def main_elph__init(structure_path, params_fd_path, supercell, log,
symmetry_tol, disp_split, stop_after_displacements,
raman_settings):
from gpaw import GPAW
if raman_settings['write_mode_intensities'] and raman_settings[
'permutations'] == 'original':
parprint(
f"--write-mode-intensities requires --no-permutations or --permutations=fast"
)
sys.exit(1)
calc = GPAW(structure_path)
if calc.wfs.kpt_u[0].C_nM is None:
parprint(
f"'{structure_path}': no wavefunctions! You must save your .gpw file with 'mode=\"all\"'!"
)
sys.exit(1)
if calc.parameters['convergence']['bands'] == 'occupied':
parprint(
f"'{structure_path}': WARNING: only occupied bands were converged! Please converge some conduction band states as these are an explicit part of the electron-phonon computation."
)
if params_fd_path is not None:
params_fd = json.load(open(params_fd_path))
else:
params_fd = {}
# atoms = Cluster(ase.build.molecule('CH4'))
# atoms.minimal_box(4)
# atoms.pbc = True
if os.path.exists('phonopy_disp.yaml'):
parprint('using saved phonopy_disp.yaml')
else:
parprint('computing phonopy_disp.yaml')
world.barrier(
) # avoid race condition where rank 0 creates file before others enter
phonon = get_minimum_displacements(
unitcell=ase_atoms_to_phonopy(calc.atoms),
supercell_matrix=np.diag(supercell),
displacement_distance=DISPLACEMENT_DIST,
phonopy_kw=dict(symprec=symmetry_tol, ),
)
if world.rank == 0:
phonon.save('phonopy_disp.yaml')
world.barrier(
) # avoid race condition where rank 0 creates file before others enter
# Structure with initial guess of wavefunctions for displacement calculations.
if os.path.exists('supercell.eq.gpw'):
parprint('using saved supercell.eq.gpw')
else:
parprint('computing supercell.eq.gpw')
supercell_atoms = make_gpaw_supercell(calc, supercell,
**dict(params_fd, txt=log))
ensure_gpaw_setups_initialized(supercell_atoms.calc, supercell_atoms)
supercell_atoms.get_potential_energy()
supercell_atoms.calc.write('supercell.eq.gpw', mode='all')
def elph_do_symmetry_expansion(supercell, calc, displacement_dist, phonon, disp_carts, disp_sites, supercell_atoms):
from gpaw.elph.electronphonon import ElectronPhononCoupling
natoms_prim = len(calc.get_atoms())
disp_values = [read_elph_input(f'sym-{index}') for index in range(len(disp_sites))]
# NOTE: phonon.symmetry includes pure translational symmetries of the supercell
# so we use an empty quotient group
quotient_perms = np.array([np.arange(len(supercell_atoms))])
super_lattice = supercell_atoms.get_cell()[...]
super_symmetry = phonon.symmetry.get_symmetry_operations()
oper_sfrac_rots = super_symmetry['rotations']
oper_sfrac_trans = super_symmetry['translations']
oper_cart_rots = np.array([super_lattice.T @ Rfrac @ np.linalg.inv(super_lattice).T for Rfrac in oper_sfrac_rots])
oper_cart_trans = oper_sfrac_trans @ super_lattice
oper_phonopy_coperms = phonon.symmetry.get_atomic_permutations()
oper_phonopy_deperms = np.argsort(oper_phonopy_coperms, axis=1)
# Convert permutations by composing the following three permutations: into phonopy order, apply oper, back to ase order
parprint('phonopy deperms:', oper_phonopy_deperms.shape)
deperm_phonopy_to_ase = interop.get_deperm_from_phonopy_sc_to_ase_sc(natoms_prim, supercell)
oper_deperms = [np.argsort(deperm_phonopy_to_ase)[deperm][deperm_phonopy_to_ase] for deperm in oper_phonopy_deperms]
del oper_phonopy_coperms, oper_phonopy_deperms
elphsym = symmetry.ElphGpawSymmetrySource.from_setups_and_ops(
setups=supercell_atoms.calc.wfs.setups,
lattice=super_lattice,
oper_cart_rots=oper_cart_rots,
oper_cart_trans=oper_cart_trans,
oper_deperms=oper_deperms,
)
if world.rank == 0:
full_derivatives = symmetry.expand_derivs_by_symmetry(
disp_sites, # disp -> atom
disp_carts, # disp -> 3-vec
disp_values, # disp -> T (displaced value, optionally minus equilibrium value)
elph_callbacks_2(supercell_atoms.calc.wfs, elphsym, supercell=supercell), # how to work with T
oper_cart_rots, # oper -> 3x3
oper_perms=oper_deperms, # oper -> atom' -> atom
quotient_perms=quotient_perms,
)
# NOTE: confusingly, Elph wants primitive atoms, but a calc for the supercell
elph = ElectronPhononCoupling(calc.atoms, calc=supercell_atoms.calc, supercell=supercell)
displaced_cell_index = elph.offset
del elph # that's all we needed it for
eq_Vt, eq_dH, eq_forces = read_elph_input('eq')
for a in range(natoms_prim):
for c in range(3):
delta_Vt, delta_dH, delta_forces = full_derivatives[natoms_prim * displaced_cell_index + a][c]
for sign in [-1, +1]:
disp = interop.AseDisplacement(atom=a, axis=c, sign=sign)
disp_Vt = eq_Vt + sign * displacement_dist * delta_Vt
disp_dH = {k: eq_dH[k] + sign * displacement_dist * delta_dH[k] for k in eq_dH}
disp_forces = eq_forces + sign * displacement_dist * delta_forces
pickle.dump(disp_forces, paropen(f'phonons.{disp}.pckl', 'wb'), protocol=2)
pickle.dump((disp_Vt, disp_dH), paropen(f'elph.{disp}.pckl', 'wb'), protocol=2)
world.barrier()
def get_mode_raman(outpath, eigendata, cart_pol_derivs):
if os.path.exists(outpath):
parprint(f'Found existing {outpath}')
return
world.barrier()
parprint(f'Computing mode raman tensors... ({outpath})')
cart_pol_derivs = np.load('raman-cart.npy')
mode_pol_derivs = []
for row in eigendata['eigenvectors']:
mode_displacements = eigendata['atom_masses'].repeat(3) ** -0.5 * row
mode_displacements /= np.linalg.norm(mode_displacements)
# ∂α_ij ∂α_ij ∂x_ak
# ----- = sum ( ----- ----- )
# ∂u_n a,k ∂x_ak ∂u_n
#
# = dot product of (3n-dimensional gradient of ∂α_ij)
# with (3n-dimensional displacement vector of mode n)
mode_pol_deriv = np.dot(
# move i and j (axes 2 and 3) to the outside and combine axes 0 and 1 (x components)
cart_pol_derivs.transpose((2, 3, 0, 1)).reshape((9, -1)),
mode_displacements,
).reshape((3, 3))
mode_pol_derivs.append(mode_pol_deriv)
np.save(outpath, mode_pol_derivs)
def main(
name,
# root="../ZnVO/",
root="/cluster/scratch/ttian/ZnVO",
model="A",
clean=False):
if name not in ("Zn", "Co"):
return False
# Directory
if rank == 0:
base_dir = os.path.join(root, "{}V2O5".format(name))
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
if clean:
return # on all ranks
base_dir = os.path.join(root, "{}V2O5".format(name))
parprint("Running {} with model type {}".format(name, model))
relax(base_dir=base_dir, model=model)
return 0
def _startup(self):
"""Initiates a run, and determines if running from previous data or
a fresh run."""
status = np.array(-1.)
exists = self._read_minima()
if world.rank == 0:
if not exists:
# Fresh run with new minima file.
status = np.array(0.)
elif not os.path.exists(self._logfile):
# Fresh run with existing or shared minima file.
status = np.array(1.)
else:
# Must be resuming from within a working directory.
status = np.array(2.)
world.barrier()
world.broadcast(status, 0)
if status == 2.:
self._resume()
else:
self._counter = 0
self._log('init')
self._log('msg', 'Performing initial optimization.')
if status == 1.:
self._log(
'msg', 'Using existing minima file with %i prior '
'minima: %s' % (len(self._minima), self._minima_traj))
self._optimize()
self._check_results()
self._counter += 1
def main(
name,
# root="../ZnVO/",
root="/cluster/scratch/ttian/ZnVO",
clean=False):
if name not in ("Zn", "Co", "ghost-Co"):
return False
# Directory
if rank == 0:
base_dir = os.path.join(root, "{}V2O5".format(name))
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
if clean:
return # on all ranks
base_dir = os.path.join(root, "{}V2O5".format(name))
# atoms = make_super(base_dir)
# add_adatom(atoms, scaled_pos=(1 / 2, 1 / 2, 1 / 2))
# parprint(atoms)
# view(atoms.copy())
if name in ("Zn", "Co"):
neb(base_dir=base_dir)
else:
neb_ghost(base_dir=base_dir)
return 0
def _startup(self):
"""Initiates a run, and determines if running from previous data or
a fresh run."""
status = np.array(-1.)
exists = self._read_minima()
if rank == 0:
if not exists:
# Fresh run with new minima file.
status = np.array(0.)
elif not os.path.exists(self._logfile):
# Fresh run with existing or shared minima file.
status = np.array(1.)
else:
# Must be resuming from within a working directory.
status = np.array(2.)
world.barrier()
world.broadcast(status, 0)
if status == 2.:
self._resume()
else:
self._counter = 0
self._log('init')
self._log('msg', 'Performing initial optimization.')
if status == 1.:
self._log('msg', 'Using existing minima file with %i prior '
'minima: %s' % (len(self._minima),
self._minima_traj))
self._optimize()
self._check_results()
self._counter += 1
def main(
name,
# root="../ZnVO/",
root="/cluster/scratch/ttian/ZnVO",
clean=False):
if name not in ("Zn", "Co"):
return False
# Directory
if rank == 0:
base_dir = os.path.join(root, "{}V2O5".format(name))
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
if clean:
return # on all ranks
atoms = get_structure(name)
parprint(atoms)
base_dir = os.path.join(root, "{}V2O5".format(name))
relax(atoms, name=name, base_dir=base_dir)
return 0
def main(name, imag="init", root="/cluster/scratch/ttian/ZnVO", clean=False):
assert imag in ("init", "final")
if name not in ("Zn", "Co"):
return False
# Directory
if rank == 0:
base_dir = os.path.join(root, "{}V2O5".format(name))
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
if clean:
return # on all ranks
base_dir = os.path.join(root, "{}V2O5".format(name))
if imag == "init":
calc_img(base_dir=base_dir, scaled_pos=(0, 0, 1 / 2), index=imag)
else:
calc_img(base_dir=base_dir,
scaled_pos=(1 / 2, 1 / 2, 1 / 2),
index=imag)
return 0
def write_gpw_file():
"""write gs dft calculation
"""
# start by cleaning up a bit
if world.rank == 0:
for name in Path().glob('*.npy'):
Path(name).unlink()
for name in Path().glob('*.tmp.*.pckl'):
Path(name).unlink()
world.barrier()
params = dict(mode=PW(400),
xc='PBE',
basis='dzp',
kpts={
'size': (6, 6, 1),
'gamma': True
},
occupations=FermiDirac(width=0.05))
slab = mx2('MoSS', '2H', 3.184, 3.127)
slab.center(vacuum=8, axis=2)
slab.pbc = (1, 1, 0)
slab.calc = GPAW(txt='gs.txt', **params)
slab.get_forces()
slab.get_stress()
slab.calc.write('gs.gpw')
def copy_chk(base, prev, now):
"""Copy chk file from previous state"""
if rank == 0:
copyfile(base / "{0}.chk".format(prev),
base / "{0}.chk".format(now))
else:
pass
world.barrier()
def make_force_sets_and_excitations(cachepath, disp_filenames, phonon, atoms,
ex_kw):
if os.path.exists(cachepath):
parprint(f'Found existing {cachepath}')
return np.load(cachepath)
world.barrier()
parprint(
f'Computing force sets and polarizability data at displacements... ({cachepath})'
)
eq_atoms = atoms.copy()
def iter_displacement_files():
eq_force_filename = disp_filenames['force']['eq']
eq_ex_filename = disp_filenames['ex']['eq']
yield 'eq', eq_force_filename, eq_ex_filename, eq_atoms
disp_phonopy_sites, disp_carts = get_phonopy_displacements(phonon)
for i, disp_atoms in enumerate(
iter_displaced_structures(atoms, disp_phonopy_sites,
disp_carts)):
force_filename = disp_filenames['force']['disp'].format(i)
ex_filename = disp_filenames['ex']['disp'].format(i)
yield 'disp', force_filename, ex_filename, disp_atoms
# Make files for one displacement at a time
for disp_kind, force_filename, ex_filename, disp_atoms in iter_displacement_files(
):
if os.path.exists(ex_filename):
continue
world.barrier()
atoms.set_positions(disp_atoms.get_positions())
disp_forces = atoms.get_forces()
ex = LrTDDFT(atoms.calc, **ex_kw)
if disp_kind == 'eq':
# For inspecting the impact of differences in the calculator
# between ionic relaxation and raman computation.
parprint('Max equilibrium force during raman:',
np.absolute(disp_forces).max())
if world.rank == 0:
np.save(force_filename, disp_forces)
ex.write(ex_filename)
# combine force sets into one file
force_sets = np.array([
np.load(disp_filenames['force']['disp'].format(i))
for i in range(len(phonon.get_displacements()))
])
np.save(cachepath, force_sets)
for i in range(len(phonon.get_displacements())):
os.unlink(disp_filenames['force']['disp'].format(i))
return force_sets
def expand_raman_by_symmetry(cachepath, phonon, disp_filenames,
get_polarizability, ex_kw,
subtract_equilibrium_polarizability):
if os.path.exists(cachepath):
parprint(f'Found existing {cachepath}')
return np.load(cachepath)
world.barrier()
parprint(f'Expanding raman data by symmetry... ({cachepath})')
disp_phonopy_sites, disp_carts = get_phonopy_displacements(phonon)
prim_symmetry = phonon.primitive_symmetry.get_symmetry_operations()
lattice = phonon.primitive.get_cell()[...]
carts = phonon.primitive.get_positions()
oper_frac_rots = prim_symmetry['rotations']
oper_frac_trans = prim_symmetry['translations']
oper_cart_rots = np.array(
[np.linalg.inv(lattice).T @ R @ lattice.T for R in oper_frac_rots])
oper_cart_trans = oper_frac_trans @ lattice
oper_deperms = []
for cart_rot, cart_trans in zip(oper_cart_rots, oper_cart_trans):
carts = phonon.primitive.get_positions()
transformed_carts = carts @ cart_rot.T + cart_trans
oper_deperms.append(get_deperm(carts, transformed_carts, lattice))
oper_deperms = np.array(oper_deperms)
disp_tensors = np.array([
get_polarizability(
LrTDDFT.read(disp_filenames['ex']['disp'].format(i), **ex_kw))
for i in range(len(disp_phonopy_sites))
])
if subtract_equilibrium_polarizability:
disp_tensors -= get_polarizability(
LrTDDFT.read(disp_filenames['ex']['eq'], **ex_kw))
pol_derivs = symmetry.expand_derivs_by_symmetry(
disp_phonopy_sites,
disp_carts,
disp_tensors,
symmetry.Tensor2Callbacks(),
oper_cart_rots,
oper_deperms,
)
pol_derivs = np.array(
pol_derivs.tolist()) # (n,3) dtype=object --> (n,3,3,3) dtype=complex
np.save(cachepath, pol_derivs)
return pol_derivs
def elph_do_supercell_matrix(log, calc, supercell):
from gpaw.elph.electronphonon import ElectronPhononCoupling
# calculate_supercell_matrix breaks if parallelized over domains so parallelize over kpt instead
# (note: it prints messages from all processes but it DOES run faster with more processes)
supercell_atoms = GPAW('supercell.eq.gpw', txt=log, parallel={'domain': (1,1,1), 'band': 1, 'kpt': world.size}).get_atoms()
elph = ElectronPhononCoupling(calc.atoms, supercell=supercell, calc=supercell_atoms.calc)
elph.set_lcao_calculator(supercell_atoms.calc)
# to initialize bfs.M_a
ensure_gpaw_setups_initialized(supercell_atoms.calc, supercell_atoms)
elph.calculate_supercell_matrix(dump=1)
world.barrier()
def relax_atoms(outpath, atoms):
from ase import optimize
if os.path.exists(outpath):
parprint(f'Found existing {outpath}')
return
world.barrier()
parprint(f'Relaxing structure... ({outpath})')
dyn = optimize.FIRE(atoms)
dyn.run(fmax=0.05)
# FIXME: consider using something else to write, like pymatgen.io.vasp.Poscar with significant_figures=15.
# ASE always writes {:11.8f} in frac coords, which can be a dangerous amount of rounding
# for large unit cells.
atoms.write(outpath, format='vasp')
def get_eigensolutions_at_q(cachepath, phonon, q):
if os.path.exists('eigensolutions-gamma.npz'):
parprint('Found existing eigensolutions-gamma.npz')
return dict(np.load(cachepath))
world.barrier()
parprint('Diagonalizing dynamical matrix at gamma... (eigensolutions-gamma.npz)')
phonon.produce_force_constants()
frequencies, eigenvectors = phonon.get_frequencies_with_eigenvectors(q)
out = dict(
atom_masses=phonon.masses,
frequencies=frequencies,
eigenvectors=eigenvectors.T, # store as rows
)
np.savez(cachepath, **out)
return out
def read_and_do_montecarlo(filename,use_gas):
d = SurfaceMonteCarloData()
d.read(filename)
print "Starting "+str(len(d))+" sims."
surfaces = data.fcc.surface_names
#for n in range(0,len(d)):
for n in range(world.rank,len(d),world.size):
file = outdir+"/a%05i.amc.gz" % n
if not os.path.exists(file):
layers = d[n][1] # Really d[n]["layers"]
atoms = FaceCenteredCubic(d.atomic_number,
surfaces, layers,latticeconstant=d.lattice_constant)
resizecluster(atoms, d.fitsize)
print "Resized number of atoms:", len(atoms)
do_monte_carlo(atoms,n,outdir,use_gas)
world.barrier()#Let the cpu's wait until all in same state.
def main(formula, root="/cluster/scratch/ttian/2D-bulk/",
clean=False):
# candidates = {}
# if rank == 0:
# If MX2 then use a larger c
if any([s in formula for s in ("I", "O", "S", "Se", "Te")]):
c = 6.0
else:
c = 3.0
candidates = get_structure(formula, c=c)
# candidates = broadcast(candidates, root=0)
parprint(rank, candidates)
# Directory manipulation
if rank == 0:
for name in candidates:
base_dir = os.path.join(root, name)
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
if clean:
return # on all ranks
# On all ranks
for name in candidates:
base_dir = os.path.join(root, name)
mol = candidates[name]
# Relaxation and gs
relax(mol, name=name,
base_dir=base_dir)
parprint("Relaxation for {} finished!".format(name))
excited(base_dir=base_dir)
parprint("Excitation for {} finished!".format(name))
permittivity(base_dir=base_dir, mode="df")
parprint("Permittivity for {} finished!".format(name))
# polarizability(base_dir=base_dir, mode="tetra") #
# parprint("Polarizability using tetra {} finished!".format(name))
return 0
def read_and_do_montecarlo(filename):
d = SurfaceMonteCarloData()
d.read(filename)
print "Starting "+str(len(d))+" sims."
surfaces = data.fcc.surface_names
#for n in range(0,len(d)):
for n in range(world.rank,len(d),world.size):
file = outdir+"/a%05i.amc.gz" % n
if not os.path.exists(file):
layers = d[n][1] # Really d[n]["layers"]
atoms = FaceCenteredCubic(d.atomic_number,
surfaces, layers,latticeconstant=d.lattice_constant)
resizecluster(atoms, d.fitsize)
print "Resized number of atoms:", len(atoms)
do_monte_carlo(atoms,n,outdir)
world.barrier()#Let the cpu's wait until all in same state.
def main(mater, n_max=16):
# Delete all previous files
if world.rank == 0:
for f in glob.glob(os.path.join(data_path, "{}/gwqeh*".format(mater))):
os.remove(f)
world.barrier()
for n in range(2, n_max):
parprint(n)
gwqeh(mater, n_layers=n) # Just try!
res = []
for n in range(1, n_max):
print(n)
gap = get_gap(mater, n)
res.append((n, gap))
res = numpy.array(res)
f_name = os.path.join(res_path, "{}-gwqeh-gap.csv".format(mater))
numpy.savetxt(f_name, X=res, delimiter=",", header="N, Eg (eV)")
return
def run_single(formula,
prototype,
root="/cluster/scratch/ttian/bulk",
clean=False):
prototype = convert_name(prototype)[0]
name = "{}-{}".format(formula, prototype)
base_dir = join(root, name)
# Directory manipulation
if rank == 0:
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not exists(base_dir):
os.makedirs(base_dir)
world.barrier()
sb = StructureBuilder()
atoms, *_ = sb.get_structure(formula, prototype)
m_calc = MaterCalc(atoms=atoms, base_dir=base_dir)
if prototype != "perovskite":
m_calc.relax(fmax=0.002)
else:
# m_calc.relax(fmax=0.02, method="UCF")
m_calc.relax(skip=True)
m_calc.ground_state()
if prototype != "perovskite":
eg_min, eg_dir, *_ = m_calc.bandgap(method="pbe")
parprint("PBE min/dir: {:.3f}\t{:.3f}".format(eg_min, eg_dir))
eg_min, eg_dir, *_ = m_calc.bandgap(method="gllb")
parprint("GLLB min/dir: {:.3f}\t{:.3f}".format(eg_min, eg_dir))
else:
pass
# eg_min, eg_dir, *_ = m_calc.bandgap(method="pbe", skip=True)
# parprint("PBE min/dir: {:.3f}\t{:.3f}".format(eg_min, eg_dir))
# eg_min, eg_dir, *_ = m_calc.bandgap(method="gllb", skip=True)
# parprint("GLLB min/dir: {:.3f}\t{:.3f}".format(eg_min, eg_dir))
# Use db values
m_calc.excited_state()
m_calc.dielectric(method="rpa")
return 0
def main(formula,
kind,
fermi_shift=0,
root="/cluster/scratch/ttian/2D/",
clean=False):
# candidates = {}
# if rank == 0:
# candidates = get_structure(formula)
# candidates = broadcast(candidates, root=0)
# parprint(rank, candidates)
name = "{}-{}".format(formula, kind)
base_dir = os.path.join(root, name)
# Directory manipulation
if rank == 0:
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
if clean:
return # on all ranks
# On all ranks
# Relaxation and gs
# relax(mol, name=name,
# base_dir=base_dir)
# parprint("Relaxation for {} finished!".format(name))
# excited(base_dir=base_dir)
# parprint("Excitation for {} finished!".format(name))
polarizability(base_dir=base_dir, mode="df",
fermi_shift=fermi_shift) # add fermilevel
parprint("Polarizability for {} with Fermi Shift {} finished!".format(
name, fermi_shift))
# polarizability(base_dir=base_dir, mode="tetra") #
# parprint("Polarizability using tetra {} finished!".format(name))
return 0
def main(formula,
prototype=None,
root="/cluster/scratch/ttian/2D",
clean=False):
# candidates = {}
# if rank == 0:
candidates = get_structure(formula, prototype)
# candidates = broadcast(candidates, root=0)
parprint(rank, candidates)
# Directory manipulation
if rank == 0:
for name in candidates:
base_dir = os.path.join(root, name)
if clean:
shutil.rmtree(base_dir, ignore_errors=True)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
if clean:
return # on all ranks
# On all ranks
for name in candidates:
base_dir = os.path.join(root, name)
parprint(name)
mol = candidates[name]
# Relaxation and gs
relax(mol, name=name, base_dir=base_dir)
parprint("Relaxation for {} finished!".format(name))
excited(base_dir=base_dir)
parprint("Excitation for {} finished!".format(name))
polarizability(base_dir=base_dir, mode="df")
parprint("Polarizability for {} finished!".format(name))
# polarizability(base_dir=base_dir, mode="tetra") #
# parprint("Polarizability using tetra {} finished!".format(name))
return 0
def read_and_do_montecarlo(filename,use_gas):
d = SurfaceMonteCarloData()
d.read(filename)
print "Starting "+str(len(d))+" sims."
surfaces = data.fcc.surface_names
#Only one worker should create the filename
outdir = determine_create_dirname(filename)
#for n in range(0,len(d)):
for n in range(world.rank,len(d),world.size):
layers = d[n][1] # Really d[n]["layers"]
multiplicity = d.get_multiplicity(n)
atoms = FaceCenteredCubic(d.atomic_number,
surfaces, layers,latticeconstant=d.lattice_constant)
print "Number of atoms:", len(atoms)
resizecluster(atoms, d.fitsize)
print "Resized number of atoms:", len(atoms)
do_monte_carlo(atoms,n,outdir,use_gas,multiplicity)
world.barrier()#Let the cpu's wait until all in same state.
def run_single(name="Si", prototype=None):
sb = StructureBuilder()
mater = sb.get_structure(formula=name, prototype=prototype)
parprint("Before", mater)
if len(mater) != 1:
return
mater = mater[0]
base_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)),
"../../tmp/", "{}-{}/".format(name, prototype))
if rank == 0:
if not os.path.exists(base_dir):
os.makedirs(base_dir)
world.barrier()
calc = GPAW(
mode=dict(name="pw", ecut=800),
occupations=dict(name="fermi-dirac", width=0.01),
basis="dzp",
xc="PBE",
kpts=dict(gamma=True, density=4.0), # Very rough k-density
txt=os.path.join(base_dir, "{}-{}.txt".format(name, prototype)))
mater.set_calculator(calc)
sf = StrainFilter(mater)
traj_filename = os.path.join(base_dir,
"{}-{}.traj".format(name, prototype))
log_filename = os.path.join(base_dir, "{}-{}.log".format(name, prototype))
# Overwrite file
with open(traj_filename, "w") as _:
pass
with open(log_filename, "w") as _:
pass
opt_strain = ase.optimize.BFGS(sf,
trajectory=traj_filename,
logfile=log_filename)
opt_force = ase.optimize.BFGS(mater,
trajectory=traj_filename,
logfile=log_filename)
opt_strain.run(fmax=0.02)
# opt_force.run(fmax=0.02)
parprint("After", mater)
def read_and_do_montecarlo(filename, use_gas):
d = SurfaceMonteCarloData()
d.read(filename)
print "Starting " + str(len(d)) + " sims."
surfaces = data.fcc.surface_names
#Only one worker should create the filename
outdir = determine_create_dirname(filename)
#for n in range(0,len(d)):
for n in range(world.rank, len(d), world.size):
layers = d[n][1] # Really d[n]["layers"]
multiplicity = d.get_multiplicity(n)
atoms = FaceCenteredCubic(d.atomic_number,
surfaces,
layers,
latticeconstant=d.lattice_constant)
print "Number of atoms:", len(atoms)
resizecluster(atoms, d.fitsize)
print "Resized number of atoms:", len(atoms)
do_monte_carlo(atoms, n, outdir, use_gas, multiplicity)
world.barrier() #Let the cpu's wait until all in same state.
def __init__(
self,
atoms, # A ase.atoms.Atoms object
base_dir,
param_file=default_json_file):
# Read the parameters
if os.path.exists(param_file):
with open(param_file, "r") as f:
params = json.load(f)
self.__params = params
else:
raise FileNotFoundError("No parameter file!")
# Base_dir for all data
if not os.path.exists(base_dir):
if rank == 0:
os.makedirs(base_dir) # Recursively makedirs
world.barrier()
# Handle file path-related issues
self.__base_dir = os.path.abspath(base_dir)
self.__relaxed_traj = os.path.join(self.__base_dir, "relaxed.traj")
self.__relaxed_gllb_traj = os.path.join(self.__base_dir,
"relaxed_gllb.traj")
self.__gs_file = os.path.join(self.__base_dir,
"gs.gpw") # ground state in PBE
self.__gs_gllb_file = os.path.join(
self.__base_dir, "gs_gllb.gpw") # ground state in PBE
self.__bg_file_template = os.path.join(self.__base_dir,
"bg_{}.npz") # to add later
self.__es_file = os.path.join(self.__base_dir,
"es.gpw") # excited states in PBE
self.__eps_file_template = os.path.join(self.__base_dir, "eps_{}.npz")
if isinstance(atoms, Atoms):
self.atoms = atoms
elif atoms is None: # Dummy instance for checking only
self.atoms = None
else:
raise TypeError("Atom must be an Atoms instance!")
return
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
# We don't call FileIOCalculator.calculate here, because that method
# calls subprocess.call(..., shell=True), which we don't want to do.
# So, we reproduce some content from that method here.
Calculator.calculate(self, atoms, properties, system_changes)
# If a parameter file exists in the working directory, delete it
# first. If we need that file, we'll recreate it later.
localparfile = os.path.join(self.directory, '.dftd3par.local')
if os.path.isfile(localparfile):
os.remove(localparfile)
# Write XYZ or POSCAR file and .dftd3par.local file if we are using
# custom damping parameters.
self.write_input(self.atoms, properties, system_changes)
command = self._generate_command()
# Finally, call dftd3 and parse results.
with paropen(self.label + '.out', 'w') as f:
if world.rank == 0:
# DFTD3 does not run in parallel
# so we only need it to run on 1 core
errorcode = subprocess.call(command,
cwd=self.directory,
stdout=f)
else:
errorcode = None
world.barrier() # Wait for the call() to complete on the master node
errorcode = broadcast(errorcode, root=0)
if errorcode:
raise RuntimeError('%s returned an error: %d' %
(self.name, errorcode))
self.read_results()
def determine_create_dirname(filename):
outdir, ext = os.path.splitext(filename)
assert (ext == ".smc")
suffix = 1
if use_gas:
outdirtmp = outdir + "_amc_gas"
else:
outdirtmp = outdir + "_amc"
while os.path.exists(outdirtmp):
if use_gas:
outdirtmp = outdir + "_amc_gas_" + str(suffix)
else:
outdirtmp = outdir + "_amc_" + str(suffix)
suffix += 1
#Create this new directory:
world.barrier()
if world.rank == 0:
os.mkdir(outdirtmp)
else:
while not os.path.exists(outdirtmp):
sleep(1)
#Now we have a unique directory, return it.
return outdirtmp
def get_minimum_displacements(
cachepath: str,
unitcell: phonopy.structure.atoms.PhonopyAtoms,
supercell_matrix: np.ndarray,
displacement_distance: float,
phonopy_kw: dict = {},
):
# note: applying phonopy_kw on load is necessary because phonopy will recompute symmetry
load = lambda: phonopy.load(cachepath, produce_fc=False, **phonopy_kw)
if os.path.exists(cachepath):
parprint(f'Found existing {cachepath}')
return load()
world.barrier() # avoid race condition where rank 0 creates file before others enter
parprint(f'Getting displacements... ({cachepath})')
if world.rank == 0:
phonon = phonopy.Phonopy(unitcell, supercell_matrix, factor=phonopy.units.VaspToTHz, **phonopy_kw)
phonon.generate_displacements(distance=displacement_distance)
parprint(f'Saving displacements...')
phonon.save(cachepath)
world.barrier()
parprint(f'Loading displacements...')
return load()
def determine_create_dirname(filename):
outdir, ext = os.path.splitext(filename)
assert(ext == ".smc")
suffix = 1
if use_gas:
outdirtmp = outdir+"_amc_gas"
else:
outdirtmp = outdir+"_amc"
while os.path.exists(outdirtmp):
if use_gas:
outdirtmp = outdir+"_amc_gas_"+str(suffix)
else:
outdirtmp = outdir+"_amc_"+str(suffix)
suffix+=1
#Create this new directory:
world.barrier()
if world.rank == 0:
os.mkdir(outdirtmp)
else:
while not os.path.exists(outdirtmp):
sleep(1)
#Now we have a unique directory, return it.
return outdirtmp
def main(begin=0, end=None):
sb = StructureBuilder()
assert begin >= 0
entries = sb.entries
if end is None:
end = len(entries)
candidates = entries[begin:end] # End is not calculated!
results_all = []
for i, line in enumerate(candidates):
name = line["formula"]
prototype = line["prototype"]
res_single = run_single(sb, name, prototype)
for entry in res_single:
results_all.append(entry)
parprint(type(results_all), results_all)
world.barrier()
if rank == 0:
with open(
os.path.join(cur_dir, "../../tmp/",
"relax_result_{}-{}.json".format(begin, end)),
"w") as f:
json.dump(results_all, f)
return
def release(self):
world.barrier()
if world.rank == 0:
os.remove(self.name)
def read_json(name):
fd = open(name, 'r')
results = loads(fd.read())
fd.close()
world.barrier()
return numpyfy(results)
def read_json(name):
fd = open(name, 'r')
results = loads(fd.read())
fd.close()
world.barrier()
return numpyfy(results)
def release(self):
world.barrier()
if world.rank == 0:
os.remove(self.name)