def test_precon(N):
a0 = bulk('Cu', cubic=True)
a0 *= (N, N, N)
# perturb the atoms
s = a0.get_scaled_positions()
s[:, 0] *= 0.995
a0.set_scaled_positions(s)
atoms = a0.copy()
atoms.calc = EMT()
# check we get a warning about small system
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
opt = PreconLBFGS(atoms, precon="auto")
if N == 1:
assert len(w) == 1
assert "The system is likely too small" in str(w[-1].message)
else:
assert len(w) == 0
# check we get a warning about bad estimate for mu with big cell
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
opt.run(1e-3)
if N == 1:
assert len(w) == 0
else:
assert len(w) == 1
assert "capping at mu=1.0" in str(w[-1].message)
def relax(atoms):
"""Performs a variable-cell optimization of the Atoms object."""
t1 = time()
# LJ parameters from G. Galassi and D.J. Tildesley,
# "Phase Diagrams of Diatomic Molecules:
# Using the Gibbs Ensemble Monte Carlo Method",
# Molecular Simulations, 13, 11 (1994).
calc = HarmonicPlusLennardJones(epsilon=37.3 * kB, sigma=3.31, rc=12.,
r0=1.12998, k=10.)
atoms.calc = calc
dyn = PreconLBFGS(atoms, variable_cell=True, maxstep=0.2,
use_armijo=True, logfile='opt.log', trajectory='opt.traj')
dyn.run(fmax=3e-2, smax=5e-4, steps=250)
e = atoms.get_potential_energy()
f = atoms.get_forces()
s = atoms.get_stress()
finalize(atoms, energy=e, forces=f, stress=s)
os.system('mv opt.log prev.log')
os.system('mv opt.traj prev.traj')
t2 = time()
print('Relaxation took %.3f seconds.' % (t2 - t1), flush=True)
def g(k, do_abs=True):
print(f'Static minimisation with k={k}, alpha={alpha0}.')
sc.k = k * k1g
sc.alpha = alpha0
sc.variable_alpha = False
sc.variable_k = False
sc.update_atoms()
atoms = sc.atoms.copy()
atoms.calc = sc.calc
atoms.set_constraint(FixAtoms(mask=~sc.regionI))
print('I think it gets to here')
if preconlbfgs:
opt = PreconLBFGS(atoms, logfile=None)
if lbfgs:
opt = LBFGS(atoms, logfile=None)
opt.run(fmax=1e-5)
print('I do not know if it gets to here')
atoms.write(traj, format="extxyz")
sc.set_atoms(atoms)
f_alpha = sc.get_crack_tip_force(mask=mask)
print(
f'Static minimisation with k={k}, alpha={alpha0} --> f_alpha={f_alpha}'
)
if do_abs:
f_alpha = abs(f_alpha)
return f_alpha
def test_precon_amin():
cu0 = bulk("Cu") * (2, 2, 2)
sigma = cu0.get_distance(0, 1) * (2.**(-1. / 6))
lj = LennardJones(sigma=sigma)
# perturb the cell
cell = cu0.get_cell()
cell *= 0.95
cell[1, 0] += 0.2
cell[2, 1] += 0.5
cu0.set_cell(cell, scale_atoms=True)
energies = []
for use_armijo in [True, False]:
for a_min in [None, 1e-3]:
atoms = cu0.copy()
atoms.calc = lj
opt = PreconLBFGS(atoms,
precon=Exp(A=3),
use_armijo=use_armijo,
a_min=a_min,
variable_cell=True)
opt.run(fmax=1e-3, smax=1e-4)
energies.append(atoms.get_potential_energy())
# check we get the expected energy for all methods
assert np.abs(np.array(energies) - -63.5032311942).max() < 1e-4
def relax(fname):
atoms = read(fname)
calc = gp.GPAW(mode=gp.PW(600),kpts=(4,4,4),xc="PBE")
atoms.set_calculator(calc)
uf = UnitCellFilter(atoms,hydrostatic_strain=True)
relaxer = PreconLBFGS( uf, logfile="logfile.log" )
relaxer.run( fmax=0.025,smax=0.003 )
write( fname, atoms )
def main(runId):
db = connect(DB_NAME)
row = db.get(id=runId)
group = row.group
atoms = row.toatoms()
niggli_reduce(atoms)
calc = EMT()
atoms.set_calculator(calc)
ucell = UnitCellFilter(atoms)
opt = PreconLBFGS(ucell)
opt.run(fmax=0.02, smax=0.003)
db.write(atoms, group=group, struct_type='relaxed')
def relax(runID):
db = connect(db_name)
atoms = db.get_atoms(id=runID)
con = sq.connect(db_name)
cur = con.cursor()
cur.execute("SELECT value FROM text_key_values WHERE id=? AND key='name'",
(runID, ))
name = cur.fetchone()[0]
con.close()
calc = gp.GPAW(mode=gp.PW(600),
xc="PBE",
kpts=(4, 4, 4),
nbands="120%",
symmetry="off")
atoms.set_calculator(calc)
precon = Exp(mu=1.0, mu_c=1.0)
save_to_db = SaveToDB(db_name, runID, name)
logfile = "logfile%d.log" % (runID)
traj = "trajectory%d.traj" % (runID)
uf = UnitCellFilter(atoms, hydrostatic_strain=True)
relaxer = PreconLBFGS(uf, logfile=logfile, use_armijo=True, precon=precon)
relaxer.attach(save_to_db, interval=1, atoms=atoms)
trajObj = Trajectory(traj, "w", atoms)
relaxer.attach(trajObj)
relaxer.run(fmax=0.05, smax=0.003)
def main(argv):
fname = argv[0]
if (int(argv[1]) == 1):
variable_cell = True
else:
variable_cell = False
atoms = read(fname)
#atoms = bulk("Al")
calc = gp.GPAW(mode=gp.PW(500), kpts=(12, 12, 12), xc="PBE", nbands=-20)
atoms.set_calculator(calc)
prc = Exp(mu=1.0, mu_c=1.0)
outfname = fname.split("/")[-1]
outfname = outfname.split(".")[0]
logfile = outfname + ".log"
traj_file = outfname + ".traj"
relaxer = PreconLBFGS(atoms,
logfile=logfile,
precon=prc,
use_armijo=True,
variable_cell=variable_cell)
trajObj = Trajectory(traj_file, 'w', atoms)
relaxer.attach(trajObj)
if (variable_cell):
relaxer.run(fmax=0.025, smax=0.003)
else:
relaxer.run(fmax=0.025)
outfname = fname.split("/")[-1]
outfname = outfname.split(".")[0]
outfname += "_relaxed.xyz"
print("Energy: {}".format(atoms.get_potential_energy()))
write(outfname, atoms)
def func(self, x):
""" Check cell shape to avoid the occasional crazy
cells attempted by the optimizer.
"""
if not self.accept_step(x):
return 1e64
return PreconLBFGS.func(self, x)
def g(k):
print(f'Static minimisation with k={k}, alpha={alpha0}.')
sc.k = k * k1g
sc.alpha = alpha0
sc.variable_alpha = False
sc.variable_k = False
sc.update_atoms()
atoms = sc.atoms.copy()
atoms.calc = sc.calc
atoms.set_constraint(FixAtoms(mask=~sc.regionI))
opt = PreconLBFGS(atoms, logfile=None)
opt.run(fmax=1e-5)
sc.set_atoms(atoms)
f_alpha = sc.get_crack_tip_force(mask=mask)
print(
f'Static minimisation with k={k}, alpha={alpha0} --> f_alpha={f_alpha}'
)
return abs(f_alpha)
def main(runID):
db = connect(db_name)
atoms = db.get_atoms(id=runID)
N = 14
calc = gp.GPAW(mode=gp.PW(500),
xc="PBE",
kpts=(N, N, N),
nbands=-50,
symmetry={'do_not_symmetrize_the_density': True})
atoms.set_calculator(calc)
precon = Exp(mu=1.0, mu_c=1.0)
uf = UnitCellFilter(atoms, hydrostatic_strain=True)
logfile = "al3mg2{}.log".format(runID)
relaxer = PreconLBFGS(uf, logfile=logfile, use_armijo=True, precon=precon)
relaxer.run(fmax=0.025, smax=0.003)
energy = atoms.get_potential_energy()
del db[db.get(id=runID)]
db.write(atoms)
def main():
atoms = bulk("Al", cubic=True)
atoms = atoms * (3, 3, 3)
for i in range(int(len(atoms) / 5)):
atoms[i].symbol = "Mg"
atoms.rattle(stdev=0.005)
calc = gp.GPAW(mode=gp.PW(500), xc="PBE", kpts=(4, 4, 4), nbands="120%")
atoms.set_calculator(calc)
logfile = "relax250.log"
traj = "relax250.traj"
trajObj = Trajectory(traj, 'w', atoms)
precon = Exp(mu=1)
relaxer = PreconLBFGS(atoms,
logfile=logfile,
use_armijo=True,
precon=precon,
memory=50)
#relaxer = PreconFIRE( atoms, logfile=logfile, use_armijo=True, precon=precon )
relaxer.attach(trajObj)
try:
relaxer.run(fmax=0.05)
except Exception as exc:
print(exc)
def main(argv):
n_mg = int(argv[0])
atoms = bulk("Al")
atoms = atoms * (4, 4, 4)
for i in range(n_mg):
atoms[i].symbol = "Mg"
atoms.rattle(stdev=0.005)
calc = gp.GPAW(mode=gp.PW(500), xc="PBE", kpts=(4, 4, 4), nbands="120%")
atoms.set_calculator(calc)
logfile = "preconTest%d.log" % (n_mg)
traj = "preconTest%d.traj" % (n_mg)
trajObj = Trajectory(traj, 'w', atoms)
precon = Exp(mu=1)
relaxer = PreconLBFGS(atoms,
logfile=logfile,
use_armijo=True,
precon=precon)
relaxer.attach(trajObj)
try:
relaxer.run(fmax=0.05)
except:
pass
print("Mu: %.2E" % (relaxer.precon.mu))
def run_dftb_precon(folder, param_file):
""" Run DFTB+ using a preconditioned optimizer
Unlike a regular DFTB+ run a result.tag file is not produced because ASE
deletes the file. Instead we dump the energy and forces to a json file so
we cna load it back in later.
Args:
folder (str): directory containing a structure to optimize
param_file (str): path to the parameter file for this structure.
"""
if param_file is None:
raise RuntimeError("A parameter file must be supplied to run \
batch_dftb+ in precon mode")
hsd_file = os.path.join(folder, 'dftb_pin.hsd')
file_name = 'dftb_pin.hsd' if os.path.isfile(hsd_file) else 'geo_end.gen'
atoms = io.read(os.path.join(folder, file_name))
params = load_input_file(param_file)
calc = make_dftb_calc(atoms, folder, params)
atoms.set_calculator(calc)
try:
opt = PreconLBFGS(atoms,
precon=Exp(A=3),
use_armijo=True,
logfile=None)
opt.run(steps=int(params['geom_steps']))
except:
return
results = {
'energy': calc.get_potential_energy(),
'forces': calc.get_forces().tolist()
}
json.dump(results, open(os.path.join(folder, "results.json"), 'w'))
def full_relaxation(self, fmax=0.025, smax=0.003):
"""
Perform a full relaxation of the system
"""
if (len(self.atoms) == 1):
strfilter = StrainFilter(self.atoms)
relaxer = BFGS(strfilter)
fmax = smax * self.atoms.get_volume()
relaxer.run(fmax=fmax)
else:
relaxer = PreconLBFGS(self.atoms, variable_cell=True)
relaxer.run(fmax=fmax, smax=smax)
db = connect(self.db_name)
db.write(self.atoms, key_value_pairs={"full_relaxation": True})
def test_precon():
cu0 = bulk("Cu") * (2, 2, 2)
lj = LennardJones(sigma=cu0.get_distance(0,1))
cu = cu0.copy()
cu.set_cell(1.2*cu.get_cell())
cu.calc = lj
ucf = UnitCellFilter(cu, constant_volume=True)
opt = PreconLBFGS(ucf, precon=Exp(mu=1.0, mu_c=1.0))
opt.run(fmax=1e-3)
assert abs(np.linalg.det(cu.cell)/np.linalg.det(cu0.cell) - 1.2**3) < 1e-3
# EcpCellFilter allows relaxing to lower tolerance
cu = cu0.copy()
cu.set_cell(1.2*cu.get_cell())
cu.calc = lj
ecf = ExpCellFilter(cu, constant_volume=True)
opt = PreconLBFGS(ecf, precon=Exp(mu=1.0, mu_c=1.0))
opt.run(fmax=1e-3)
assert abs(np.linalg.det(cu.cell)/np.linalg.det(cu0.cell) - 1.2**3) < 1e-7
def optimise_positions(self, fmax=0.01, use_precon=None, use_armijo=None):
""" Relax atoms positions with the fixed cell to a given force
threshold """
if use_precon is None:
use_precon = self.parameters.use_precon
if use_armijo is None:
use_armijo = self.parameters.use_armijo
if use_precon:
precon = Exp(A=3, use_pyamg=False)
else:
precon = None
if self.parameters.optimizer == 'BFGS':
relax = BFGS(self.atoms)
elif self.parameters.optimizer == 'FIRE':
relax = PreconFIRE(self.atoms, precon=precon)
elif self.parameters.optimizer == 'ase-FIRE':
relax = ASEFIRE(self.atoms)
elif self.parameters.optimizer == 'LBFGS':
relax = PreconLBFGS(self.atoms,
precon=precon,
use_armijo=use_armijo)
elif self.parameters.optimizer == 'ase-LBFGS':
relax = ASELBFGS(self.atoms)
else:
parprint("ERROR: unknown optimizer {}. "
"Reverting to BFGS".format(self.parameters.optimizer))
relax = BFGS(self.atoms)
name = self.atoms.get_chemical_formula()
relax.attach(
lambda: self.atoms.calc.write(name + '_relax.gpw', mode='all'))
relax.attach(lambda: write_atat_input(self.atoms, 'str_last.out'))
relax.run(fmax=fmax, steps=100)
if not relax.converged():
relax = ASELBFGS(self.atoms)
relax.run(fmax=fmax, steps=100)
if not relax.converged():
max_force = self.atoms.get_forces()
max_force = np.sqrt((max_force**2).sum(axis=1).max())
print('WARNING: optimisation not converged.' +
' Maximum force: %.4f' % max_force)
def test_preconlbfgs():
N = 1
a0 = bulk('Cu', cubic=True)
a0 *= (N, N, N)
# perturb the atoms
s = a0.get_scaled_positions()
s[:, 0] *= 0.995
a0.set_scaled_positions(s)
nsteps = []
energies = []
for OPT in [PreconLBFGS, PreconFIRE]:
for precon in [None, Exp(A=3, mu=1.0)]:
atoms = a0.copy()
atoms.calc = EMT()
opt = OPT(atoms, precon=precon, use_armijo=True)
opt.run(1e-4)
energies += [atoms.get_potential_energy()]
nsteps += [opt.get_number_of_steps()]
# check we get the expected energy for all methods
assert np.abs(np.array(energies) - -0.022726045433998365).max() < 1e-4
# test with fixed bondlength and fixed atom constraints
cu0 = bulk("Cu") * (2, 2, 2)
cu0.rattle(0.01)
a0 = cu0.get_distance(0, 1)
cons = [FixBondLength(0, 1), FixAtoms([2, 3])]
for precon in [None, Exp(mu=1.0)]:
cu = cu0.copy()
cu.calc = EMT()
cu.set_distance(0, 1, a0 * 1.2)
cu.set_constraint(cons)
opt = PreconLBFGS(cu, precon=precon, use_armijo=True)
opt.run(fmax=1e-3)
assert abs(cu.get_distance(0, 1) / a0 - 1.2) < 1e-3
assert np.all(abs(cu.positions[2] - cu0.positions[2]) < 1e-3)
assert np.all(abs(cu.positions[3] - cu0.positions[3]) < 1e-3)
bulk_mat = bulk('Fe','bcc',a)*(2,1,1)
#bulk_mat.set_initial_magnetic_moments([2.2, 2.2])
print(bulk_mat.get_positions())
bulk_mat = bulk_mat#*(atoms,atoms,atoms)
is_varying = 'nothing'
calc = GPAW(mode=PW(e_cut), nbands = nbands,
xc='PBE', spinpol = True, kpts=(k_pts,k_pts,k_pts),
occupations=FermiDirac(smear , fixmagmom = True), txt='Fe.out')
bulk_mat.set_calculator(calc)
traj = Trajectory('some_test.traj', 'w', bulk_mat)
bulk_mat = unitcellfilter...(bulk_mat, hydrotstatic_strain=True)
relaxer = PreconLBFGS(bulk_mat, variable_cell = True, logfile = 'my_log.txt')
relaxer.attach(traj)
relaxer.run(fmax = 0.025, smax = 0.003)
energy = bulk_mat.get_potential_energy()
print(bulk_mat.get_magnetic_moments())
print(bulk_mat.get_positions())
print(energy)
calc.write('Fe.gpw')
import gpaw as gp
from ase.build import bulk
from ase.visualize import view
from ase.optimize.precon import PreconLBFGS
from ase.io import write
from ase.calculators.emt import EMT
atoms = bulk("Mg", crystalstructure="fcc", a=4.1)
atoms = atoms * (2, 2, 2)
si_indx = [1, 2, 4, 7]
for indx in si_indx:
atoms[indx].symbol = "Si"
calc = gp.GPAW(mode=gp.PW(600), xc="PBE", kpts=(2, 2, 2), nbands=-100)
atoms.set_calculator(calc)
opt = PreconLBFGS(atoms, variable_cell=True)
opt.run(fmax=0.025, smax=0.003)
write("data/relaxed_mgsi.xyz", atoms)
def main(argv):
uid = int(argv[0])
attempt_restart = 1
kpts_density = 1.37
lattice_param = 4.05
relax_atoms = 0
final_structure = 0
optimizer = "lbfgs"
init_from_traj = 0
for arg in argv:
if arg.find("--restart=") != -1:
attempt_restart = int(arg.split("--restart")[1])
elif "--kpt=" in arg:
kpts_density = float(arg.split("--kpt=")[1])
elif "--a=" in arg:
lattice_param = float(arg.split("--a=")[1])
elif "--relax=" in arg:
relax_atoms = int(arg.split("--relax=")[1])
elif "--final=" in arg:
final_structure = int(arg.split("--final=")[1])
elif "--opt=" in arg:
optimizer = arg.split("--opt=")[1]
elif "--traj=" in arg:
init_from_traj = int(arg.split("--traj=")[1])
db = connect(db_name)
atoms = db.get(id=uid).toatoms()
atoms = delete_vacancies(atoms)
name = db.get(id=uid).name
kpt = {"density": kpts_density, "even": True}
# calc = gp.GPAW(h=0.32, kpts=kpt, xc="PBE", nbands="120%")
calc = gp.GPAW(mode=gp.PW(600), kpts=kpt, xc="PBE", nbands="120%")
atoms.set_calculator(calc)
restart_file = db.get(id=uid).get("restart_file", "")
if relax_atoms == 0 and final_structure == 0:
atoms.get_potential_energy()
# Store the energy of the atoms object with the correct name
# and lattice parameter
db.write(atoms,
name=name,
lattice_param=lattice_param,
run_type="lattice_param_estimation")
elif relax_atoms == 1:
if os.path.exists(restart_file) and attempt_restart == 1:
atoms, calc = gp.restart(restart_file)
elif init_from_traj:
trajfile = "trajectory{}.traj".format(name)
traj = Trajectory(trajfile, 'r')
atoms = traj[-1]
atoms.set_calculator(calc)
else:
db.update(uid, restart_file=SaveRestartFiles.restart_name(name))
restart_saver = SaveRestartFiles(calc, name)
trajObj = Trajectory("trajectory{}.traj".format(name), 'a', atoms)
ucf = UnitCellFilter(atoms, hydrostatic_strain=True)
logfile = "log_{}.txt".format(name)
if optimizer == "cg":
relaxer = SciPyFminCG(ucf, logfile=logfile)
elif optimizer == "fire":
relaxer = PreconFIRE(ucf, logfile=logfile)
else:
relaxer = PreconLBFGS(ucf, logfile=logfile)
relaxer.attach(trajObj)
relaxer.attach(restart_saver, interval=1)
relaxer.run(fmax=0.025)
db.write(atoms,
name=name,
lattice_param=lattice_param,
run_type="geometry_opt",
restart_file=SaveRestartFiles.restart_name(name))
elif final_structure:
atoms.get_potential_energy()
uid = db.write(atoms,
name=name,
struct_type="final",
kpts_density=kpts_density)
init_id = db.get(name=name, struct_type='initial').id
db.update(init_id, final_struct_id=uid, converged=1)
dimer.positions[3:, 0] += 2.8
dimer.constraints = FixBondLengths([
((selection[i] + 3) % 6, (selection[i - 1] + 3) % 6) for i in range(3)
])
dimer.calc = EIQMMM(selection,
GPAW(txt=name + '.txt', h=0.16),
TIP4P(),
interaction,
vacuum=4,
embedding=Embedding(rc=0.2, rc2=20, width=1),
output=name + '.out')
opt = LBFGS(dimer, trajectory=name + '.traj')
opt.run(0.02)
monomer = dimer[selection]
monomer.center(vacuum=4)
monomer.calc = GPAW(txt=name + 'M.txt', h=0.16)
opt = PreconLBFGS(monomer, precon=Exp(A=3), trajectory=name + 'M.traj')
opt.run(0.02)
e0 = monomer.get_potential_energy()
be = dimer.get_potential_energy() - e0
d = dimer.get_distance(0, 3)
print(name, be, d)
if name == '012':
assert abs(be - -0.288) < 0.002
assert abs(d - 2.76) < 0.02
else:
assert abs(be - -0.316) < 0.002
assert abs(d - 2.67) < 0.02
def relax_config(atoms,
calculator,
relax_pos,
relax_cell,
tol=1e-3,
method='lbfgs',
max_steps=200,
traj_file=None,
constant_volume=False,
refine_symmetry_tol=None,
keep_symmetry=False,
strain_mask=None,
config_label=None,
from_base_model=False,
save_config=False,
fix_cell_dependence=False,
applied_P=0.0,
**kwargs):
# get from base model if requested
#import model
if from_base_model:
if config_label is None:
raise ValueError(
'from_base_model is set but no config_label provided')
try:
base_run_file = os.path.join(
'..', base_run_root,
base_run_root + '-' + config_label + '-relaxed.xyz')
atoms_in = read(base_run_file, format='extxyz')
# set positions from atoms_in rescaling to match current cell
saved_cell = atoms.get_cell().copy()
atoms.set_cell(atoms_in.get_cell())
atoms.set_positions(atoms_in.get_positions())
atoms.set_cell(saved_cell, scale_atoms=True)
print("relax_config read config from ", base_run_file)
except:
try:
print("relax_config failed to read base run config from ",
base_run_root + '-' + config_label + '-relaxed.xyz')
except:
print("relax_config failed to determined base_run_root")
print("relax_config symmetry before refinement at default tol 1.0e-6")
check_symmetry(atoms, 1.0e-6, verbose=True)
if refine_symmetry_tol is not None:
refine_symmetry(atoms, refine_symmetry_tol)
print("relax_config symmetry after refinement")
check_symmetry(atoms, refine_symmetry_tol, verbose=True)
if keep_symmetry:
print("relax_config trying to maintain symmetry")
atoms.set_constraint(FixSymmetry(atoms))
atoms.set_calculator(calculator)
# if needed, fix cell dependence before running
# if fix_cell_dependence and hasattr(model, "fix_cell_dependence"):
# model.fix_cell_dependence(atoms)
if method == 'lbfgs' or method == 'sd2':
if 'move_mask' in atoms.arrays:
atoms.set_constraint(
FixAtoms(np.where(atoms.arrays['move_mask'] == 0)[0]))
if relax_cell:
atoms_cell = ExpCellFilter(atoms,
mask=strain_mask,
constant_volume=constant_volume,
scalar_pressure=applied_P * GPa)
else:
atoms_cell = atoms
atoms.info["n_minim_iter"] = 0
if method == 'sd2':
(traj,
run_stat) = sd2_run("", atoms_cell, tol,
lambda i: sd2_converged(i, atoms_cell, tol),
max_steps)
#if traj_file is not None:
#write(traj_file, traj)
else:
# precon="Exp" specified to resolve an error with the lbfgs not optimising
opt = PreconLBFGS(atoms_cell, use_armijo=False, **kwargs)
if traj_file is not None:
traj = open(traj_file, "w")
def write_trajectory():
if "n_minim_iter" in atoms.info:
atoms.info["n_minim_iter"] += 1
write(traj, atoms, format='extxyz')
#opt.attach(write_trajectory)
elif method == 'cg_n':
raise ValueError(
'minim method cg_n not supported in new python3 quippy')
# if strain_mask is not None:
# raise(Exception("strain_mask not supported with method='cg_n'"))
# atoms.info['Minim_Constant_Volume'] = constant_volume
# opt = Minim(atoms, relax_positions=relax_pos, relax_cell=relax_cell, method='cg_n')
else:
raise ValueError('unknown method %s!' % method)
if method != 'sd2':
opt.run(tol, max_steps)
if refine_symmetry_tol is not None:
print("symmetry at end of relaxation at desired tol")
check_symmetry(atoms, refine_symmetry_tol, verbose=True)
print("symmetry at end of relaxation at default tol 1e-6")
check_symmetry(atoms, 1.0e-6, verbose=True)
# in case we had a trajectory saved
try:
traj.close()
except:
pass
if save_config:
if config_label is None:
raise ValueError('save_config is set but no config_label provided')
#write('-'+config_label+'-relaxed.xyz', atoms, format='extxyz')
if keep_symmetry:
for (i_c, c) in enumerate(atoms.constraints):
if isinstance(c, FixSymmetry):
del atoms.constraints[i_c]
break
# undo fix cell dependence
# if fix_cell_dependence and hasattr(model, "fix_cell_dependence"):
# sys.stderr.write("WARNING: relax_config undoing fix_cell_dependence, whether or not it was set before it started\n")
# model.fix_cell_dependence()
return atoms
atoms.set_cell(atoms.cell * np.diag([1.0 + s, 1.0 - s * nu, 1.0 - s * nu]),
scale_atoms=True)
# simple header for the output
print(" Iteration Time Energy max Force")
# loop to perform the successive small strain increments
for i in range(50):
# record and print the current strain
atoms.info["strain"] = (atoms.cell[0, 0] -
origLx) / origLx # Engineering strain
print "strain: ", atoms.info["strain"]
# set up an optimizer, this is a particularly efficient one
opt = PreconLBFGS(atoms, precon=Exp(3.0))
# attach the optimiser to the atoms object, asking it to call our helper function
# that writes out the atomic positions, after every 2nd iterations of the optimisation
opt.attach(write_frame, 2, atoms)
# run the optimizer, until the maximum force on any atom is less than a tolerance in eV/Ang
opt.run(fmax=0.02)
# update the "grip" by applying the small strain increment.
s = 0.01 # small strain increment
atoms.set_cell(atoms.cell * np.diag([1.0 + s, 1.0 - s * nu, 1.0 - s * nu]),
scale_atoms=True)
#######################################################################
#
vasp_client = VaspClient(client_id=0,
npj=96,
ppn=1,
exe=vasp,
mpirun=mpirun,
parmode='mpi',
ibrion=13,
nsw=1000000,
npar=4,
**vasp_args)
if not args.no_relax:
traj = io.Trajectory('relaxation.traj', 'a', gam_cell)
qm_pot = SocketCalculator(vasp_client)
gam_cell.set_calculator(qm_pot)
opt = PreconLBFGS(gam_cell)
opt.attach(traj.write, interval=1)
opt.run(fmax=args.fmax)
traj.close()
qm_pot.shutdown()
#remove defect atom with symbol
del gam_cell[[atom.symbol == args.symbol for atom in gam_cell]]
defect_cell = gam_cell.copy()
defect_cell.write('no_impurity.xyz')
#Need accurate forces
vasp_args['ediff'] = 1e-5
vasp_client = VaspClient(client_id=0,
npj=96,
ppn=1,
import numpy as np
from ase.build import bulk
from ase.calculators.lj import LennardJones
from ase.optimize.precon import PreconLBFGS, Exp
from ase.constraints import UnitCellFilter
cu0 = bulk("Cu") * (2, 2, 2)
lj = LennardJones(sigma=cu0.get_distance(0, 1))
cu = cu0.copy()
cu.set_cell(1.2 * cu.get_cell())
cu.set_calculator(lj)
ucf = UnitCellFilter(cu, constant_volume=True)
opt = PreconLBFGS(ucf, precon=Exp(mu=1.0, mu_c=1.0))
opt.run(fmax=1e-3)
assert abs(np.linalg.det(cu.cell) / np.linalg.det(cu0.cell) - 1.2**3) < 1e-3
def do_lattice(test_dir,
lattice_type,
dV=0.025,
n_steps=(-10, 10),
tol=1.0e-2,
method='lbfgs',
applied_P=0.0):
bulk = ase.io.read(test_dir + "/bulk.xyz", format="extxyz")
results_dict = {}
print("relax bulk")
# relax the initial unit cell and atomic positions
(orig_cell, new_cell) = (None, None)
while new_cell is None or np.max(
np.abs(np.dot(np.linalg.inv(new_cell), orig_cell) -
np.eye(3))) > 0.05:
if hasattr(model, "fix_cell_dependence"):
model.fix_cell_dependence(bulk)
orig_cell = bulk.get_cell()
bulk = relax_config(bulk,
relax_pos=True,
relax_cell=True,
tol=tol,
traj_file="lattice_bulk_traj.xyz",
method=method,
refine_symmetry_tol=1.0e-2,
keep_symmetry=True,
config_label="bulk",
from_base_model=True,
save_config=True,
applied_P=applied_P)
new_cell = bulk.get_cell()
if hasattr(model, "fix_cell_dependence"):
model.fix_cell_dependence()
else:
break
print("final relaxed bulk")
ase.io.write(sys.stdout, bulk, format='extxyz')
ase.io.write(os.path.join("..", "relaxed.xyz"), bulk, format='extxyz')
print("calculating E vs. V")
E_vs_V = calc_E_vs_V(bulk, dV=dV, n_steps=n_steps, tol=tol)
results_dict.update({'E_vs_V': E_vs_V})
print("calculating elastic constants")
if hasattr(model, "fix_cell_dependence"):
model.fix_cell_dependence(bulk)
opt = lambda atoms, **kwargs: PreconLBFGS(atoms, **kwargs)
if lattice_type == 'cubic':
elastic_consts = matscipy.elasticity.fit_elastic_constants(
bulk, symmetry='cubic', optimizer=opt, logfile=sys.stdout)
c11 = elastic_consts[0][0, 0] / GPa
c12 = elastic_consts[0][0, 1] / GPa
c44 = elastic_consts[0][3, 3] / GPa
results_dict.update({
'c11': c11,
'c12': c12,
'c44': c44,
'B': (c11 + 2.0 * c12) / 3.0
})
elif lattice_type == 'orthorhombic':
elastic_consts = matscipy.elasticity.fit_elastic_constants(
bulk, optimizer=opt, logfile=sys.stdout)
c11 = elastic_consts[0][0, 0] / GPa
c22 = elastic_consts[0][1, 1] / GPa
c33 = elastic_consts[0][2, 2] / GPa
c12 = elastic_consts[0][0, 1] / GPa
c13 = elastic_consts[0][0, 2] / GPa
c23 = elastic_consts[0][1, 2] / GPa
c44 = elastic_consts[0][3, 3] / GPa
c55 = elastic_consts[0][4, 4] / GPa
c66 = elastic_consts[0][5, 5] / GPa
results_dict.update({
'c11': c11,
'c22': c22,
'c33': c33,
'c12': c12,
'c13': c13,
'c23': c23,
'c44': c44,
'c55': c55,
'c66': c66
})
elif lattice_type == 'tetragonal':
elastic_consts = matscipy.elasticity.fit_elastic_constants(
bulk,
symmetry='tetragonal_high',
optimizer=opt,
logfile=sys.stdout)
c11 = elastic_consts[0][0, 0] / GPa
c33 = elastic_consts[0][2, 2] / GPa
c12 = elastic_consts[0][0, 1] / GPa
c13 = elastic_consts[0][0, 2] / GPa
c44 = elastic_consts[0][3, 3] / GPa
c66 = elastic_consts[0][5, 5] / GPa
results_dict.update({
'c11': c11,
'c33': c33,
'c12': c12,
'c13': c13,
'c44': c44,
'c66': c66,
'B': VRH_B(c11, c33, c12, c13, c44, c66)
})
elif lattice_type == 'hexagonal':
# Need to check if hexagonal structures are truly trigonal_high
# symmetry=triginal_high not hexagonal until matscipy is debugged
elastic_consts = matscipy.elasticity.fit_elastic_constants(
bulk, symmetry='trigonal_high', optimizer=opt, logfile=sys.stdout)
c11 = elastic_consts[0][0, 0] / GPa
c33 = elastic_consts[0][2, 2] / GPa
c12 = elastic_consts[0][0, 1] / GPa
c13 = elastic_consts[0][0, 2] / GPa
c44 = elastic_consts[0][3, 3] / GPa
c14 = elastic_consts[0][0, 3] / GPa
c15 = elastic_consts[0][0, 4] / GPa
c25 = elastic_consts[0][1, 4] / GPa
c66 = elastic_consts[0][5, 5] / GPa
results_dict.update({
'c11': c11,
'c33': c33,
'c12': c12,
'c13': c13,
'c44': c44,
'c14': c14,
'c15': c15,
'c25': c25,
'c66': c66,
'B': HTT_B(c11, c33, c12, c13)
})
elif lattice_type == 'trigonal':
elastic_consts = matscipy.elasticity.fit_elastic_constants(
bulk, symmetry='trigonal_high', optimizer=opt, logfile=sys.stdout)
c11 = elastic_consts[0][0, 0] / GPa
c33 = elastic_consts[0][2, 2] / GPa
c12 = elastic_consts[0][0, 1] / GPa
c13 = elastic_consts[0][0, 2] / GPa
c44 = elastic_consts[0][3, 3] / GPa
c14 = elastic_consts[0][0, 3] / GPa
c15 = elastic_consts[0][0, 4] / GPa
c25 = elastic_consts[0][1, 4] / GPa
c66 = elastic_consts[0][5, 5] / GPa
results_dict.update({
'c11': c11,
'c33': c33,
'c12': c12,
'c13': c13,
'c44': c44,
'c14': c14,
'c15': c15,
'c25': c25,
'c66': c66,
'B': HTT_B(c11, c33, c12, c13)
})
if hasattr(model, "fix_cell_dependence"):
model.fix_cell_dependence()
return results_dict
# creates: precon.png
from ase.build import bulk
from ase.calculators.emt import EMT
from ase.optimize.precon import Exp, PreconLBFGS
from ase.calculators.loggingcalc import LoggingCalculator
import matplotlib.pyplot as plt
a0 = bulk('Cu', cubic=True)
a0 *= [3, 3, 3]
del a0[0]
a0.rattle(0.1)
nsteps = []
energies = []
log_calc = LoggingCalculator(EMT())
for precon, label in [(None, 'None'), (Exp(A=3), 'Exp(A=3)')]:
log_calc.label = label
atoms = a0.copy()
atoms.set_calculator(log_calc)
opt = PreconLBFGS(atoms, precon=precon, use_armijo=True)
opt.run(fmax=1e-3)
log_calc.plot(markers=['r-', 'b-'], energy=False, lw=2)
plt.savefig('precon.png')
if os.path.isfile('./' + system_name + '_relaxed.gpw'):
#Recover past done calculations if available
bulk_mat, calc = restart(system_name + '_relaxed.gpw', txt = None)
bulk_mat.set_calculator(calc)
else:
#Initialize new calculations
db = connect(sys.argv[8])
bulk_mat = db.get_atoms(id = sys.argv[9])
calc = GPAW(mode=PW(e_cut), nbands = nbands,
xc='PBE', spinpol=True, kpts=(k_pts,k_pts,k_pts),
occupations=FermiDirac(smear), txt=system_name + '.out')
bulk_mat.set_calculator(calc)
save_atoms(bulk_mat, e_cut, nbands, k_pts, smear, a, initial_magmom, 1, str(sys.argv[6]))
saver = Gpw_save(calc, system_name + '_relaxed.gpw')
traj = Trajectory(system_name + '_relaxed.traj', 'w', bulk_mat)
relaxer = PreconLBFGS(bulk_mat, variable_cell = True, logfile = system_name + '.txt')
relaxer.attach(traj)
relaxer.attach(saver)
relaxer.run(fmax = 0.025, smax = 0.003)
bulk_mat.get_potential_energy()
#Save the final state of the calculations
calc.write(system_name + '_relaxer_final.gpw')
save_atoms(bulk_mat, e_cut, nbands, k_pts, smear, a, initial_magmom, 0, str(sys.argv[6]))
import numpy as np
from ase.build import bulk
from ase.calculators.lj import LennardJones
from ase.optimize.precon import Exp, PreconLBFGS
cu0 = bulk("Cu") * (2, 2, 2)
sigma = cu0.get_distance(0,1)*(2.**(-1./6))
lj = LennardJones(sigma=sigma)
# perturb the cell
cell = cu0.get_cell()
cell *= 0.95
cell[1,0] += 0.2
cell[2,1] += 0.5
cu0.set_cell(cell, scale_atoms=True)
energies = []
for use_armijo in [True, False]:
for a_min in [None, 1e-3]:
atoms = cu0.copy()
atoms.set_calculator(lj)
opt = PreconLBFGS(atoms, precon=Exp(A=3), use_armijo=use_armijo,
a_min=a_min, variable_cell=True)
opt.run(fmax=1e-3, smax=1e-4)
energies.append(atoms.get_potential_energy())
# check we get the expected energy for all methods
assert np.abs(np.array(energies) - -63.5032311942).max() < 1e-4
def main(argv):
relax_mode = "both" # both, cell, positions
system = "AlMg"
runID = int(argv[0])
nkpt = int(argv[1])
single_point = False
if (len(argv) >= 3):
single_point = (int(argv[2]) == 1)
print("Running job: %d" % (runID))
db_paths = [
"/home/ntnu/davidkl/GPAWTutorial/CE/almg_fcc_vac.db",
"almg_fcc_vac.db", "/home/davidkl/GPAWTutorial/CE/almg_fcc_vac.db"
]
for path in db_paths:
if (os.path.isfile(path)):
db_name = path
break
#db_name = "almgsi_test_db.db"
db = ase.db.connect(db_name)
name = db.get(id=runID).key_value_pairs["name"]
new_run = not db.get(id=runID).key_value_pairs["started"]
# Update the databse
db.update(runID, started=True, converged=False)
db.update(runID, nkpt=nkpt)
atoms = db.get_atoms(id=runID)
atoms = delete_vacancies(atoms)
if (len(atoms) == 1):
nbands = -10
else:
nbands = "120%"
kpts = (nkpt, nkpt, nkpt)
try:
restart_name = SaveRestartFiles.restart_name(name)
atoms, calc = gp.restart(restart_name)
except:
calc = gp.GPAW(mode=gp.PW(500), xc="PBE", kpts=kpts, nbands=nbands)
atoms.set_calculator(calc)
if (single_point):
calc = gp.GPAW(mode=gp.PW(500), xc="PBE", kpts=kpts, nbands=nbands)
atoms.set_calculator(calc)
logfile = "almg_fcc_vac{}.log".format(name)
traj = "almg_bcc{}.traj".format(name)
db.update(runID, trajfile=traj)
trajObj = Trajectory(traj, 'w', atoms)
#storeBest = SaveToDB(db_name,runID,name,mode=relax_mode)
save_calc = SaveRestartFiles(calc, name)
update_db_info = UpdateDBInfo(db_name, runID, atoms)
volume = atoms.get_volume()
try:
precon = Exp(mu=1.0, mu_c=1.0)
fmax = 0.025
smax = 0.003
if (relax_mode == "both"):
relaxer = PreconLBFGS(atoms,
logfile=logfile,
use_armijo=True,
variable_cell=True)
elif (relax_mode == "positions"):
#relaxer = SciPyFminCG( atoms, logfile=logfile )
relaxer = BFGS(atoms, logfile=logfile)
elif (relax_mode == "cell"):
str_f = StrainFilter(atoms, mask=[1, 1, 1, 0, 0, 0])
relaxer = BFGS(str_f, logfile=logfile)
fmax = smax * volume
relaxer.attach(trajObj)
#relaxer.attach( storeBest, interval=1, atoms=atoms )
relaxer.attach(save_calc, interval=1)
relaxer.attach(update_db_info, interval=1)
if (not single_point):
if (relax_mode == "both"):
relaxer.run(fmax=fmax, smax=smax)
else:
relaxer.run(fmax=fmax)
energy = atoms.get_potential_energy()
orig_atoms = db.get_atoms(runID)
single_p_calc = SinglePointCalculator(orig_atoms, energy=energy)
orig_atoms.set_calculator(single_p_calc)
kvp = db.get(name=name).key_value_pairs
del db[runID]
newID = db.write(orig_atoms, key_value_pairs=kvp)
if (relax_mode == "positions"):
db.update(newID, converged_force=True)
elif (relax_mode == "cell"):
db.update(newID, converged_stress=True)
else:
db.update(newID, converged_stress=True, converged_force=True)
db.update(newID, single_point=single_point)
db.update(newID, restart_file=SaveRestartFiles.restart_name(name))
row = db.get(id=newID)
conv_force = row.get("converged_force", default=0)
conv_stress = row.get("converged_stress", default=0)
if ((conv_force == 1) and (conv_stress == 1) and (nkpt == 4)):
db.update(newID, converged=True)
except Exception as exc:
print(exc)