def gen_test_data(datadir: str, params_fd: dict, supercell):
from gpaw.elph.electronphonon import ElectronPhononCoupling
params_gs = copy.deepcopy(params_fd)
atoms = Cluster(ase.build.bulk('C'))
calc_gs = GPAW(**params_gs)
atoms.calc = calc_gs
atoms.get_potential_energy()
atoms.calc.write("gs.gpw", mode="all")
# Make sure the real space grid matches the original.
# (basically we multiply the number of grid points in each dimension by the supercell dimension)
params_fd['gpts'] = calc_gs.wfs.gd.N_c * list(supercell)
if 'h' in params_fd:
del params_fd['h']
del calc_gs
if world.rank == 0:
os.makedirs(datadir, exist_ok=True)
calc_fd = GPAW(**params_fd)
elph = ElectronPhononCoupling(atoms,
calc=calc_fd,
supercell=supercell,
calculate_forces=True,
name=f'{datadir}/elph')
elph.run()
calc_fd.wfs.gd.comm.barrier()
elph = ElectronPhononCoupling(atoms, calc=calc_fd, supercell=supercell)
elph.set_lcao_calculator(calc_fd)
elph.calculate_supercell_matrix(dump=1)
from ase.build import molecule
from ase import optimize
from ase.vibrations.infrared import InfraRed
from gpaw.cluster import Cluster
from gpaw import GPAW, FermiDirac
h = 0.22
atoms = Cluster(molecule('H2'))
atoms.minimal_box(3.5, h=h)
# relax the molecule
calc = GPAW(h=h, occupations=FermiDirac(width=0.1))
atoms.calc = calc
dyn = optimize.FIRE(atoms)
dyn.run(fmax=0.05)
atoms.write('relaxed.traj')
# finite displacement for vibrations
ir = InfraRed(atoms)
ir.run()
def main__raman_ch4(structure, supercell, log):
import ase.build
from gpaw.lrtddft.spectrum import polarizability
from gpaw.cluster import Cluster
from gpaw import GPAW, FermiDirac
#=============================================
# Settings
# Input structure
relax_grid_sep = 0.22 # GPAW finite grid size
vacuum_sep = 3.5
pbc = False
if structure == 'ch4':
def get_unrelaxed_structure():
atoms = Cluster(ase.build.molecule('CH4'))
atoms.minimal_box(vacuum_sep, h=relax_grid_sep)
return atoms
elif structure == 'mos2':
def get_unrelaxed_structure():
atoms = Cluster(ase.build.mx2('MoS2'))
atoms.center(vacuum=vacuum_sep, axis=2)
return atoms
# Calculator (general settings)
make_calc = functools.partial(GPAW,
occupations=FermiDirac(width=0.1),
symmetry={'point_group': False},
txt=log,
)
# Relaxation settings
make_calc_relax = functools.partial(make_calc,
h=relax_grid_sep,
)
# Args for computations on displaced structures
raman_grid_sep = 0.25 # In the example, they use a larger spacing here than during relaxation.
# (TODO: but why? On CH4 I observe that this to leads to equilibrium forces of
# 0.067 ev/A, which seems to compromise our "energy minimum" state...)
num_converged_bands = 10
num_total_bands = 20
make_calc_raman = functools.partial(make_calc,
h=raman_grid_sep,
convergence={
'eigenstates': 1.e-5,
'bands': num_converged_bands,
},
eigensolver='cg',
nbands=num_total_bands,
)
supercell_matrix = [[supercell[0], 0, 0], [0, supercell[1], 0], [0, 0, supercell[2]]]
displacement_distance = 1e-2
# ----------
# Excitation settings (for polarizability)
ex_kw = {'restrict': {'jend':num_converged_bands-1}}
omega = 5.0 # eV
get_polarizability = functools.partial(polarizability, omega=omega, form='v', tensor=True)
subtract_equilibrium_polarizability = False
#=============================================
# Process
disp_filenames = {
'ex': {'eq': 'raman-eq.ex.gz', 'disp': 'raman-{:04}.ex.gz'},
'force': {'eq': 'force-set-eq.npy', 'disp': 'force-set-{:04}.npy'},
}
# Relax
unrelaxed_atoms = get_unrelaxed_structure()
unrelaxed_atoms.pbc = pbc
unrelaxed_atoms.calc = make_calc_relax()
relax_atoms(outpath='relaxed.vasp', atoms=unrelaxed_atoms)
# Phonopy displacements
phonon = get_minimum_displacements(cachepath='phonopy_disp.yaml',
unitcell=phonopy.interface.calculator.read_crystal_structure('relaxed.vasp', interface_mode='vasp')[0],
supercell_matrix=supercell_matrix,
displacement_distance=displacement_distance,
)
# Computing stuff at displacements
eq_atoms = Cluster(phonopy_atoms_to_ase(phonon.supercell))
eq_atoms.pbc = pbc
if raman_grid_sep != relax_grid_sep:
eq_atoms.minimal_box(vacuum_sep, h=raman_grid_sep)
eq_atoms.calc = make_calc_raman()
force_sets = make_force_sets_and_excitations(cachepath='force-sets.npy',
disp_filenames=disp_filenames, phonon=phonon,
atoms=eq_atoms, ex_kw=ex_kw,
)
phonon.set_forces(force_sets)
# Applying symmetry
cart_pol_derivs = expand_raman_by_symmetry(cachepath='raman-cart.npy',
phonon=phonon,
disp_filenames=disp_filenames, get_polarizability=get_polarizability, ex_kw=ex_kw,
subtract_equilibrium_polarizability=subtract_equilibrium_polarizability,
)
# Phonopy part 2
gamma_eigendata = get_eigensolutions_at_q(cachepath='eigensolutions-gamma.npz',
phonon=phonon, q=[0, 0, 0],
)
# Raman of modes
get_mode_raman(outpath='mode-raman-gamma.npy',
eigendata=gamma_eigendata, cart_pol_derivs=cart_pol_derivs,
)
epsinf = 78.36
rhomin = 0.0001 / Bohr**3
rhomax = 0.0050 / Bohr**3
st = 50. * 1e-3 * Pascal * m
p = -0.35 * 1e9 * Pascal
convergence = {
'energy': 0.05 / 8.,
'density': 10.,
'eigenstates': 10.,
}
atoms = Cluster(molecule('H2O'))
atoms.minimal_box(vac, h)
if not SKIP_VAC_CALC:
atoms.calc = GPAW(xc='PBE', h=h, convergence=convergence)
Evac = atoms.get_potential_energy()
print(Evac)
else:
# h=0.24, vac=4.0, setups: 0.9.11271, convergence: only energy 0.05 / 8
Evac = -14.857414548
with warnings.catch_warnings():
# ignore production code warning for ADM12PoissonSolver
warnings.simplefilter("ignore")
psolver = ADM12PoissonSolver()
atoms.calc = SolvationGPAW(xc='PBE',
h=h,
poissonsolver=psolver,
convergence=convergence,
epsinf = 78.36
rho0 = 0.00078 / Bohr**3
beta = 1.3
st = 72. * 1e-3 * Pascal * m
convergence = {
'energy': 0.05 / 8.,
'density': 10.,
'eigenstates': 10.,
}
atoms = Cluster(Atoms('Cl'))
atoms.minimal_box(vac, h)
if not SKIP_VAC_CALC:
atoms.calc = GPAW(xc='PBE', h=h, charge=-1, convergence=convergence)
Evac = atoms.get_potential_energy()
print(Evac)
else:
# h=0.24, vac=4.0, setups: 0.9.11271, convergence: only energy 0.05 / 8
Evac = -3.83245253419
atoms.calc = SolvationGPAW(
xc='PBE',
h=h,
charge=-1,
convergence=convergence,
cavity=FG02SmoothStepCavity(rho0=rho0,
beta=beta,
density=ElDensity(),
surface_calculator=GradientSurface()),
T = 298.15
vdw_radii = vdw_radii.copy()
vdw_radii[1] = 1.09
atomic_radii = lambda atoms: [vdw_radii[n] for n in atoms.numbers]
convergence = {
'energy': 0.05 / 8.,
'density': 10.,
'eigenstates': 10.,
}
atoms = Cluster(molecule('H2O'))
atoms.minimal_box(vac, h)
atoms.pbc = True
with warnings.catch_warnings():
# ignore production code warning for ADM12PoissonSolver
warnings.simplefilter("ignore")
psolver = ADM12PoissonSolver(eps=1e-7)
atoms.calc = SolvationGPAW(
xc='LDA', h=h, convergence=convergence,
cavity=EffectivePotentialCavity(
effective_potential=Power12Potential(atomic_radii=atomic_radii, u0=u0),
temperature=T
),
dielectric=LinearDielectric(epsinf=epsinf),
poissonsolver=psolver
)
atoms.get_potential_energy()
atoms.get_forces()
SKIP_VAC_CALC = True
h = 0.24
vac = 4.0
convergence = {
'energy': 0.05 / 8.,
'density': 10.,
'eigenstates': 10.,
}
atoms = Cluster(molecule('H2O'))
atoms.minimal_box(vac, h)
if not SKIP_VAC_CALC:
atoms.calc = GPAW(xc='PBE', h=h, convergence=convergence)
Evac = atoms.get_potential_energy()
print(Evac)
else:
# h=0.24, vac=4.0, setups: 0.9.11271, convergence: only energy 0.05 / 8
Evac = -14.857414548
atoms.calc = SolvationGPAW(
xc='PBE', h=h, convergence=convergence,
**get_HW14_water_kwargs()
)
Ewater = atoms.get_potential_energy()
Eelwater = atoms.calc.get_electrostatic_energy()
Esurfwater = atoms.calc.get_solvation_interaction_energy('surf')
atoms.get_forces()
DGSol = (Ewater - Evac) / (kcal / mol)
atoms2 = atoms.copy()
atoms2.set_initial_magnetic_moments(None)
atomss = (atoms, atoms2)
Es = []
Fs = []
for atoms in atomss:
atoms.calc = SolvationGPAW(
xc='LDA',
h=h,
charge=-1,
cavity=EffectivePotentialCavity(effective_potential=Power12Potential(
atomic_radii, u0),
temperature=T,
surface_calculator=GradientSurface(),
volume_calculator=KB51Volume()),
dielectric=LinearDielectric(epsinf=epsinf),
interactions=[
SurfaceInteraction(surface_tension=100. * 1e-3 * Pascal * m),
VolumeInteraction(pressure=-1.0 * 1e9 * Pascal),
LeakedDensityInteraction(voltage=1.0)
])
Es.append(atoms.get_potential_energy())
Fs.append(atoms.get_forces())
# compare to expected difference of a gas phase calc
print('difference E: ', Es[0] - Es[1])
equal(Es[0], Es[1], 0.0002)
print('difference F: ', np.abs(Fs[0] - Fs[1]).max())
equal(Fs[0], Fs[1], 0.003)