def cjson_reader(cjsonfile, trajfile=None):
"""Read CJSON files
Parameters
----------
cjsonfile : str
Path to the CJSON file.
trajfile : str, optional
Name of trajectory file to be saved, by default None.
Returns
-------
atoms
A list of Atoms objects.
"""
collection = json.loads(open(cjsonfile, "r").read())
atoms = []
if trajfile is not None:
traj = Trajectory(trajfile, mode="w")
for document in collection:
cjson = json.loads(document)
molecule, energy = cjson_to_ase(cjson)
molecule.set_calculator(FakeCalculator())
molecule.calc.results["energy"] = energy
atoms.append(molecule)
if trajfile is not None:
traj.write(molecule, energy=energy)
return atoms
def train_test():
"""Gaussian/KRR train test."""
label = 'train_test/calc'
train_images = generate_data(2)
traj = Trajectory('trainingset.traj', mode='w')
for image in train_images:
traj.write(image)
calc = Amp(descriptor=Gaussian(),
model=KernelRidge(forcetraining=True, trainingimages='trainingset.traj'),
label=label,
cores=1)
calc.train(images=train_images,)
for image in train_images:
print("energy = %s" % str(calc.get_potential_energy(image)))
print("forces = %s" % str(calc.get_forces(image)))
# Test that we can re-load this calculator and call it again.
del calc
calc2 = Amp.load(label + '.amp')
for image in train_images:
print("energy = %s" % str(calc2.get_potential_energy(image)))
print("forces = %s" % str(calc2.get_forces(image)))
def integrate_atoms(
self,
atoms,
traj_file,
n_steps,
save_interval,
steps=0,
timestep=5.0,
traj_dir="trajs",
convert=False,
):
if not os.path.exists(traj_dir):
os.mkdir(traj_dir)
traj_file = os.path.join(traj_dir, traj_file)
if not os.path.exists(traj_file):
traj = Trajectory(traj_file, "w")
print("Creating trajectory {}...".format(traj_file))
dyn = VelocityVerlet(atoms, timestep=timestep * units.fs)
count = n_steps // save_interval
for i in range(count):
dyn.run(save_interval)
energy = atoms.get_total_energy()
forces = atoms.get_forces()
traj.write(atoms)
steps += save_interval
print("Steps: {}, total energy: {}".format(steps, energy))
else:
print("Trajectory {} already exists!".format(traj_file))
if convert:
self.convert_trajectory(traj_file)
return steps, traj_file
def __call__(self):
""" Writes trajectory file for current atoms list. """
from ase import Trajectory
traj = Trajectory('%s_it%i.trj' % (self.name, self.i), 'w')
for image in self.images:
traj.write(image)
self.i += 1
def nudged_elastic_band(images,
fmax=0.01,
algo='BFGS',
trajectory='path-neb.traj',
final='neb.traj'):
calc = cline.gen_active_calc()
load1 = calc.size[0]
master = calc.rank == 0
for image in images:
image.calc = calc
# calculate for the first and last images
# (for more efficient ML)
images[0].get_potential_energy()
images[-1].get_potential_energy()
# define and run NEB
neb = NEB(images, allow_shared_calculator=True)
Min = getattr(optimize, algo)
dyn = Min(neb, trajectory=trajectory, master=master)
dyn.run(fmax)
load2 = calc.size[0]
if master:
print(f'\tTotal number of Ab initio calculations: {load2-load1}\n')
# output
if master:
out = Trajectory(final, 'w')
for image in images:
image.get_potential_energy()
if master:
out.write(image)
def test_info():
from ase import Atoms
from ase.io import Trajectory
# Create a molecule with an info attribute
info = dict(
creation_date='2011-06-27',
chemical_name='Hydrogen',
# custom classes also works provided that it is
# imported and pickleable...
foo={'seven': 7})
molecule = Atoms('H2', positions=[(0., 0., 0.), (0., 0., 1.1)], info=info)
assert molecule.info == info
# Copy molecule
atoms = molecule.copy()
assert atoms.info == info
# Save molecule to trajectory
traj = Trajectory('info.traj', 'w', atoms=molecule)
traj.write()
del traj
# Load molecule from trajectory
t = Trajectory('info.traj')
atoms = t[-1]
print(atoms.info)
assert atoms.info == info
def main():
args = sys.argv
imgs = read(args[1], index=":")
random.shuffle(imgs)
imgs_selected_Pd = imgs[:200]
random.shuffle(imgs)
imgs_selected_H = imgs[:100]
expansions = [0.1 * (i + 1) for i in range(8)]
traj = Trajectory('expanded.traj', 'w')
for img in imgs_selected_Pd:
Pds = [atom.index for atom in img if atom.symbol == 'Pd']
com = img.get_center_of_mass()
d_atoms = []
for Pd in Pds:
d_atoms.append([np.linalg.norm(img[Pd].position - com), Pd])
ordered_atoms = sorted(d_atoms, key=itemgetter(0), reverse=False)
imags_expanded = expand_particle(img, expansions,
random.choice(ordered_atoms[-5:])[1])
for im in imags_expanded:
traj.write(im)
for img in imgs_selected_H:
Hs = [atom.index for atom in img if atom.symbol == 'H']
com = img.get_center_of_mass()
d_Hs = []
for H in Hs:
d_Hs.append([np.linalg.norm(img[H].position - com), H])
ordered_atoms = sorted(d_Hs, key=itemgetter(0), reverse=False)
imags_expanded = expand_particle(img, expansions, ordered_atoms[-1][1])
for im in imags_expanded:
traj.write(im)
def eos(self, atoms, name):
args = self.args
traj = Trajectory(self.get_filename(name, 'traj'), 'w', atoms)
N, eps = args.equation_of_state.split(',')
N = int(N)
eps = float(eps) / 100
strains = np.linspace(1 - eps, 1 + eps, N)
v1 = atoms.get_volume()
volumes = strains**3 * v1
energies = []
cell1 = atoms.cell
for s in strains:
atoms.set_cell(cell1 * s, scale_atoms=True)
energies.append(atoms.get_potential_energy())
traj.write(atoms)
traj.close()
eos = EquationOfState(volumes, energies, args.eos_type)
v0, e0, B = eos.fit()
atoms.set_cell(cell1 * (v0 / v1)**(1 / 3), scale_atoms=True)
from ase.parallel import parprint as p
p('volumes:', volumes)
p('energies:', energies)
p('fitted energy:', e0)
p('fitted volume:', v0)
p('bulk modulus:', B)
p('eos type:', args.eos_type)
def main():
imgs = read('train.traj', index='0::10', format='traj')
natoms = len(imgs[0])
cutoff = 3.3
mindist = 2.7
traj = Trajectory('traj.traj', 'w')
for atoms in imgs:
nl = NeighborList([cutoff / 2] * len(atoms),
self_interaction=False,
bothways=False)
nl.update(atoms)
neighbor_info = {}
n_pairs = 0
for i in range(natoms):
i_indices, i_offsets = nl.get_neighbors(i)
neighbor_info[i] = i_indices
n_pairs += len(i_indices)
print len(i_indices)
#randomvalues=np.random.random((n_pairs,)) + mindist
randomvalues = np.random.normal(mindist, 0.5, (n_pairs, ))
pullcloser = {}
pointer = 0
for key in neighbor_info.keys():
pullcloser[key] = randomvalues[pointer:len(neighbor_info[key]) +
pointer:1]
pointer += len(neighbor_info[key])
atoms.set_positions(
pull_closer(atoms.get_positions(), neighbor_info, pullcloser))
#write('CONTCAR',atoms,format='vasp')
traj.write(atoms)
def main():
args = sys.argv
imgs = read(args[1], index="::40")
#layers = find_layers(atoms.copy())
traj = Trajectory('traj.traj','w')
H_indices = random.sample([a.index for a in imgs[0] if a.symbol == 'H'],8)
n_img = 0
for atoms in imgs:
nl=NeighborList([2.5/2]*len(atoms), self_interaction=False, bothways=True)
nl.update(atoms)
pair_selected = []
for H_index in H_indices:
nl_indices, nl_offsets = nl.get_neighbors(H_index)
pair_selected.append([H_index, random.sample(nl_indices, 1)[0]])
for HPd_dist in [1.0, 1.1, 1.2, 1.3, 1.4]:
img = atoms.copy()
for pair in pair_selected:
H_index = pair[0]
Pd_selected = pair[1]
v = atoms[H_index].position - atoms[Pd_selected].position
vn = v/np.linalg.norm(v)
del img[H_index]
img.append(Atom('H',atoms[Pd_selected].position + vn * HPd_dist))
traj.write(img)
print n_img
n_img+=1
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--traj',
type=str,
nargs='+',
metavar='trajFile',
default=None,
help='filename of the trajectory')
parser.add_argument('--runtype',
type=str,
nargs='+',
metavar='type',
default=None,
help='run type: split or match')
args = parser.parse_args()
print(args)
if args.traj[0].split('.')[1] == 'xyz':
configs, es, fnorms, fmins, fmaxs = read_images(args.traj[0])
if args.traj[0].split('.')[1] == 'traj':
configs, es, fnorms, fmins, fmaxs = read_traj(args.traj[0])
if args.runtype[0] == 'split':
configs.sort(key=lambda x: x[1])
dn = int(len(configs) / 14)
for i in range(14):
print(i)
test_traj = Trajectory(str(i) + '.traj', 'w')
start = dn * i
if i == 13:
end = len(configs)
else:
end = dn * (i + 1)
for config in configs[start:end]:
test_traj.write(config[0])
if args.runtype[0] == 'match':
outtraj = Trajectory('filter.traj', 'w')
for i in range(len(configs) - 1):
#calc = force_setter(energy=config.get_potential_energy(), forces=config.get_forces())
#config.set_cell([[40.,0,0],[0,40.,0],[0,0,40.]],scale_atoms=False)
#config.set_pbc((True, True, True))
#config.center()
#config.set_calculator(calc)
e0 = configs[i][0].get_potential_energy()
fs0 = configs[i][0].get_forces()
matched = False
for j in range(i + 1, len(configs)):
e1 = configs[j][0].get_potential_energy()
if abs(e1 - e0) <= 0.05:
matched = match(configs[i][0],
configs[j][0],
0.02,
3.3,
indistinguishable=True)
if matched:
break
print(i, matched)
if matched:
continue
outtraj.write(configs[i][0])
def _test_timestepping(self, t):
#XXX DEBUG START
if debug and os.path.isfile('%s_%d.gpw' % (self.tdname, t)):
return
#XXX DEBUG END
timestep = self.timesteps[t]
self.assertAlmostEqual(self.duration % timestep, 0.0, 12)
niter = int(self.duration / timestep)
ndiv = 1 #XXX
traj = Trajectory('%s_%d.traj' % (self.tdname, t), 'w',
self.tdcalc.get_atoms())
t0 = time.time()
f = paropen('%s_%d.log' % (self.tdname, t), 'w')
print('propagator: %s, duration: %6.1f as, timestep: %5.2f as, ' \
'niter: %d' % (self.propagator, self.duration, timestep, niter), file=f)
for i in range(1, niter + 1):
# XXX bare bones propagation without all the nonsense
self.tdcalc.propagator.propagate(self.tdcalc.time,
timestep * attosec_to_autime)
self.tdcalc.time += timestep * attosec_to_autime
self.tdcalc.niter += 1
if i % ndiv == 0:
rate = 60 * ndiv / (time.time() - t0)
ekin = self.tdcalc.atoms.get_kinetic_energy()
epot = self.tdcalc.get_td_energy() * Hartree
F_av = np.zeros((len(self.tdcalc.atoms), 3))
print('i=%06d, time=%6.1f as, rate=%6.2f min^-1, ' \
'ekin=%13.9f eV, epot=%13.9f eV, etot=%13.9f eV' \
% (i, timestep * i, rate, ekin, epot, ekin + epot), file=f)
t0 = time.time()
# Hack to prevent calls to GPAW::get_potential_energy when saving
spa = self.tdcalc.get_atoms()
spc = SinglePointCalculator(spa, energy=epot, forces=F_av)
spa.set_calculator(spc)
traj.write(spa)
f.close()
traj.close()
self.tdcalc.write('%s_%d.gpw' % (self.tdname, t), mode='all')
# Save density and wavefunctions to binary
gd, finegd = self.tdcalc.wfs.gd, self.tdcalc.density.finegd
if world.rank == 0:
big_nt_g = finegd.collect(self.tdcalc.density.nt_g)
np.save('%s_%d_nt.npy' % (self.tdname, t), big_nt_g)
del big_nt_g
big_psit_nG = gd.collect(self.tdcalc.wfs.kpt_u[0].psit_nG)
np.save('%s_%d_psit.npy' % (self.tdname, t), big_psit_nG)
del big_psit_nG
else:
finegd.collect(self.tdcalc.density.nt_g)
gd.collect(self.tdcalc.wfs.kpt_u[0].psit_nG)
world.barrier()
def calculate_eos(atoms, npoints=5, eps=0.04, trajectory=None, callback=None):
"""Calculate equation-of-state.
atoms: Atoms object
System to calculate EOS for. Must have a calculator attached.
npoints: int
Number of points.
eps: float
Variation in volume from v0*(1-eps) to v0*(1+eps).
trajectory: Trjectory object or str
Write configurations to a trajectory file.
callback: function
Called after every energy calculation.
>>> from ase.build import bulk
>>> from ase.calculators.emt import EMT
>>> a = bulk('Cu', 'fcc', a=3.6)
>>> a.calc = EMT()
>>> eos = calculate_eos(a, trajectory='Cu.traj')
>>> v, e, B = eos.fit()
>>> a = (4 * v)**(1 / 3.0)
>>> print('{0:.6f}'.format(a))
3.589825
"""
# Save original positions and cell:
p0 = atoms.get_positions()
c0 = atoms.get_cell()
if isinstance(trajectory, basestring):
from ase.io import Trajectory
trajectory = Trajectory(trajectory, 'w', atoms)
if trajectory is not None:
trajectory.set_description({
'type': 'eos',
'npoints': npoints,
'eps': eps
})
try:
energies = []
volumes = []
for x in np.linspace(1 - eps, 1 + eps, npoints)**(1 / 3):
atoms.set_cell(x * c0, scale_atoms=True)
volumes.append(atoms.get_volume())
energies.append(atoms.get_potential_energy())
if callback:
callback()
if trajectory is not None:
trajectory.write()
return EquationOfState(volumes, energies)
finally:
atoms.cell = c0
atoms.positions = p0
if trajectory is not None:
trajectory.close()
def split(images,
trainingname='trainingimages.traj',
testname='testimages.traj',
shuffle=True,
test_set=20,
logfile='log.txt'):
"""Split data set in training and test sets.
images : str
Path to images to be split.
trainingname : str
Name of the training set trajectory file. By default is
trainingimages.traj
testname : str
Name of the test set trajectory file. By default is
testimages.traj
test_set : integer
Porcentage of training data that will be used as test set.
shuffle : bool
Whether or not the data will be randomized.
logfile : str
Name of logfile. By default is log.txt.
"""
images = Trajectory(images)
total_length = len(images)
test_length = int((test_set * total_length / 100))
training_leght = int(total_length - test_length)
_images = list(range(len(images)))
if shuffle is True:
random.shuffle(_images)
trainingimages = []
ti = Trajectory(trainingname, mode='w')
log = open(logfile, 'w')
for i in _images[0:training_leght]:
trainingimages.append(i)
ti.write(images[i])
log.write(str(trainingimages))
log.write('\n')
if test_set > 0:
testimages = []
test = Trajectory(testname, mode='w')
for i in _images[-test_length:-1]:
testimages.append(i)
test.write(images[i])
log.write(str(testimages))
log.close()
return
def calculate_eos(atoms, npoints=5, eps=0.04, trajectory=None, callback=None):
"""Calculate equation-of-state.
atoms: Atoms object
System to calculate EOS for. Must have a calculator attached.
npoints: int
Number of points.
eps: float
Variation in volume from v0*(1-eps) to v0*(1+eps).
trajectory: Trjectory object or str
Write configurations to a trajectory file.
callback: function
Called after every energy calculation.
>>> from ase.build import bulk
>>> from ase.calculators.emt import EMT
>>> a = bulk('Cu', 'fcc', a=3.6)
>>> a.calc = EMT()
>>> eos = calculate_eos(a, trajectory='Cu.traj')
>>> v, e, B = eos.fit()
>>> a = (4 * v)**(1 / 3.0)
>>> print('{0:.6f}'.format(a))
3.589825
"""
# Save original positions and cell:
p0 = atoms.get_positions()
c0 = atoms.get_cell()
if isinstance(trajectory, basestring):
from ase.io import Trajectory
trajectory = Trajectory(trajectory, 'w', atoms)
if trajectory is not None:
trajectory.set_description({'type': 'eos',
'npoints': npoints,
'eps': eps})
try:
energies = []
volumes = []
for x in np.linspace(1 - eps, 1 + eps, npoints)**(1 / 3):
atoms.set_cell(x * c0, scale_atoms=True)
volumes.append(atoms.get_volume())
energies.append(atoms.get_potential_energy())
if callback:
callback()
if trajectory is not None:
trajectory.write()
return EquationOfState(volumes, energies)
finally:
atoms.cell = c0
atoms.positions = p0
if trajectory is not None:
trajectory.close()
def test_pull():
import numpy as np
from ase import Atoms
from ase.calculators.emt import EMT
from ase.io import Trajectory
Cu = Atoms('Cu', pbc=(1, 0, 0), calculator=EMT())
traj = Trajectory('Cu.traj', 'w')
for a in np.linspace(2.0, 4.0, 20):
Cu.set_cell([a, 1, 1], scale_atoms=True)
traj.write(Cu)
def ani_to_ase(hdf5file, data_keys, trajfile=None):
"""ANI to ASE
Parameters
----------
hdf5file : hdf5, list
hdf5 file loaded using pyanitools (or list of them).
data_keys : list
List of keys to extract data.
trajfile : str, optional
Name of trajectory file to be saved, by default None.
Returns
-------
atoms
A list of Atoms objects.
"""
if isinstance(hdf5file, list) is False:
hdf5file = [hdf5file]
atoms = []
prop = {"energies": "energy", "energy": "energy"}
if trajfile is not None:
traj = Trajectory(trajfile, mode="w")
for hdf5 in hdf5file:
for data in hdf5:
symbols = data["species"]
conformers = data["coordinates"]
for index, conformer in enumerate(conformers):
molecule = Atoms(positions=conformer, symbols=symbols)
molecule.set_calculator(SinglePointCalculator())
_prop = {}
for key in data_keys:
value = data[key][index]
# Mutate key because ANI naming is not standard.
key = prop[key]
_prop[key] = value
molecule.calc.results[key] = value
atoms.append(molecule)
if trajfile is not None:
traj.write(molecule, **_prop)
return atoms
def main():
args = sys.argv
imgs = read(args[1], index=":")
random.shuffle(imgs)
imgs_selected = imgs[:200]
expansions = [0.05*(i+1) for i in range(8)]
traj=Trajectory('expanded.traj','w')
for img in imgs_selected:
imags_expanded=expand_particle(img, expansions)
for im in imags_expanded:
traj.write(im)
def test(*args, r='::', o='test.traj'):
if 'calculator' in cline.ARGS and cline.ARGS['calculator'] is not None:
raise RuntimeError('set calculator = None in ARGS!')
traj = Trajectory(o, 'w')
calc = cline.gen_active_calc()
for arg in args:
data = [read(arg)] if (r is None or ':' not in r) else read(arg, r)
for atoms in data:
atoms.set_calculator(calc)
atoms.get_forces()
if calc.rank == 0:
traj.write(atoms)
def traj_from_qe_xml(fileobj, index=-1, results_required=True):
"""Reads Quantum ESPRESSO output files.
The atomistic configurations as well as results (energy, force, stress,
magnetic moments) of the calculation are read for all configurations
within the output file.
Will probably raise errors for broken or incomplete files.
Parameters
----------
fileobj : file|str
A file like object or filename
index : slice
The index of configurations to extract.
results_required : bool
If True, atomistic configurations that do not have any
associated results will not be included. This prevents double
printed configurations and incomplete calculations from being
returned as the final configuration with no results data.
Yields
------
structure : Atoms
The next structure from the index slice. The Atoms has a
SinglePointCalculator attached with any results parsed from
the file.
"""
root = ET.parse(fileobj).getroot()
output = root.find('output')
steps = root.findall('step')
atoms, input_parameters = xml2atoms(output)
trajectory = None
trajectory = Trajectory('t1.traj', 'a')
atoms_list = []
for step in steps:
aaa, _ = xml2atoms(step)
trajectory.write(aaa)
atoms_list.append(aaa)
trajectory.close()
return atoms, input_parameters, atoms_list
def backup_outcar():
# it needs some improvement. Use with caution.
import os
import numpy as np
from ase.io import read, write, Trajectory
calc_id = int(np.loadtxt('db_id'))
if os.path.isfile(
'OUTCAR') and not os.path.isfile(f'opt_id_{calc_id}.traj'):
write(f'opt_id_{calc_id}.traj', read('OUTCAR', index=':'))
elif os.path.isfile('OUTCAR') and os.path.isfile(f'opt_id_{calc_id}.traj'):
t1 = Trajectory(f'opt_id_{calc_id}.traj', 'a')
t2 = read('OUTCAR', index=':')
for atoms in t2:
t1.write(atoms)
t1.close()
return print('OUTCAR backup complete')
def main():
arg = sys.argv
paras = readinputs(arg[1])
distances = paras['distance'].split()
md_traj = read('3w-pos-1.xyz', index=slice(-3000, None), format='xyz')
for p in md_traj:
dist = p.get_distance(7, 13) + p.get_distance(9, 11)
for distance in distances:
if dist > float(distance) - 0.05 and dist < float(distance) + 0.05:
make_dir(distance)
write(distance + '/geometry.xyz', p, format='xyz')
break
traj = Trajectory('selected.traj', 'w')
for distance in distances:
traj.write(
read(distance + '/geometry.xyz', index=':', format='xyz')[0])
def run(T, sysID):
ceBulk = init_BC()
prec = 1E-4
db = dataset.connect("sqlite:///" + mc_db_name)
entry = db["systems"].find_one(id=sysID)
chem_pot = {"c1_0": entry["c1_0"], "c1_1": entry["c1_1"]}
if entry["status"] == "finished":
return
equil_params = {"window_length": 30 * len(ceBulk.atoms), "mode": "fixed"}
max_steps = 1000 * len(ceBulk.atoms)
trajfile = "data/almgsi_sgc/traj_{}.traj".format(sysID)
traj = None
if rank == 0:
traj = Trajectory(trajfile, mode='w')
for temp in T:
print("Current temperature {}K".format(temp))
mc_obj = SGCMonteCarlo(ceBulk.atoms,
temp,
mpicomm=comm,
symbols=["Al", "Mg", "Si"])
mc_obj.runMC(mode="prec",
prec=prec,
chem_potential=chem_pot,
equil_params=equil_params,
steps=max_steps)
thermo = mc_obj.get_thermodynamic()
thermo["temperature"] = temp
thermo["prec"] = prec
thermo["internal_energy"] = thermo.pop("energy")
thermo["converged"] = True
thermo["muc1_0"] = chem_pot["c1_0"]
thermo["muc1_1"] = chem_pot["c1_1"]
if (rank == 0):
thermo["sysID"] = sysID
newID = db["thermodynamic"].insert(thermo)
cf = ceBulk.atoms._calc.get_cf()
cf["resultID"] = newID
db["correlation"].insert(cf)
atoms_cpy = ceBulk.atoms.copy()
atoms_cpy.set_calculator(None)
traj.write(atoms_cpy)
if (rank == 0):
db["systems"].update({"status": "finished", "id": sysID}, ["id"])
def main():
arg = sys.argv
try:
configs = read(arg[1], index=":")
except:
configs = read_atoms(arg[1])
traj = Trajectory('selected_' + arg[1], 'w')
chem_symbols = ['H', 'Pd']
H_indices = [atom.index for atom in configs[0] if atom.symbol == 'H']
Pd_indices = [atom.index for atom in configs[0] if atom.symbol == 'Pd']
#temp = copy.deepcopy(configs)
for itrj in range(len(configs)):
print itrj
config = configs[itrj]
delete = False
for i in range(len(H_indices) - 1):
for j in range(i + 1, len(H_indices)):
if config.get_distance(H_indices[i], H_indices[j]) < 0.5:
delete = True
break
if delete:
break
for pd in Pd_indices:
if config.get_distance(H_indices[i], pd) < 1.00:
delete = True
break
if delete:
break
if delete:
continue
for i in range(len(Pd_indices) - 1):
for j in range(i + 1, len(Pd_indices)):
if config.get_distance(Pd_indices[i], Pd_indices[j]) < 2.00:
delete = True
break
if delete:
break
if delete:
continue
traj.write(config)
def init_model(atoms, samples=5, rattle=0.05, trajectory='init.traj'):
"""
atoms: ASE atoms
samples: number of samples
rattle: stdev for random displacements
trajectory: traj file name
"""
calc = cline.gen_active_calc()
master = calc.rank == 0
if master:
traj = Trajectory(trajectory, 'w')
for _ in range(samples):
tmp = atoms.copy()
tmp.rattle(rattle, rng=np.random)
tmp.set_calculator(calc)
tmp.get_potential_energy()
if master:
traj.write(tmp)
def main():
#config = ConfigParser.SafeConfigParser()
config = ConfigParser.ConfigParser()
config.read('config.ini')
#print config
main_paras = dict(config.items('main'))
#print main_paras
atoms = read(main_paras['structurefile'],
index=main_paras['structure_slice'],
format=main_paras['fileformat'])
h_distances = np.array([0.6 + float(i) / 10.0 for i in range(10)])
bondlength = 1.6
traj = Trajectory('traj.traj', 'w')
h_index = []
for index in range(len(atoms[0])):
if atoms[0][index].symbol == 'H':
h_index.append(index)
h_index.sort(reverse=True)
for p in atoms:
for index in h_index:
p.pop(i=index)
center = np.mean(p.get_positions(), axis=0)
print center
for atom in p:
distance = np.linalg.norm(center - atom.position)
if distance > 2.0:
dot = atom.position + bondlength * (atom.position -
center) / distance
perp_vector = perpendicular_vector(atom.position - center)
unit_perp_vector = perp_vector / np.linalg.norm(perp_vector)
for h_distance in h_distances:
image = p.copy()
image.append(
Atom('H', dot + h_distance * unit_perp_vector / 2.0))
image.append(
Atom('H', dot - h_distance * unit_perp_vector / 2.0))
#image=image.wrap(center=(0.5, 0.5, 0.5))
traj.write(image)
break
def test_hcp():
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
print('%.4f %.3f' % (a0, c0 / a0))
for i in range(3):
traj = Trajectory('Ni.traj', 'w')
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 4):
for c in c0 * np.linspace(1 - eps, 1 + eps, 4):
ni = bulk('Ni', 'hcp', a=a, covera=c / a)
ni.calc = EMT()
ni.get_potential_energy()
traj.write(ni)
traj.close()
configs = read('Ni.traj', index=':')
energies = [config.get_potential_energy() for config in configs]
ac = [(config.cell[0, 0], config.cell[2, 2]) for config in configs]
p = polyfit(ac, energies, 2)
a0, c0 = fmin_bfgs(p, (a0, c0))
print('%.4f %.3f' % (a0, c0 / a0))
assert abs(a0 - 2.466) < 0.001
assert abs(c0 / a0 - 1.632) < 0.005
def main():
arg = sys.argv
paras = readinputs(arg[1])
distances = paras['distance'].split()
#output = open('freeEnergy.dat','w')
dx = float(paras['dx'])
avg_force = []
free_energy = []
md_steps = []
atom_distance = {}
tag = None
atoms = None
traj = Trajectory('reaction.traj', 'w', atoms)
#traj=[]
cellsize = 20.0
for distance in distances:
cp2k_inp = open(distance + '/' + paras['cp2k_inp'], 'r')
lines = cp2k_inp.readlines()
for line in lines:
if 'PROJECT_NAME' in line:
tag = line.split()[1]
break
try:
p = read(distance + '/' + tag + '-pos-1.xyz',
index=slice(-1, None),
format='xyz')[0]
p.set_cell([[cellsize, 0, 0], [0, cellsize, 0], [0, 0, cellsize]],
scale_atoms=False)
p.set_pbc((True, True, True))
except:
print(distance)
continue
p.center()
print(p)
#traj.append(p)
traj.write(p)
# Make a mask of zeros and ones that select fixed atoms - the two
# bottom layers:
mask = initial.positions[:, 2] - min(initial.positions[:, 2]) < 1.5 * h
constraint = FixAtoms(mask=mask)
initial.set_constraint(constraint)
# Calculate using EMT:
initial.calc = EMT()
# Relax the initial state:
QuasiNewton(initial).run(fmax=0.05)
e0 = initial.get_potential_energy()
traj = Trajectory('dimer_along.traj', 'w', initial)
traj.write()
# Making dimer mask list:
d_mask = [False] * (N - 1) + [True]
# Set up the dimer:
d_control = DimerControl(initial_eigenmode_method='displacement',
displacement_method='vector',
logfile=None,
mask=d_mask)
d_atoms = MinModeAtoms(initial, d_control)
# Displacement settings:
displacement_vector = np.zeros((N, 3))
# Strength of displacement along y axis = along row:
displacement_vector[-1, 1] = 0.001
# Set calculator
# loop a number of times to capture if minimization stops with high force
# due to the VariansBreak calls
niter = 0
# If the structure is already fully relaxed just return it
traj = Trajectory(label + '_lcao.traj', 'w', structure)
while (structure.get_forces()**
2).sum(axis=1).max()**0.5 > forcemax and niter < niter_max:
dyn = BFGS(structure, logfile=label + '.log')
vb = VariansBreak(structure, dyn, min_stdev=0.01, N=15)
dyn.attach(traj)
dyn.attach(vb)
dyn.run(fmax=forcemax, steps=steps)
niter += 1
#print('relaxgpaw over',flush=True)
return structure
calc = GPAW(mode=PW(500), xc='PBE', basis='dzp', kpts=(3, 3, 1))
traj = Trajectory('V2O5_H2OTiO2_101_DFTrelaxed.traj', 'w')
name = 'V2O5_H2OTiO2_101surface_gm'
data = read('BE_V2O5_H2O_TiO2_101_I8.traj@:')
for i in range(0, len(data)):
name = 'V2O5H2OTiO2_101surface_isomer_{}'.format(i)
a = data[i]
a.set_calculator(calc)
a_relaxed = relaxGPAW(a, name, forcemax=0.01, niter_max=2, steps=100)
traj.write(a_relaxed)
class globalOptim():
"""
--Input--
MLmodel:
Model that given training data can predict energy and gradient of a structure.
Hint: must include a fit, predict_energy and predict_force methods.
Natoms:
Number of atoms in structure.
Niter:
Number of monte-carlo steps.
rattle_maxDist:
Max translation of each coordinate when perturbing the current structure to
form a new candidate.
min_saveDifference:
Defines the energy which a new trajectory point has to be lover than the previous, to be saved for training.
minSampleStep:
if minSampleStep=10, every tenth point in the relaxation trajectory is used for training, and so on..
Unless min_saveDifference have not been ecxeeded.
"""
def __init__(self, traj_namebase, MLmodel, startGenerator, mutationSelector, calc=None, startStructures=None, population_size=5, kappa=2, Niter=50, Ninit=2, sigma=20, min_saveDifference=0.3, minSampleStep=10, dualPoint=False, relaxFinalPop=False, stat=True):
self.traj_namebase = traj_namebase
self.MLmodel = MLmodel
self.startGenerator = startGenerator
self.mutationSelector = mutationSelector
self.calc = calc
self.startStructures = startStructures
self.population = population(population_size=population_size, comparator=self.MLmodel.comparator)
self.kappa = kappa
self.Natoms = len(self.startGenerator.slab) + len(self.startGenerator.atom_numbers)
self.Niter = Niter
self.Ninit = Ninit
try:
len(sigma)
self.sigma = list(sigma)
except:
self.sigma = [sigma]
self.min_saveDifference = min_saveDifference
self.minSampleStep = minSampleStep
self.dualPoint = dualPoint
self.relaxFinalPop = relaxFinalPop
self.stat = stat
self.opNameList = [op.descriptor for op in self.mutationSelector.oplist]
# List of structures to be added in next training
self.a_add = []
self.traj_counter = 0
self.ksaved = 0
# Define parallel communication
self.comm = world.new_communicator(np.array(range(world.size)))
self.master = self.comm.rank == 0
# Make new folders
self.ML_dir = 'all_MLcandidates/'
self.pop_dir = 'relaxedPop/'
if self.master:
os.makedirs(self.ML_dir)
os.makedirs(self.pop_dir)
# Trajectory names
self.writer_initTrain = Trajectory(filename=traj_namebase+'initTrain.traj', mode='a', master=self.master)
self.writer_spTrain = Trajectory(filename=traj_namebase+'spTrain.traj', mode='a', master=self.master)
self.writer_spPredict = Trajectory(filename=traj_namebase+'spPredict.traj', mode='a', master=self.master)
self.writer_current = Trajectory(filename=traj_namebase+'current.traj', mode='a', master=self.master)
# make txt file
open(traj_namebase + 'sigma.txt', 'a').close()
open(traj_namebase + 'MLerror_Ntries.txt', 'a').close()
open(traj_namebase + 'E_MLerror.txt', 'a').close()
open(traj_namebase + 'time.txt', 'a').close()
def runOptimizer(self):
# Initial structures
if self.startStructures is None:
for i in range(self.Ninit):
a_init, _ = self.startGenerator.get_new_individual()
a, E, F = self.relaxTrue(a_init)
self.population.add_structure(a, E, F)
else:
for a in self.startStructures:
Ei = a.get_potential_energy()
Fi = a.get_forces()
self.a_add.append(a)
self.writer_initTrain.write(a, energy=Ei)
self.population.add_structure(a, Ei, Fi)
# Reset traj_counter for ML-relaxations
self.traj_counter = 0
# Run global search
for i in range(self.Niter):
# Train ML model if new data is available
t0_all = time()
t0_train = time()
if len(self.a_add) > 0:
self.trainModel()
t1_train = time()
# Clean similar structures from population
self.update_MLrelaxed_pop()
# Generate new rattled + MLrelaxed candidate
t_newCand_start = time()
a_new = self.newCandidate_beyes()
t_newCand_end = time()
# Singlepoint with objective potential
t_sp_start = time()
Enew, Fnew = self.singlePoint(a_new)
t_sp_end = time()
# Get dual-point if relevant
Fnew_max = (Fnew**2).sum(axis=1).max()**0.5
if self.dualPoint and i > 50 and Fnew_max > 0.5:
a_dp = self.get_dualPoint(a_new, Fnew)
E, error, _ = self.MLmodel.predict_energy(a_dp, return_error=True)
# If dual-point looks promising - perform sp-calculation
if E - self.kappa*error < self.population.largest_energy:
E_dp, F_dp = self.singlePoint(a_dp)
if E_dp < Enew:
a_new = a_dp.copy()
Enew = E_dp
Fnew = F_dp
# Try to add the new structure to the population
t1_all = time()
#self.update_MLrelaxed_pop()
self.population.add_structure(a_new, Enew, Fnew)
if self.master:
for i, a in enumerate(self.population.pop):
E = a.get_potential_energy()
print('pop{0:d}={1:.2f} '.format(i, E), end='')
# write population to file
self.writer_current.write(a, energy=E, forces=a.get_forces())
print('')
print('Enew={}'.format(Enew))
t2_all = time()
if self.master:
with open(self.traj_namebase + 'time.txt', 'a') as f:
f.write('{}\t{}\t{}\t{}\t{}\n'.format(t_newCand_end-t_newCand_start,
t_sp_end-t_sp_start,
t1_train - t0_train,
t1_all - t0_all,
t2_all - t0_all))
self.traj_counter += 1
# Save final population
self.update_MLrelaxed_pop()
pop = self.population.pop
write(self.traj_namebase + 'finalPop.traj', pop)
# relax final pop with true potential
if self.relaxFinalPop:
relaxed_pop = []
for i, a in enumerate(pop):
# Only promicing structures
if (a.get_forces()**2).sum(axis = 1).max()**0.5 < 2:
name = savefiles_namebase + 'pop{}'.format(i)
a_relaxed = relaxGPAW(a, name, forcemax=0.05, steps=30, niter_max=2)
relaxed_pop.append(a_relaxed)
write(self.traj_namebase + 'finalPop_relaxed.traj', relaxed_pop)
def update_MLrelaxed_pop(self):
# Initialize MLrelaxed population
self.population.pop_MLrelaxed = []
for a in self.population.pop:
self.population.pop_MLrelaxed.append(a.copy())
E_relaxed_pop = np.zeros(len(self.population.pop))
error_relaxed_pop = np.zeros(len(self.population.pop))
if self.comm.rank < len(self.population.pop):
index = self.comm.rank
a_MLrelaxed = self.relaxML(self.population.pop[index], Fmax=0.01)
self.population.pop_MLrelaxed[index] = a_MLrelaxed
E_temp, error_temp, _ = self.MLmodel.predict_energy(a_MLrelaxed, return_error=True)
E_relaxed_pop[index] = E_temp
error_relaxed_pop[index] = error_temp
for i in range(len(self.population.pop)):
pos = self.population.pop_MLrelaxed[i].positions
self.comm.broadcast(pos, i)
self.population.pop_MLrelaxed[i].set_positions(pos)
E = np.array([E_relaxed_pop[i]])
error = np.array([error_relaxed_pop[i]])
self.comm.broadcast(E, i)
self.comm.broadcast(error, i)
self.population.pop_MLrelaxed[i].info['key_value_pairs']['predictedEnergy'] = E[0]
self.population.pop_MLrelaxed[i].info['key_value_pairs']['predictedError'] = error[0]
self.population.pop_MLrelaxed[i].info['key_value_pairs']['fitness'] = E[0] - self.kappa*error[0]
label = self.pop_dir + 'ML_relaxed_pop{}'.format(self.traj_counter)
write(label+'.traj', self.population.pop_MLrelaxed)
"""
# Initialize MLrelaxed population
self.population.pop_MLrelaxed = []
for a in self.population.pop:
self.population.pop_MLrelaxed.append(a.copy())
if self.comm.rank < len(self.population.pop):
index = self.comm.rank
self.population.pop_MLrelaxed[index] = self.relaxML(self.population.pop[index], Fmax=0.01)
for i in range(len(self.population.pop)):
pos = self.population.pop_MLrelaxed[i].positions
self.comm.broadcast(pos, i)
self.population.pop_MLrelaxed[i].set_positions(pos)
"""
def get_dualPoint(self, a, F, lmax=0.10, Fmax_flat=5):
"""
lmax:
The atom with the largest force will be displaced by this distance
Fmax_flat:
max displaced distance is increased linearely with force until
Fmax = Fmax_flat, over which it will be constant as lmax.
"""
a_dp = a.copy()
# Calculate and set new positions
Fmax = np.sqrt((F**2).sum(axis=1).max())
pos_displace = lmax * F*min(1/Fmax_flat, 1/Fmax)
pos_dp = a.positions + pos_displace
a_dp.set_positions(pos_dp)
return a_dp
def get_force_mutated_population(self, lmax=[0.02, 0.07]):
Npop = len(self.population.pop)
Nl = len(lmax)
E_list = np.zeros(Npop*Nl)
error_list = np.zeros(Npop*Nl)
pos_list = np.zeros((Npop*Nl, 3*self.Natoms))
for i, a in enumerate(self.population.pop):
F = a.get_forces()
for n, l in enumerate(lmax):
anew = self.get_dualPoint(a, F, lmax=l)
pos_new = anew.get_positions()
E, error, theta0 = self.MLmodel.predict_energy(anew, return_error=True)
E_list[i*Nl+n] = E
error_list[i*Nl+n] = error
pos_list[i*Nl+n] = pos_new.reshape(-1)
return pos_list, E_list, error_list
def mutate(self, Ntasks_each):
a_mutated_list = []
for k in range(Ntasks_each):
# draw random structure to mutate from population
a = self.population.get_structure()
a_copy = a.copy()
a_mutated, _ = self.mutationSelector.get_new_individual([a_copy])
a_mutated_list.append(a_mutated)
self.comm.barrier()
return a_mutated_list
def newCandidate_beyes(self):
N_newCandidates = 30
# the maximum number of candidates a core need to make N_newCandidates on a single node.
N_tasks = int(np.ceil(N_newCandidates / self.comm.size))
# Use all cores on nodes.
N_newCandidates = N_tasks * N_newCandidates
# perform mutations
if self.master:
t0 = time()
anew_mutated_list = self.mutate(N_tasks)
if self.master:
print('mutation time:', time() - t0, flush=True)
# Relax with MLmodel
anew_list = []
E_list = []
error_list = []
for anew_mutated in anew_mutated_list:
anew = self.relaxML(anew_mutated, with_error=True)
anew_list.append(anew)
E, error, theta0 = self.MLmodel.predict_energy(anew, return_error=True)
E_list.append(E)
error_list.append(error)
E_list = np.array(E_list)
error_list = np.array(error_list)
if self.master:
print('theta0:', theta0, flush=True)
oplist_index = np.array([self.opNameList.index(a.info['key_value_pairs']['origin']) for a in anew_list]).astype(int)
# Gather data from slaves to master
pos_new_list = np.array([anew.positions for anew in anew_list])
pos_new_mutated_list = np.array([anew_mutated.positions for anew_mutated in anew_mutated_list])
if self.comm.rank == 0:
E_all = np.empty(N_tasks * self.comm.size, dtype=float)
error_all = np.empty(N_tasks * self.comm.size, dtype=float)
pos_all = np.empty(N_tasks * 3*self.Natoms*self.comm.size, dtype=float)
pos_all_mutated = np.empty(N_tasks * 3*self.Natoms*self.comm.size, dtype=float)
oplist_index_all = np.empty(N_tasks * self.comm.size, dtype=int)
else:
E_all = None
error_all = None
pos_all = None
pos_all_mutated = None
oplist_index_all = None
self.comm.gather(E_list, 0, E_all)
self.comm.gather(error_list, 0, error_all)
self.comm.gather(pos_new_list.reshape(-1), 0, pos_all)
self.comm.gather(pos_new_mutated_list.reshape(-1), 0, pos_all_mutated)
self.comm.gather(oplist_index, 0, oplist_index_all)
# Pick best candidate on master + broadcast
pos_new = np.zeros((self.Natoms, 3))
pos_new_mutated = np.zeros((self.Natoms, 3))
if self.master:
fitness_all = E_all - self.kappa * error_all
index_best = fitness_all.argmin()
print('{}:\n'.format(self.traj_counter), np.c_[E_all, error_all])
print('{} best:\n'.format(self.traj_counter), E_all[index_best], error_all[index_best])
with open(self.traj_namebase + 'E_MLerror.txt', 'a') as f:
f.write('{0:.4f}\t{1:.4f}\n'.format(E_all[index_best], error_all[index_best]))
pos_all = pos_all.reshape((-1, self.Natoms, 3))
pos_new = pos_all[index_best] # old
pos_all_mutated = pos_all_mutated.reshape((N_tasks * self.comm.size, self.Natoms, 3))
pos_new_mutated = pos_all_mutated[index_best] # old
if self.stat:
a_all = []
a_all_mutated = []
for i, (pos, pos_mutated) in enumerate(zip(pos_all, pos_all_mutated)):
a = anew.copy()
a_mutated = anew.copy()
a.positions = pos
a_mutated.positions = pos_mutated
a.info['key_value_pairs']['predictedEnergy'] = E_all[i]
a.info['key_value_pairs']['predictedError'] = error_all[i]
a.info['key_value_pairs']['fitness'] = E_all[i] - self.kappa*error_all[i]
a.info['key_value_pairs']['origin'] = self.opNameList[oplist_index_all[index_best]]
a_all.append(a)
a_all_mutated.append(a_mutated)
label_relaxed = self.ML_dir + 'ML_relaxed{}'.format(self.traj_counter)
write(label_relaxed+'.traj', a_all, parallel=False)
label_unrelaxed = self.ML_dir + 'ML_unrelaxed{}'.format(self.traj_counter)
write(label_unrelaxed+'.traj', a_all_mutated, parallel=False)
# Write unrelaxed + relaxed versions of best candidate to file
label = self.ML_dir + 'ML_best{}'.format(self.traj_counter)
write(label+'.traj', [a_all_mutated[index_best], a_all[index_best]], parallel=False)
#try:
# pos_new = pos_all[index_best]
# pos_new_mutated = pos_all_mutated[index_best]
#except IndexError:
# pos_new = self.population.pop_MLrelaxed[index_best % N_newCandidates].get_positions()
# pos_new_mutated = self.population.pop[index_best % N_newCandidates].get_positions()
self.comm.broadcast(pos_new, 0)
anew.positions = pos_new
self.comm.broadcast(pos_new_mutated, 0)
anew_mutated = anew.copy()
anew_mutated.positions = pos_new_mutated
self.comm.barrier()
# Write unrelaxed + relaxed versions of best candidate to file
#label = self.ML_dir + 'ML_best{}'.format(self.traj_counter)
#write(label+'.traj', [anew_mutated, anew])
return anew
def trainModel(self):
"""
# Reduce training data - If there is too much
if self.ksaved > self.maxNtrain:
Nremove = self.ksaved - self.maxNtrain
self.ksaved = self.maxNtrain
self.MLmodel.remove_data(Nremove)
"""
#GSkwargs = {'reg': [1e-5], 'sigma': np.logspace(1, 3, 5)}
# GSkwargs = {'reg': [1e-5], 'sigma': [30]} # C24
GSkwargs = {'reg': [1e-5], 'sigma': self.sigma} # SnO
FVU, params = self.MLmodel.train(atoms_list=self.a_add,
add_new_data=True,
k=3,
**GSkwargs)
self.a_add = []
if self.master:
with open(self.traj_namebase + 'sigma.txt', 'a') as f:
f.write('{0:.2f}\n'.format(params['sigma']))
def add_trajectory_to_training(self, trajectory_file):
atoms = read(filename=trajectory_file, index=':', parallel=False)
E = [a.get_potential_energy() for a in atoms]
Nstep = len(atoms)
# Always add+save start structure
self.a_add.append(atoms[0])
self.writer_initTrain.write(atoms[0], energy=E[0])
n_last = 0
Ecurrent = E[0]
for i in range(1,Nstep-int(self.minSampleStep/2)):
n_last += 1
if Ecurrent - E[i] > self.min_saveDifference and n_last > self.minSampleStep:
self.a_add.append(atoms[i])
Ecurrent = E[i]
self.ksaved += 1
n_last = 0
# Save to initTrain-trajectory
self.writer_initTrain.write(atoms[i], energy=E[i])
# Always save+add last structure
self.a_add.append(atoms[-1])
self.writer_initTrain.write(atoms[-1], energy=E[-1])
def relaxML(self, anew, Fmax=0.1, with_error=True):
a = anew.copy()
# Relax
label = self.traj_namebase + 'ML{}'.format(self.traj_counter)
if with_error:
krr_calc = krr_calculator(self.MLmodel, kappa=self.kappa)
else:
krr_calc = krr_calculator(self.MLmodel)
a_relaxed = relax_VarianceBreak(a, krr_calc, label, niter_max=1, forcemax=Fmax)
return a_relaxed
def relaxTrue(self, a):
pos = a.positions
if self.master:
pos = a.positions
self.comm.broadcast(pos, 0)
a.positions = pos
self.comm.barrier()
label = self.traj_namebase + '{}'.format(self.traj_counter)
pos_relaxed = a.positions
Erelaxed = np.zeros(1)
Frelaxed = np.zeros((3,self.Natoms))
if self.master:
# Relax
a_relaxed = relaxGPAW(a, label, calc=self.calc)
pos_relaxed = a_relaxed.positions
Erelaxed = np.array([a_relaxed.get_potential_energy()])
Frelaxed = a_relaxed.get_forces()
self.comm.broadcast(pos_relaxed, 0)
self.comm.broadcast(Erelaxed, 0)
Erelaxed = Erelaxed[0]
self.comm.broadcast(Frelaxed, 0)
a_relaxed = a.copy()
a_relaxed.positions = pos_relaxed
self.comm.barrier()
# Add sampled trajectory to training data.
self.add_trajectory_to_training(label+'_lcao.traj')
self.traj_counter += 1
return a_relaxed, Erelaxed, Frelaxed
def singlePoint(self, anew):
a = anew.copy()
# Save structure with ML-energy
if self.master:
self.writer_spPredict.write(a)
# broadcast structure, so all cores have the same
pos = a.positions
if self.master:
pos = a.positions
self.comm.broadcast(pos, 0)
a.positions = pos
self.comm.barrier()
# Perform single-point
E = np.zeros(1)
F = np.zeros((self.Natoms,3))
if self.master:
label = self.traj_namebase + '{}'.format(self.traj_counter)
E, F = singleGPAW(a, label, calc=self.calc)
E = np.array([E])
self.comm.broadcast(E, 0)
E = E[0]
self.comm.broadcast(F, 0)
# save structure for training
a.energy = E
results = {'energy': E}
calc = SinglePointCalculator(a, **results)
a.set_calculator(calc)
self.a_add.append(a)
# Save to spTrain-trajectory
self.writer_spTrain.write(a, energy=E, forces=F)
self.ksaved += 1
return E, F
if sys.platform in ['win32']:
raise NotAvailable('Fails on Windows '
'https://trac.fysik.dtu.dk/projects/ase/ticket/62')
import os
from ase import Atom, Atoms
from ase.io import Trajectory, read
from ase.constraints import FixBondLength
co = Atoms([Atom('C', (0, 0, 0)),
Atom('O', (0, 0, 1.2))])
traj = Trajectory('1.traj', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
traj = Trajectory('1.traj', 'a')
co = read('1.traj')
print(co.positions)
co.positions[:] += 1
traj.write(co)
for a in Trajectory('1.traj'):
print(1, a.positions[-1, 2])
co.positions[:] += 1
t = Trajectory('1.traj', 'a')
t.write(co)
assert len(t) == 7
co[0].number = 1
from ase.test import NotAvailable, must_raise
if sys.platform in ['win32']:
raise NotAvailable('Fails on Windows '
'https://trac.fysik.dtu.dk/projects/ase/ticket/62')
import os
from ase import Atom, Atoms
from ase.io import Trajectory, read
co = Atoms([Atom('C', (0, 0, 0)),
Atom('O', (0, 0, 1.2))])
traj = Trajectory('1.traj', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
traj = Trajectory('1.traj', 'a')
co = read('1.traj')
print(co.positions)
co.positions[:] += 1
traj.write(co)
for a in Trajectory('1.traj'):
print(1, a.positions[-1, 2])
co.positions[:] += 1
t = Trajectory('1.traj', 'a')
t.write(co)
assert len(t) == 7
co[0].number = 1
relativistic=relativistic,
constant_basis=constant_basis,
x=x)
if id is None:
continue
# perform EOS step
atoms.set_cell(cell * x, scale_atoms=True)
# set calculator
atoms.calc = GPAW(
txt=name + '_' + code + '_' + str(n) + '.txt',
xc='PBE',
kpts=kpts,
width=width,
parallel={'band': 1},
idiotproof=False)
atoms.calc.set(**kwargs) # remaining calc keywords
t = time.time()
atoms.get_potential_energy()
c.write(atoms,
category=category,
name=name, e=e, linspacestr=linspacestr,
kptdensity=kptdensity, width=width,
relativistic=relativistic,
constant_basis=constant_basis,
x=x,
magnetic_moment=atoms.calc.get_magnetic_moment(),
niter=atoms.calc.get_number_of_iterations(),
time=time.time()-t)
traj.write(atoms)
del c[id]
import numpy as np
from ase import Atoms
from ase.calculators.emt import EMT
from ase.io import Trajectory
Cu = Atoms('Cu', pbc=(1, 0, 0), calculator=EMT())
traj = Trajectory('Cu.traj', 'w')
for a in np.linspace(2.0, 4.0, 20):
Cu.set_cell([a, 1, 1], scale_atoms=True)
traj.write(Cu)
# Make a mask of zeros and ones that select fixed atoms - the two
# bottom layers:
mask = initial.positions[:, 2] - min(initial.positions[:, 2]) < 1.5 * h
constraint = FixAtoms(mask=mask)
initial.set_constraint(constraint)
# Calculate using EMT:
initial.set_calculator(EMT())
# Relax the initial state:
QuasiNewton(initial).run(fmax=0.05)
e0 = initial.get_potential_energy()
traj = Trajectory('dimer_along.traj', 'w', initial)
traj.write()
# Making dimer mask list:
d_mask = [False] * (N - 1) + [True]
# Set up the dimer:
d_control = DimerControl(initial_eigenmode_method='displacement',
displacement_method='vector',
logfile=None,
mask=d_mask)
d_atoms = MinModeAtoms(initial, d_control)
# Displacement settings:
displacement_vector = np.zeros((N, 3))
# Strength of displacement along y axis = along row:
displacement_vector[-1, 1] = 0.001
import numpy as np
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
from ase.io import Trajectory
traj = Trajectory('Ni.traj', 'w')
from ase.lattice import bulk
from ase.calculators.emt import EMT
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 3):
for c in c0 * np.linspace(1 - eps, 1 + eps, 3):
ni = bulk('Ni', 'hcp', a=a, c=c)
ni.set_calculator(EMT())
ni.get_potential_energy()
traj.write(ni)
from ase.io import read
configs = read('Ni.traj@:')
energies = [config.get_potential_energy() for config in configs]
a = np.array([config.cell[0, 0] for config in configs])
c = np.array([config.cell[2, 2] for config in configs])
functions = np.array([a**0, a, c, a**2, a * c, c**2])
p = np.linalg.lstsq(functions.T, energies)[0]
p0 = p[0]
p1 = p[1:3]
p2 = np.array([(2 * p[3], p[4]),
(p[4], 2 * p[5])])
a0, c0 = np.linalg.solve(p2.T, -p1)