from ase import *
from ase.dft.bee import BEEF_Ensemble
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.test import equal
import numpy as np
xc = 'mBEEF'
conv = {'eigenstates':1.e-6, 'density':1.e-6, 'energy':1.e-6}
h = 0.18
tol1 = 1.e-3
tol2 = 1.e-1
# N2 molecule
n2 = Cluster(Atoms('N2',[[0.,0.,0.],[0.,0.,1.09]]))
n2.minimal_box(3.0, h=h)
cell = n2.get_cell()
calc = GPAW(h=h, xc='PBE', convergence=conv)
n2.set_calculator(calc)
n2.get_potential_energy()
n2.calc.set(xc=xc)
e_n2 = n2.get_potential_energy()
f = n2.get_forces()
ens = BEEF_Ensemble(n2)
de_n2 = ens.get_ensemble_energies()
del n2, calc, ens
# N atom
n = Atoms('N')
n.set_cell(cell)
n.center()
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)
def read(self, filename='trajectory.vmol', position=0):
"""Read atom configurations of step position"""
self.file = None
f = open(filename)
# find coordinates
loa = Cluster([])
coords = False
for l in f.readlines():
if coords:
w = l.split()
loa.append(Atom(w[3].replace ("\n", "" ),
(float(w[0]), float(w[1]), float(w[2]))))
def read(self, filename='trajectory.vmol', position=0):
"""Read atom configurations of step position"""
self.file = None
f = open(filename)
# find coordinates
loa = Cluster([])
coords = False
for l in f.readlines():
if coords:
w = l.split()
loa.append(Atom(w[3].replace("\n", ""),
(float(w[0]), float(w[1]), float(w[2]))))
def read_viewmol(self, filename):
f = open(filename)
# read the definition first
definition=False
for line in f:
w = line.split()
if not definition:
if w[0] == '$coord':
definition=True
self.scale = float(w[1])
loa = Cluster([])
else:
if w[0] == '$grad':
# definition ends here
self.definition = loa
break
else:
# we assume this is a coordinate entry
coo = (float(w[0]), float(w[1]), float(w[2]))
loa.append(Atom(w[3], coo))
# get the iterations
cycle = False
for line in f:
w = line.split()
if not cycle:
# search for the cycle keyword
if w[0] == 'cycle=':
cycle=True
n_coo=0
n_F=0
self.images.append(Cluster([]))
else:
if n_coo < len(self.definition):
n_coo += 1
coo = (float(w[0]), float(w[1]), float(w[2]))
self[-1].append(Atom(w[3], coo))
elif n_F < len(self.definition):
F = (float(w[0]), float(w[1]), float(w[2]))
self[-1][n_F].F = F
n_F += 1
if n_F == len(self.definition):
cycle=False
def read_viewmol(self, filename):
f = open(filename)
# read the definition first
definition = False
for line in f:
w = line.split()
if not definition:
if w[0] == '$coord':
definition = True
self.scale = float(w[1])
loa = Cluster([])
else:
if w[0] == '$grad':
# definition ends here
self.definition = loa
break
else:
# we assume this is a coordinate entry
coo = (float(w[0]), float(w[1]), float(w[2]))
loa.append(Atom(w[3], coo))
# get the iterations
cycle = False
for line in f:
w = line.split()
if not cycle:
# search for the cycle keyword
if w[0] == 'cycle=':
cycle = True
n_coo = 0
n_F = 0
self.images.append(Cluster([]))
else:
if n_coo < len(self.definition):
n_coo += 1
coo = (float(w[0]), float(w[1]), float(w[2]))
self[-1].append(Atom(w[3], coo))
elif n_F < len(self.definition):
F = (float(w[0]), float(w[1]), float(w[2]))
self[-1][n_F].F = F
n_F += 1
if n_F == len(self.definition):
cycle = False
import os
import sys
from ase import Atoms, Atom, QuasiNewton, PickleTrajectory
from gpaw import *
from gpaw.cluster import Cluster
from gpaw.utilities.viewmol import ViewmolTrajectory, write_viewmol
s = Cluster([Atom('H'), Atom('H',(0,0,3))])
s.minimal_box(2)
c = GPAW(h=0.3, nbands=2)
s.set_calculator(c)
vfname='traj.vmol'
pfname='traj.pickle'
vmt = ViewmolTrajectory(s, vfname)
traj = PickleTrajectory(pfname, 'w', s)
#c.attach(vmt.add, 100000)
#sys.exit()
# Find the theoretical bond length:
dyn = QuasiNewton(s)
dyn.attach(traj.write)
dyn.attach(vmt.add)
dyn.run(fmax=0.05)
traj = PickleTrajectory(pfname, 'r')
vfname2='pickle.vmol'
write_viewmol(traj, vfname2)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
return results
# calculate
parprint('fresh:')
mol = Cluster(molecule('H2O'))
mol.minimal_box(3, h=h)
calc = GPAW(nbands=6,
h = h,
txt=None)
calc.calculate(mol)
calc.write(gpwname)
lastres = run()
# load previous calculation
parprint('reloaded:')
calc = GPAW(gpwname, txt=None)
mol = calc.get_atoms()
run(lastres)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
return results
mol = Cluster(molecule('H2O'))
mol.minimal_box(2.5, h=h)
# calculate
if 1:
parprint('### fresh:')
calc = GPAW(nbands=6, h=h, txt=None)
if 1:
calc.calculate(mol)
calc.write(gpwname)
lastres = run()
# load previous calculation
if 1:
parprint('### reloaded:')
calc = GPAW(gpwname, txt=None)
CO.translate(-CO.get_center_of_mass())
p = CO.positions.copy()
for i in range(2):
equal(p[i, 1], 0, 1e-10)
equal(p[i, 2], 0, 1e-10)
# rotate the nuclear axis to the direction (1,1,1)
CO.rotate(p[1] - p[0], (1, 1, 1))
q = CO.positions.copy()
for c in range(3):
equal(q[0, c], p[0, 0] / sqrt(3), 1e-10)
equal(q[1, c], p[1, 0] / sqrt(3), 1e-10)
# minimal box
b = 4.0
CO = Cluster([Atom('C', (1, 0, 0)), Atom('O', (1, 0, R))])
CO.minimal_box(b)
cc = CO.get_cell()
for c in range(3):
width = 2 * b
if c == 2:
width += R
equal(cc[c, c], width, 1e-10)
# minimal box, ensure multiple of 4
h = .13
b = [2, 3, 4]
CO.minimal_box(b, h=h)
cc = CO.get_cell()
for c in range(3):
# print "cc[c,c], cc[c,c] / h % 4 =", cc[c, c], cc[c, c] / h % 4
from __future__ import print_function
from ase import Atom
from ase.neb import SingleCalculatorNEB
from ase.optimize import FIRE
from gpaw import GPAW
from gpaw.cluster import Cluster
txt = None
mol = Cluster(
[Atom('H'), Atom('H', [1, 0, 0]),
Atom('H', [.5, .5, .5])],
cell=[2, 2, 2],
pbc=True)
def set_calculators(all=False):
c = GPAW(h=.3,
convergence={
'eigenstates': 0.1,
'energy': 0.1,
'density': 0.01
},
txt=txt)
# c = EMT()
n = len(images)
if not all:
n -= 2
neb.set_calculators([c] * n)
from gpaw import GPAW, FermiDirac
from gpaw.cluster import Cluster
from gpaw.lrtddft import LrTDDFT
from gpaw.lrtddft.excited_state import ExcitedState
box = 5. # box dimension
h = 0.25 # grid spacing
width = 0.01 # Fermi width
nbands = 6 # bands in GS calculation
nconv = 4 # bands in GS calculation to converge
R = 2.99 # starting distance
iex = 1 # excited state index
d = 0.01 # step for numerical force evaluation
exc = 'LDA' # xc for the linear response TDDFT kernel
s = Cluster([Atom('Na'), Atom('Na', [0, 0, R])])
s.minimal_box(box, h=h)
c = GPAW(h=h, nbands=nbands, eigensolver='cg',
occupations=FermiDirac(width=width),
setups={'Na': '1'},
convergence={'bands':nconv})
c.calculate(s)
lr = LrTDDFT(c, xc=exc, eps=0.1, jend=nconv-1)
ex = ExcitedState(lr, iex, d=d)
s.set_calculator(ex)
ftraj='relax_ex' + str(iex)
ftraj += '_box' + str(box) + '_h' + str(h)
ftraj += '_d' + str(d) + '.traj'
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 do_elph_symmetry(
data_subdir: str,
params_fd: dict,
supercell,
all_displacements: tp.Iterable[AseDisplacement],
symmetry_type: tp.Optional[str],
):
atoms = Cluster(ase.build.bulk('C'))
# a supercell exactly like ElectronPhononCoupling makes
supercell_atoms = atoms * supercell
quotient_perms = list(
interop.ase_repeat_translational_symmetry_perms(len(atoms), supercell))
# Make sure the grid matches our calculations (we repeated the grid of the groundstate)
params_fd = copy.deepcopy(params_fd)
params_fd['gpts'] = GPAW('gs.gpw').wfs.gd.N_c * list(supercell)
if 'h' in params_fd:
del params_fd['h']
wfs_with_sym = get_wfs_with_sym(params_fd=params_fd,
supercell_atoms=supercell_atoms,
symmetry_type=symmetry_type)
calc_fd = GPAW(**params_fd)
# GPAW displaces the center cell for some reason instead of the first cell
elph = ElectronPhononCoupling(atoms,
calc=calc_fd,
supercell=supercell,
calculate_forces=True)
displaced_cell_index = elph.offset
del elph # just showing that we don't use these anymore
del calc_fd
get_displaced_index = lambda prim_atom: displaced_cell_index * len(
atoms) + prim_atom
all_displacements = list(all_displacements)
disp_atoms = [get_displaced_index(disp.atom) for disp in all_displacements]
disp_carts = [
disp.cart_displacement(DISPLACEMENT_DIST) for disp in all_displacements
]
disp_values = [
read_elph_input(data_subdir, disp) for disp in all_displacements
]
full_Vt = np.empty((len(supercell_atoms), 3) + disp_values[0][0].shape)
full_dH = np.empty((len(supercell_atoms), 3), dtype=object)
full_forces = np.empty((len(supercell_atoms), 3) + disp_values[0][2].shape)
lattice = supercell_atoms.get_cell()[...]
oper_cart_rots = interop.gpaw_op_scc_to_cart_rots(
wfs_with_sym.kd.symmetry.op_scc, lattice)
if world.rank == 0:
full_values = symmetry.expand_derivs_by_symmetry(
disp_atoms, # disp -> atom
disp_carts, # disp -> 3-vec
disp_values, # disp -> T (displaced value, optionally minus equilibrium value)
elph_callbacks(wfs_with_sym, supercell), # how to work with T
oper_cart_rots, # oper -> 3x3
oper_perms=wfs_with_sym.kd.symmetry.a_sa, # oper -> atom' -> atom
quotient_perms=quotient_perms,
)
for a in range(len(full_values)):
for c in range(3):
full_Vt[a][c] = full_values[a][c][0]
full_dH[a][c] = full_values[a][c][1]
full_forces[a][c] = full_values[a][c][2]
else:
# FIXME
# the symmetry part is meant to be done in serial but we should return back to
# our original parallel state after it...
pass
return full_Vt, full_dH, full_forces
import sys
import numpy as np
from ase.structure import molecule
from ase.parallel import parprint
from gpaw import GPAW, PW
from gpaw.analyse.multipole import Multipole
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.3
s = Cluster(molecule('H2O'))
s.minimal_box(3., h)
gpwname = 'H2O_h' + str(h) + '.gpw'
try:
# XXX check why this fails in parallel
calc = GPAW(gpwname + 'failsinparallel', txt=None)
atoms = calc.get_atoms()
calc.density.set_positions(atoms.get_scaled_positions() % 1.0)
calc.density.interpolate_pseudo_density()
calc.density.calculate_pseudo_charge()
except IOError:
calc = GPAW(h=h, charge=0, txt=None)
calc.calculate(s)
calc.write(gpwname)
dipole_c = calc.get_dipole_moment()
parprint('Dipole', dipole_c)
from __future__ import print_function
import sys
import numpy as np
from ase.structure import molecule
from ase.parallel import parprint
from gpaw import GPAW, PW
from gpaw.analyse.multipole import Multipole
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.3
s = Cluster(molecule("H2O"))
s.minimal_box(3.0, h)
gpwname = "H2O_h" + str(h) + ".gpw"
try:
# XXX check why this fails in parallel
calc = GPAW(gpwname + "failsinparallel", txt=None)
atoms = calc.get_atoms()
calc.density.set_positions(atoms.get_scaled_positions() % 1.0)
calc.density.interpolate_pseudo_density()
calc.density.calculate_pseudo_charge()
except IOError:
calc = GPAW(h=h, charge=0, txt=None)
calc.calculate(s)
calc.write(gpwname)
dipole_c = calc.get_dipole_moment()
from ase import Atom
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.test import equal
h=0.40
txt = None
txt = 'mgga_sc.txt'
s = Cluster([Atom('H')])
s.minimal_box(4., h=h)
s.set_initial_magnetic_moments([1])
# see https://trac.fysik.dtu.dk/projects/gpaw/ticket/244
s.set_cell((8.400000,8.400000,8.400000))
c = GPAW(xc='TPSS', h=h, nbands=5, txt=txt,
eigensolver='rmm-diis',
fixmom=True,
maxiter=300)
c.calculate(s)
cpbe = GPAW(xc='PBE', h=h, nbands=5, txt=txt,
eigensolver='rmm-diis',
fixmom=True,
maxiter=300)
cpbe.calculate(s)
cpbe.set(xc='TPSS')
cpbe.calculate()
print "Energy difference", (cpbe.get_potential_energy() -
c.get_potential_energy())
butadiene = """10
C 3.649801161546418 5.442281389577507 3.863313703750026
C 5.051651240044169 5.368220758269772 4.162165876906096
C 5.750174626862403 4.162261915959347 4.240449977068684
C 7.150130182125531 4.155384186721486 4.537328602062397
H 3.218154657585170 4.565210696328925 3.522601038049320
H 3.077656122062729 6.375092902842770 3.826039498180272
H 5.478464901706067 6.370680001794822 4.422235395756437
H 5.320549047980879 3.220584852467720 3.974551561510350
H 7.723359150977955 3.224855971783890 4.574146712279462
H 7.580803493981530 5.034479218283977 4.877211530909463
"""
h = 0.3
atoms = Cluster(read_xyz(StringIO.StringIO(butadiene)))
atoms.minimal_box(3.0, h)
atoms.set_calculator(GPAW(h=h))
if 0:
dyn = FIRE(atoms)
dyn.run(fmax=0.05)
atoms.write("butadiene.xyz")
vibname = "fcvib"
vib = Vibrations(atoms, name=vibname)
vib.run()
# Modul
a = FranckCondon(atoms, vibname, minfreq=250)
# excited state forces
import numpy as np
from ASE import Atom
from gpaw.utilities import equal
from gpaw.cluster import Cluster
from gpaw import Calculator
from gpaw.analyse.expandyl import ExpandYl
R = 1.
H2 = Cluster([Atom('H',(0,0,0)), Atom('H',(0,0,R))])
H2.minimal_box(3.)
calc = Calculator(h=0.2, width=0.01, nbands=2)
H2.SetCalculator(calc)
H2.GetPotentialEnergy()
yl = ExpandYl(H2.center_of_mass(), calc.wfs.gd, Rmax=2.5)
gl = []
for n in range(calc.nbands):
psit_G = calc.kpt_u[0].psit_nG[n]
norm = calc.wfs.gd.integrate(psit_G**2)
g = yl.expand(psit_G)
gsum = np.sum(g)
# allow for 10 % inaccuracy in the norm
print "norm, sum=", norm, gsum
equal(norm, gsum, 0.1)
gl.append(g/gsum*100)
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,
)
def get_unrelaxed_structure():
atoms = Cluster(ase.build.mx2('MoS2'))
atoms.center(vacuum=vacuum_sep, axis=2)
return atoms
import numpy as np
import ase.io
from ase.calculators.vdwcorrection import vdWTkatchenko09prl
from ase.parallel import barrier
from ase.build import molecule
from gpaw import GPAW
from gpaw.analyse.hirshfeld import HirshfeldPartitioning
from gpaw.analyse.vdwradii import vdWradii
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.4
s = Cluster(molecule('LiH'))
s.minimal_box(3., h=h)
def print_charge_and_check(hp, q=0, label='unpolarized'):
q_a = np.array(hp.get_charges())
print('Charges ({0})='.format(label), q_a, ', sum=', q_a.sum())
equal(q_a.sum(), q, 0.03)
return q_a
# spin unpolarized
if 1:
out_traj = 'LiH.traj'
out_txt = 'LiH.txt'
from ase.data.s22 import data, s22
from ase.calculators.vdwcorrection import vdWTkatchenko09prl
from gpaw import *
from gpaw.cluster import Cluster
from gpaw.analyse.hirshfeld import HirshfeldDensity, HirshfeldPartitioning
from gpaw.analyse.vdwradii import vdWradii
h = 0.18
box = 4.
xc = 'TS09'
f = paropen('energies_' + xc +'.dat', 'w')
print >> f, '# h=', h
print >> f, '# box=', box
print >> f, '# molecule E[1] E[2] E[1+2] E[1]+E[2]-E[1+2]'
for molecule in data:
print >> f, molecule,
ss = Cluster(Atoms(data[molecule]['symbols'],
data[molecule]['positions']))
# split the structures
s1 = ss.find_connected(0)
s2 = ss.find_connected(-1)
assert(len(ss) == len(s1) + len(s2))
if xc == 'TS09' or xc == 'TPSS' or xc == 'M06L':
c = GPAW(xc='PBE', h=h, nbands=-6, occupations=FermiDirac(width=0.1))
else:
c = GPAW(xc=xc, h=h, nbands=-6, occupations=FermiDirac(width=0.1))
E = []
for s in [s1, s2, ss]:
s.set_calculator(c)
s.minimal_box(box, h=h)
if xc == 'TS09':
s.get_potential_energy()
cc = vdWTkatchenko09prl(HirshfeldPartitioning(c),
from ase.parallel import parprint
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.analyse.hirshfeld import HirshfeldDensity, HirshfeldPartitioning
from gpaw.analyse.wignerseitz import WignerSeitz
from gpaw.test import equal
h = 0.3
gpwname = 'H2O' + str(h) + '.gpw'
try:
calc = GPAW(gpwname + 'notfound', txt=None)
# calc = GPAW(gpwname, txt=None)
mol = calc.get_atoms()
except:
mol = Cluster(molecule('H2O'))
mol.minimal_box(3, h=h)
calc = GPAW(nbands=6, h=h, txt=None)
calc.calculate(mol)
calc.write(gpwname)
# Hirshfeld ----------------------------------------
if 1:
hd = HirshfeldDensity(calc)
# check for the number of electrons
expected = [
[None, 10],
[[0, 1, 2], 10],
b = [2, 3, 4]
CO.minimal_box(b, h=h)
cc = CO.get_cell()
for c in range(3):
# print "cc[c,c], cc[c,c] / h % 4 =", cc[c, c], cc[c, c] / h % 4
for a in CO:
print(a.symbol, b[c], a.position[c], cc[c, c] - a.position[c])
assert(a.position[c] > b[c])
equal(cc[c, c] / h % 4, 0.0, 1e-10)
# .............................................
# connected atoms
assert(len(CO.find_connected(0, 1.1 * R)) == 2)
assert(len(CO.find_connected(0, 0.9 * R)) == 1)
H2O = Cluster(molecule('H2O'))
assert (len(H2O.find_connected(0)) == 3)
assert (len(H2O.find_connected(0, scale=0.9)) == 1)
# .............................................
# I/O
fxyz='CO.xyz'
fpdb='CO.pdb'
cell = [2.,3.,R+2.]
CO.set_cell(cell, scale_atoms=True)
barrier()
CO.write(fxyz)
barrier()
CO_b = Cluster(filename=fxyz)
assert(len(CO) == len(CO_b))
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.pes.state import BoundState, H1s
from gpaw.pes.ds_beta import CrossSectionBeta
xc = 'PBE'
ngauss = 2
h = .3
box = 3.
gpwname = 'H1s.gpw'
if 1:
c = GPAW(xc='PBE', nbands=-1, h=h)
s = Cluster([Atom('H')])
s.minimal_box(box, h=h)
c.calculate(s)
c.write(gpwname, 'all')
else:
c = GPAW(gpwname)
s = c.get_atoms()
c.converge_wave_functions()
cm = s.get_center_of_mass()
Ekin = 1.
ekin = Ekin / Ha
for form, title in [('L', 'length form'), ('V', 'velocity form')]:
parprint('--', title)
ds = []
for analytic in [True, False]:
from ase import Atom
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.analyse.eed import ExteriorElectronDensity
fwfname = 'H2_kpt441_wf.gpw'
txt = None
#txt = '-'
# write first if needed
try:
c = GPAW(fwfname, txt=txt)
s = c.get_atoms()
except:
s = Cluster([Atom('H'), Atom('H', [0, 0, 1])], pbc=[1, 1, 0])
s.minimal_box(3.)
c = GPAW(xc='PBE',
h=.3,
kpts=(4, 4, 1),
convergence={
'density': 1e-3,
'eigenstates': 1e-3
})
c.calculate(s)
c.write(fwfname, 'all')
eed = ExteriorElectronDensity(c.wfs.gd, s)
eed.write_mies_weights(c.wfs)
from gpaw import GPAW, setup_paths
from gpaw.cluster import Cluster
from gpaw.eigensolvers import RMMDIIS
from gpaw.xc.hybrid import HybridXC
from gpaw.occupations import FermiDirac
from gpaw.test import equal, gen
if setup_paths[0] != '.':
setup_paths.insert(0, '.')
for atom in ['Be']:
gen(atom, xcname='PBE', scalarrel=True, exx=True,
yukawa_gamma=0.83, gpernode=149)
h = 0.35
be = Cluster(Atoms('Be', positions=[[0, 0, 0]]))
be.minimal_box(3.0, h=h)
c = {'energy': 0.05, 'eigenstates': 0.05, 'density': 0.05}
IP = 8.79
xc = HybridXC('LCY-PBE', omega=0.83)
fname = 'Be_rsf.gpw'
calc = GPAW(txt='Be.txt', xc=xc, convergence=c,
eigensolver=RMMDIIS(), h=h,
occupations=FermiDirac(width=0.0), spinpol=False)
be.set_calculator(calc)
# energy = na2.get_potential_energy()
# calc.set(xc=xc)
import os
import sys
from gpaw.test import equal
from ase import Atom
from gpaw import GPAW, MixerDif
from gpaw.cluster import Cluster
h = .25
q = 0
box = 3.
spin=True
# B should not have spin contamination
s = Cluster([Atom('B')])
s.minimal_box(box, h=h)
s.set_initial_magnetic_moments([-1])
c = GPAW(xc='LDA', nbands=-3,
charge=q, spinpol=spin, h=h,
convergence={'eigenstates':1e-3, 'density':1e-2, 'energy':0.1},
)
c.calculate(s)
equal(c.density.get_spin_contamination(s, 1), 0., 0.01)
# setup H2 at large distance with differnt spins for the atoms
s = Cluster([Atom('H'), Atom('H',[0,0,3.0])])
s.minimal_box(box, h=h)
s.set_initial_magnetic_moments([-1,1])
from ase import Atom
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.test import equal
fname='H2_PBE.gpw'
fwfname='H2_wf_PBE.gpw'
txt = None
# write first if needed
try:
c = GPAW(fname, txt=txt)
c = GPAW(fwfname, txt=txt)
except:
s = Cluster([Atom('H'), Atom('H', [0,0,1])])
s.minimal_box(3.)
c = GPAW(xc='PBE', h=.3, convergence={'density':1e-3, 'eigenstates':1e-3})
c.calculate(s)
c.write(fname)
c.write(fwfname, 'all')
# full information
c = GPAW(fwfname, txt=txt)
E_PBE = c.get_potential_energy()
try: # number of iterations needed in restart
niter_PBE = c.get_number_of_iterations()
except: pass
dE = c.get_xc_difference('TPSS')
E_1 = E_PBE + dE
print "E PBE, TPSS=", E_PBE, E_1
from gpaw.analyse.overlap import Overlap
from gpaw.lrtddft import LrTDDFT
"""Evaluate the overlap between two independent calculations
Differences are forced by different eigensolvers and differing number
of Kohn-Sham states.
"""
h = 0.4
box = 2
nbands = 4
txt = '-'
txt = None
np.set_printoptions(precision=3, suppress=True)
H2 = Cluster(molecule('H2'))
H2.minimal_box(box, h)
c1 = GPAW(h=h,
txt=txt,
eigensolver='dav',
nbands=nbands,
convergence={'eigenstates': nbands})
c1.calculate(H2)
lr1 = LrTDDFT(c1)
parprint('sanity --------')
ov = Overlap(c1).pseudo(c1)
parprint('pseudo(normalized):\n', ov)
ov = Overlap(c1).pseudo(c1, False)
parprint('pseudo(not normalized):\n', ov)
from ase.structure import molecule
from ase.parallel import parprint
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.occupations import FixedOccupations, ZeroKelvin
from gpaw.test import equal
h = 0.4
box = 2
nbands = 2
txt = '-'
txt = None
H2 = Cluster(molecule('H2'))
H2.minimal_box(box, h)
convergence = {'energy':0.01, 'eigenstates':1.e-3, 'density':1.e-2}
if 1:
# test ZeroKelvin vs FixedOccupations
c = GPAW(h=h, nbands=nbands,
occupations=ZeroKelvin(True),
convergence=convergence,
txt=txt)
H2.set_calculator(c)
E_zk = H2.get_potential_energy()
c = GPAW(h=h, nbands=nbands,
occupations=FixedOccupations([[2, 0]]),
convergence=convergence,
txt=txt)
H2.set_calculator(c)
import os
import sys
from ase import Atoms, Atom, QuasiNewton, PickleTrajectory
from gpaw import *
from gpaw.cluster import Cluster
from gpaw.utilities.viewmol import ViewmolTrajectory, write_viewmol
s = Cluster([Atom('H'), Atom('H', (0, 0, 3))])
s.minimal_box(2)
c = GPAW(h=0.3, nbands=2)
s.set_calculator(c)
vfname = 'traj.vmol'
pfname = 'traj.pickle'
vmt = ViewmolTrajectory(s, vfname)
traj = PickleTrajectory(pfname, 'w', s)
#c.attach(vmt.add, 100000)
#sys.exit()
# Find the theoretical bond length:
dyn = QuasiNewton(s)
dyn.attach(traj.write)
dyn.attach(vmt.add)
dyn.run(fmax=0.05)
traj = PickleTrajectory(pfname, 'r')
vfname2 = 'pickle.vmol'
write_viewmol(traj, vfname2)
h = 0.3
vac = 3.0
u0 = .180
epsinf = 80.
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),
from gpaw.cluster import Cluster
from gpaw.analyse.hirshfeld import HirshfeldPartitioning
from gpaw.analyse.vdwradii import vdWradii
h = 0.25
box = 3.0
molecule = 'Adenine-thymine_complex_stack'
Energy = {
'PBE': [],
'vdW-DF': [],
'TS09': []}
for molecule in ['Adenine-thymine_complex_stack']:
ss = Cluster(Atoms(data[molecule]['symbols'],
data[molecule]['positions']))
# split the structures
s1 = ss.find_connected(0)
s2 = ss.find_connected(-1)
assert len(ss) == len(s1) + len(s2)
c = GPAW(xc='PBE', h=h, nbands=-6,
occupations=FermiDirac(width=0.1), txt=None)
cdf = GPAW(xc='vdW-DF', h=h, nbands=-6, occupations=FermiDirac(width=0.1),
txt=None)
for s in [s1, s2, ss]:
s.set_calculator(c)
s.minimal_box(box, h=h)
Energy['PBE'].append(s.get_potential_energy())
"""Test Hirshfeld for spin/no spin consitency"""
from ase import Atom
from gpaw import GPAW
from ase.parallel import parprint
from gpaw.analyse.hirshfeld import HirshfeldPartitioning
from gpaw import FermiDirac
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.25
box = 3
atoms = Cluster()
atoms.append(Atom('H'))
atoms.minimal_box(box)
volumes = []
for spinpol in [False, True]:
calc = GPAW(h=h,
occupations=FermiDirac(0.1, fixmagmom=True),
experimental={'niter_fixdensity': 2},
spinpol=spinpol)
calc.calculate(atoms)
volumes.append(HirshfeldPartitioning(calc).get_effective_volume_ratios())
parprint(volumes)
equal(volumes[0][0], volumes[1][0], 4e-9)
from ase.io.plt import write_plt, read_plt
from gpaw.test import equal
from gpaw import GPAW
from gpaw.cluster import Cluster
txt='-'
txt='/dev/null'
load = False
#load = True
R=0.7 # approx. experimental bond length
a = 4.
c = 4.
H2 = Cluster([Atom('H', (a/2,a/2,(c-R)/2)),
Atom('H', (a/2,a/2,(c+R)/2))],
cell=(a,a,c))
H2.rotate([1.,1.,1.])
##H2.write('H2.xyz')
fname = 'H2.gpw'
if (not load) or (not os.path.exists(fname)):
calc = GPAW(xc='PBE', nbands=2, spinpol=False, txt=txt)
H2.set_calculator(calc)
H2.get_potential_energy()
if load:
calc.write(fname, 'all')
else:
calc = GPAW(fname, txt=txt)
calc.initialize_wave_functions()
from __future__ import print_function
import sys
import numpy as np
from ase.build import molecule
from ase.parallel import parprint
from gpaw import GPAW, PW
from gpaw.analyse.multipole import Multipole
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.3
s = Cluster(molecule('H2O'))
s.minimal_box(3., h)
gpwname = 'H2O_h' + str(h) + '.gpw'
try:
# XXX check why this fails in parallel
calc = GPAW(gpwname + 'failsinparallel', txt=None)
atoms = calc.get_atoms()
calc.density.set_positions(atoms.get_scaled_positions() % 1.0)
calc.density.interpolate_pseudo_density()
calc.density.calculate_pseudo_charge()
except IOError:
calc = GPAW(h=h, charge=0, txt=None)
calc.calculate(s)
calc.write(gpwname)
dipole_c = calc.get_dipole_moment()
from __future__ import print_function
from ase.build import molecule
from ase.parallel import parprint
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.occupations import FixedOccupations, ZeroKelvin
from gpaw.test import equal
h = 0.4
box = 2
nbands = 2
txt = '-'
txt = None
H2 = Cluster(molecule('H2'))
H2.minimal_box(box, h)
convergence = {'energy': 0.01, 'eigenstates': 1.e-3, 'density': 1.e-2}
if 1:
# test ZeroKelvin vs FixedOccupations
c = GPAW(h=h,
nbands=nbands,
occupations=ZeroKelvin(True),
convergence=convergence,
txt=txt)
H2.set_calculator(c)
E_zk = H2.get_potential_energy()
c = GPAW(h=h,
nbands=nbands,
occupations=FixedOccupations([[2, 0]]),
SKIP_VAC_CALC = True
h = 0.24
vac = 4.0
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,
def get_unrelaxed_structure():
atoms = Cluster(ase.build.molecule('CH4'))
atoms.minimal_box(vacuum_sep, h=relax_grid_sep)
return atoms
from ase.vibrations.resonant_raman import ResonantRaman
from gpaw.cluster import Cluster
from gpaw import GPAW, FermiDirac
from gpaw.lrtddft import LrTDDFT
h = 0.25
atoms = Cluster('relaxed.traj')
atoms.minimal_box(3.5, h=h)
# relax the molecule
calc = GPAW(h=h,
occupations=FermiDirac(width=0.1),
eigensolver='cg',
symmetry={'point_group': False},
nbands=10,
convergence={
'eigenstates': 1.e-5,
'bands': 4
})
atoms.set_calculator(calc)
# use only the 4 converged states for linear response calculation
rr = ResonantRaman(atoms, LrTDDFT, exkwargs={'jend': 3})
rr.run()
from ase.vibrations.resonant_raman import ResonantRaman
from gpaw.cluster import Cluster
from gpaw import GPAW, FermiDirac
from gpaw.lrtddft import LrTDDFT
h = 0.25
atoms = Cluster('relaxed.traj')
atoms.minimal_box(3.5, h=h)
# relax the molecule
calc = GPAW(h=h,
occupations=FermiDirac(width=0.1),
eigensolver='cg',
symmetry={'point_group': False},
nbands=10,
convergence={
'eigenstates': 1.e-5,
'bands': 4
})
atoms.calc = calc
# use only the 4 converged states for linear response calculation
rr = ResonantRaman(atoms, LrTDDFT, exkwargs={'jend': 3})
rr.run()
h = 0.24
vac = 4.0
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()
from __future__ import print_function
from ase import Atom
from ase.units import Hartree
from gpaw import GPAW, FermiDirac, Davidson, PoissonSolver
from gpaw.cluster import Cluster
from gpaw.test import equal
h = .35
box = 3.
energy_tolerance = 0.0004
s = Cluster([Atom('Zn')])
s.minimal_box(box, h=h)
E = {}
E_U = {}
for spin in [0, 1]:
c = GPAW(h=h,
spinpol=spin,
xc='oldLDA',
mode='lcao',
basis='sz(dzp)',
poissonsolver=PoissonSolver(relax='GS', eps=1e-7),
parallel=dict(kpt=1),
charge=1,
occupations=FermiDirac(width=0.1, fixmagmom=spin))
s.set_calculator(c)
E[spin] = s.get_potential_energy()
c.set(setups=':d,3.0,1')
E_U[spin] = s.get_potential_energy()
import gpaw.mpi as mpi
from gpaw import GPAW
from gpaw.cluster import Cluster
txt = '-'
txt = '/dev/null'
load = False
# load = True
R = 0.7 # approx. experimental bond length
a = 4.
c = 4.
H2 = Cluster([Atom('H', (a / 2, a / 2, (c - R) / 2)),
Atom('H', (a / 2, a / 2, (c + R) / 2))],
cell=(a, a, c))
H2.rotate(57, [1, 1, 1])
fname = 'H2.gpw'
if (not load) or (not os.path.exists(fname)):
calc = GPAW(xc='PBE', nbands=2, spinpol=False, txt=txt)
H2.set_calculator(calc)
H2.get_potential_energy()
if load:
calc.write(fname, 'all')
else:
calc = GPAW(fname, txt=txt)
calc.initialize_wave_functions()
fname = 'aed.plt'
from gpaw import GPAW, FermiDirac
from gpaw.cluster import Cluster
from gpaw.test import equal
h =.3
box = 4.
energy_tolerance = 0.0004
l=2 # d-orbitals
U_ev=3 # U in eV
U_au=U_ev / Hartree # U in atomic units
scale=1 # Do not scale (does not seem to matter much)
store=0 # Do not store (not in use yet)
s = Cluster([Atom('Zn')])
s.minimal_box(box, h=h)
E = {}
E_U = {}
for spin in [0, 1]:
c = GPAW(h=h, spinpol=bool(spin),
charge=1, occupations=FermiDirac(width=0.1)
)
s.set_calculator(c)
E[spin] = s.get_potential_energy()
for setup in c.hamiltonian.setups:
setup.set_hubbard_u(U_au, l, scale, store) # Apply U
c.scf.reset()
E_U[spin] = s.get_potential_energy()
results.append(vr)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
return results
mol = Cluster(molecule('H2O'))
mol.minimal_box(2.5, h=h)
# calculate
if 1:
parprint('### fresh:')
calc = GPAW(nbands=6,
h = h,
txt=None)
if 1:
calc.calculate(mol)
calc.write(gpwname)
lastres = run()
# load previous calculation
if 1: