
Al = bulk("Al", "fcc", a=4.5, cubic=True)
calc = Vasp(xc="LDA")
Al.set_calculator(calc)
from ase.constraints import StrainFilter
sf = StrainFilter(Al)
qn = QuasiNewton(sf, logfile="relaxation.log")
qn.run(fmax=0.1, steps=5)
print("Stress:\n", calc.read_stress())
print("Al post ASE volume relaxation\n", calc.get_atoms().get_cell())
return Al
def setup_dvol_corrections_evq(self):
from ase.calculators.vasp import Vasp
calc = Vasp(restart=True)
atoms = calc.get_atoms()
cell = atoms.get_cell()
#Create small and large lattice matrices
small = cell*0.99
large = cell*1.01
# Setup the large and small POSCAR files
atoms.set_cell(small, scale_atoms=True)
ase.io.write('POSCAR99pc',atoms,format='vasp', direct=1)
atoms.set_cell(large, scale_atoms=True)
ase.io.write('POSCAR101pc',atoms,format='vasp', direct=1
)
# copy the basic VASP files to the new directories
directories = ['0x99pc','1x00pc','1x01pc']
files = ['KPOINTS','POTCAR','WAVECAR','CHGCAR']
for dir in directories:
if not os.path.exists(dir):
os.makedirs(dir)
for file in files:
if os.path.exists(file):
shutil.copy(file,dir)
# copy the new POSCAR files to the new directories
shutil.copy('POSCAR','1x00pc')
shutil.copy('POSCAR99pc','0x99pc/POSCAR')
shutil.copy('POSCAR101pc','1x01pc/POSCAR')
# Edit INCAR to create a single point calculations, and save in new directories
EVQ_INCAR = 'INCAR_EVQ'
bad_words = ['NSW', 'LVTOT', 'NELM ', 'ISTART', 'ICHARG']
with open('INCAR') as oldfile, open(EVQ_INCAR, 'w') as newfile:
for line in oldfile:
if not any(bad_word in line for bad_word in bad_words):
newfile.write(line)
newfile.write('ISTART = 0\nICHARGE = 2\nNSW = 0\nLVTOT = .TRUE.\nNELM = 60\n')
# Save the new INCAR in directories
shutil.copy(EVQ_INCAR,'1x00pc/INCAR')
shutil.copy(EVQ_INCAR,'0x99pc/INCAR')
shutil.copy(EVQ_INCAR,'1x01pc/INCAR')
def ase_run_vasp(mol, calc, job_dir, init_only=False):
"""
This is used to set a vasp calculation in an ASE-based script
mode = 0: only create input files needed to run a vasp calculation
mode
"""
wdir = os.getcwd()
if init_only:
if not os.path.isdir(job_dir):
os.mkdir(job_dir)
os.chdir(job_dir)
mol.set_calculator(calc)
calc.initialize(mol)
calc.write_input(mol)
os.chdir(wdir)
return 0.0
if not os.path.isdir(job_dir):
os.mkdir(job_dir)
os.chdir(job_dir)
mol.set_calculator(calc)
else:
os.chdir(job_dir)
calc = Vasp(restart=True)
mol = calc.get_atoms()
try:
ene = mol.get_potential_energy()
except:
print "ERROR: Fail when running vasp in " + job_dir
os.system("touch ERROR")
ene = 0.0
os.chdir(wdir)
return ene
def output_cell_params():
import fnmatch
from ase.calculators.vasp import Vasp
outfile = 'cell_params.txt'
fout = open(outfile,'w')
prelim_matches = []
matches = []
for root, dirnames, filenames in os.walk('.'):
for filename in fnmatch.filter(filenames, 'OUTCAR'):
prelim_matches.append(os.path.abspath(root))
for dir in prelim_matches:
if os.path.isfile(os.path.join(dir,"CONTCAR")):
matches.append(dir)
for dir in matches:
os.chdir(dir)
label = os.path.abspath(".")
print>>fout, label
print>>fout, "{:<14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ".format('volume','a','b','c','alpha','beta','gamma')
calc = Vasp(restart=1)
atoms = calc.get_atoms()
params = asetools.cellparam(atoms)
volume = atoms.get_volume()
print>>fout, "{:<14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ".format(volume,params[0],params[1],params[2],params[3],params[4],params[5])
fout.close
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:
if Optimizer.calc_method=='VASP':
en=totalsol.get_potential_energy()
calcb=Vasp(restart=True)
totalsol=calcb.get_atoms()
stress=calcb.read_stress()
else:
OUT=indiv.calc.calculate(indiv)
en=OUT['thermo'][-1]['pe']
#indiv.set_positions(OUT['atoms'].get_positions())
#indiv.set_cell(OUT['atoms'].get_cell())
indiv=OUT['atoms']
indiv.set_pbc(True)
stress=numpy.array([OUT['thermo'][-1][i] for i in ('pxx','pyy','pzz','pyz','pxz','pxy')])*(-1e-4*GPa)
if Optimizer.fitness_scheme == 'enthalpyfit':
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]
#!/usr/bin/env python
import os
from ase.io import read, write
from ase.calculators.vasp import Vasp
import sys
try:
tar = sys.argv[1]
except IndexError:
print "please give the name of the folder"
exit()
if os.path.isfile('fin.traj'):
calc = Vasp(restart=True)
p = calc.get_atoms()
p.set_initial_magnetic_moments(p.get_magnetic_moments())
write('fin.traj', p)
os.system('vfin.pl ' + str(tar))
os.system('cp init.traj fin.traj ' + str(tar))
os.system('cp ' + str(tar) + '/fe.dat .')
os.system('rm init.traj')
else:
os.system('vfin.pl ' + str(tar))
os.system('cp init.traj ' + str(tar))
ptmp = read(str(tar) + '/CONTCAR')
pini = read(str(tar) + '/init.traj')
mag = pini.get_initial_magnetic_moments()
ptmp.set_initial_magnetic_moments(mag)
write('init.traj', ptmp)
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:
if Optimizer.calc_method == 'VASP':
en = totalsol.get_potential_energy()
calcb = Vasp(restart=True)
totalsol = calcb.get_atoms()
stress = calcb.read_stress()
else:
OUT = indiv.calc.calculate(indiv)
en = OUT['thermo'][-1]['pe']
#indiv.set_positions(OUT['atoms'].get_positions())
#indiv.set_cell(OUT['atoms'].get_cell())
indiv = OUT['atoms']
indiv.set_pbc(True)
stress = numpy.array([
OUT['thermo'][-1][i]
for i in ('pxx', 'pyy', 'pzz', 'pyz', 'pxz', 'pxy')
]) * (-1e-4 * GPa)
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure = indiv.get_isotropic_pressure(stress)
cell_max = numpy.maximum.reduce(indiv.get_positions())
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:
prec = 'Low',
algo = 'Fast',
ismear= 0,
sigma = 1.,
istart = 0,
lwave = False,
lcharg = False)
co.set_calculator(calc)
en = co.get_potential_energy()
assert abs(en + 14.918933) < 1e-4
# Secondly, check that restart from the previously created VASP output works
calc2 = Vasp(restart=True)
co2 = calc2.get_atoms()
# Need tolerance of 1e-14 because VASP itself changes coordinates
# slightly between reading POSCAR and writing CONTCAR even if no ionic
# steps are made.
assert array_almost_equal(co.positions, co2.positions, 1e-14)
assert en - co2.get_potential_energy() == 0.
assert array_almost_equal(calc.get_stress(co), calc2.get_stress(co2))
assert array_almost_equal(calc.get_forces(co), calc2.get_forces(co2))
assert array_almost_equal(calc.get_eigenvalues(), calc2.get_eigenvalues())
assert calc.get_number_of_bands() == calc2.get_number_of_bands()
assert calc.get_xc_functional() == calc2.get_xc_functional()
# Cleanup
calc.clean()
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False)
co.set_calculator(calc)
en = co.get_potential_energy()
assert abs(en + 14.918933) < 1e-4
# Secondly, check that restart from the previously created VASP output works
calc2 = Vasp(restart=True)
co2 = calc2.get_atoms()
# Need tolerance of 1e-14 because VASP itself changes coordinates
# slightly between reading POSCAR and writing CONTCAR even if no ionic
# steps are made.
assert array_almost_equal(co.positions, co2.positions, 1e-14)
assert en - co2.get_potential_energy() == 0.
assert array_almost_equal(calc.get_stress(co), calc2.get_stress(co2))
assert array_almost_equal(calc.get_forces(co), calc2.get_forces(co2))
assert array_almost_equal(calc.get_eigenvalues(), calc2.get_eigenvalues())
assert calc.get_number_of_bands() == calc2.get_number_of_bands()
assert calc.get_xc_functional() == calc2.get_xc_functional()
# Cleanup
calc.clean()
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: