def test_bs(self): sb = StructureBuilder() atoms, *_ = sb.get_structure("C", "diamond") # print(atoms) base_dir = os.path.join(os.path.dirname(__file__), "../../tmp/C-class/") m_calc = MaterCalc(atoms=atoms, base_dir=base_dir) self.assertTrue(m_calc.relax(fmax=0.002)) # Very tight limit! self.assertTrue(m_calc.ground_state()) # get the PBE BS lattice_type = get_cellinfo(m_calc.atoms.cell).lattice self.assertTrue(lattice_type in special_paths.keys()) kpts_bs = dict(path=special_paths[lattice_type], npoints=120) # HSE06 base generate gs_file = os.path.join(base_dir, "gs.gpw") _calc = GPAW(restart=gs_file) atoms = _calc.atoms.copy() calc = GPAW(**_calc.parameters) calc.set(kpts=dict(gamma=True, density=4)) # low density calculations calc.atoms = atoms del _calc calc.get_potential_energy() calc.write(os.path.join(base_dir, "hse.gpw"), mode="all") calc = GPAW(restart=os.path.join(base_dir, "hse.gpw"), txt=None) ns = calc.get_number_of_spins() nk = len(calc.get_ibz_k_points()) nbands = calc.get_number_of_bands() eigen_pbe = numpy.array([[calc.get_eigenvalues(spin=s, kpt=k) \ for k in range(nk)]\ for s in range(ns)]) parprint("EIGEN_PBE", eigen_pbe.shape) vxc_pbe = vxc(calc, "PBE") parprint("VXC_PBE", vxc_pbe.shape) # world.barrier() # HSE06 now calc_hse = EXX(os.path.join(base_dir, "hse.gpw"), xc="HSE06", bands=[0, nbands]) calc_hse.calculate() vxc_hse = calc_hse.get_eigenvalue_contributions() parprint(vxc_hse.shape) parprint(vxc_hse) eigen_hse = eigen_pbe - vxc_pbe + vxc_hse # HSE bandgap from just kpts bg_hse_min, *_ = bandgap(eigenvalues=eigen_hse, efermi=calc.get_fermi_level(), direct=False) bg_hse_dir, *_ = bandgap(eigenvalues=eigen_hse, efermi=calc.get_fermi_level(), direct=True) parprint("HSE: E_min \t E_dir") parprint("{:.3f}\t{:.3f}".format(bg_hse_min, bg_hse_dir)) """
def calculate_exact_exchange(self): name = self.filename + '.exx.npy' fd = opencew(name) if fd is None: print('Reading EXX contribution from file:', name, file=self.fd) with open(name) as fd: self.exx_sin = np.load(fd) assert self.exx_sin.shape == self.shape, self.exx_sin.shape return print('Calculating EXX contribution', file=self.fd) exx = EXX(self.calc, kpts=self.kpts, bands=self.bands, txt=self.filename + '.exx.txt', timer=self.timer) exx.calculate() self.exx_sin = exx.get_eigenvalue_contributions() / Hartree np.save(fd, self.exx_sin)
def calculate_exact_exchange(self): name = self.filename + '.exx.npy' fd = opencew(name) if fd is None: print('Reading EXX contribution from file:', name, file=self.fd) with open(name) as fd: self.exx_sin = np.load(fd) assert self.exx_sin.shape == self.shape, self.exx_sin.shape return print('Calculating EXX contribution', file=self.fd) exx = EXX(self.calc, kpts=self.kpts, bands=self.bands, txt=self.filename + '.exx.txt', timer=self.timer) exx.calculate() self.exx_sin = exx.get_eigenvalue_contributions() / Hartree np.save(fd, self.exx_sin)
def xc(filename, xc, ecut=None): """Calculate non self-consitent energy. filename: str Name of restart-file. xc: str Functional ecut: float Plane-wave cutoff for exact exchange. """ name, ext = filename.rsplit('.', 1) assert ext == 'gpw' if xc in ['EXX', 'PBE0', 'B3LYP']: from gpaw.xc.exx import EXX exx = EXX(filename, xc, ecut=ecut, txt=name + '-exx.txt') exx.calculate() e = exx.get_total_energy() else: from gpaw import GPAW calc = GPAW(filename, txt=None) e = calc.get_potential_energy() + calc.get_xc_difference(xc) print(e, 'eV')
def xc(filename, xc, ecut=None): """Calculate non self-consitent energy. filename: str Name of restart-file. xc: str Functional ecut: float Plane-wave cutoff for exact exchange. """ name, ext = filename.rsplit(".", 1) assert ext == "gpw" if xc in ["EXX", "PBE0", "B3LYP"]: from gpaw.xc.exx import EXX exx = EXX(filename, xc, ecut=ecut, txt=name + "-exx.txt") exx.calculate() e = exx.get_total_energy() else: from gpaw import GPAW calc = GPAW(filename, txt=None) e = calc.get_potential_energy() + calc.get_xc_difference(xc) print(e, "eV")
isolated_calc = GPAW( mode=PW(pwcutoff), dtype=complex, kpts=(1, 1, 1), xc="PBE", txt="si_isolated_pbe.txt", occupations=FermiDirac(0.01, fixmagmom=True), spinpol=True, hund=True, convergence={"density": 1.0e-6}, mixer=Mixer(beta=0.05, nmaxold=5, weight=50.0), ) isolated_silicon.set_calculator(isolated_calc) e0_isolated_pbe = isolated_silicon.get_potential_energy() isolated_calc.write("si.pbe+exx.isolated.gpw", mode="all") # Now the exact exchange exx = EXX("si.pbe+exx.isolated.gpw", txt="si_isolated_exx.txt") exx.calculate() si_isolated_exx = exx.get_total_energy() s = str(L) s += " " s += str(e0_isolated_pbe) s += " " s += str(si_isolated_exx) s += "\n" myresults.write(s)
'size': (k, k, k), 'gamma': True }, xc='PBE', occupations=FermiDirac(0.01), txt='si.pbe+exx.pbe_output.txt', parallel={'band': 1}) bulk_crystal.set_calculator(bulk_calc) e0_bulk_pbe = bulk_crystal.get_potential_energy() # Write to file bulk_calc.write('bulk.gpw', mode='all') # Now the exact exchange exx_bulk = EXX('bulk.gpw', txt='si.pbe+exx.exx_output.txt') exx_bulk.calculate() e0_bulk_exx = exx_bulk.get_total_energy() s = str(alat) s += ' ' s += str(k) s += ' ' s += str(pwcutoff) s += ' ' s += str(e0_bulk_pbe) s += ' ' s += str(e0_bulk_exx) s += '\n' resultfile.write(s)
N2 = molecule('N2') N2.center(vacuum=2.0) calc = GPAW(mode=PW(force_complex_dtype=True), xc='PBE', parallel={'domain': 1}, eigensolver='rmm-diis') N2.set_calculator(calc) E_n2_pbe = N2.get_potential_energy() calc.diagonalize_full_hamiltonian(nbands=104, scalapack=True) calc.write('N2.gpw', mode='all') exx = EXX('N2.gpw') exx.calculate() E_n2_hf = exx.get_total_energy() rpa = RPACorrelation('N2.gpw', nfrequencies=8) E_n2_rpa = rpa.calculate(ecut=[ecut]) N = molecule('N') N.set_cell(N2.cell) calc = GPAW(mode=PW(force_complex_dtype=True), xc='PBE', parallel={'domain': 1}, eigensolver='rmm-diis') N.set_calculator(calc) E_n_pbe = N.get_potential_energy()
ibzk_kc = atoms.calc.get_ibz_k_points() n = int(atoms.calc.get_number_of_electrons()) // 2 ibzk = [] eps_kn = [] for k_c in [(0, 0, 0), (0.5, 0.5, 0), (0.5, 0.5, 0.5)]: k = abs(ibzk_kc - k_c).max(1).argmin() ibzk.append(k) eps_kn.append(atoms.calc.get_eigenvalues(k)[n - 1:n + 1]) if name == 'Ar': break deps_kn = vxc(atoms.calc, 'PBE')[0, ibzk, n - 1:n + 1] pbe0 = EXX(name + '.gpw', 'PBE0', ibzk, (n - 1, n + 1), txt=name + '.exx') pbe0.calculate() deps0_kn = pbe0.get_eigenvalue_contributions()[0] eps0_kn = eps_kn - deps_kn + deps0_kn data = {} for k, point in enumerate('GXL'): data[point] = [eps_kn[k][1] - eps_kn[0][0], eps0_kn[k, 1] - eps0_kn[0, 0]] data[point] += bfb[name][2 + k * 4:6 + k * 4] if name == 'Ar': break c.write(atoms, name=name, data=data) del c[id]
ibzk_kc = atoms.calc.get_ibz_k_points() n = int(atoms.calc.get_number_of_electrons()) // 2 ibzk = [] eps_kn = [] for k_c in [(0, 0, 0), (0.5, 0.5, 0), (0.5, 0.5, 0.5)]: k = abs(ibzk_kc - k_c).max(1).argmin() ibzk.append(k) eps_kn.append(atoms.calc.get_eigenvalues(k)[n - 1:n + 1]) if name == 'Ar': break deps_kn = vxc(atoms.calc, 'PBE')[0, ibzk, n - 1:n + 1] pbe0 = EXX(name, 'PBE0', ibzk, (n - 1, n + 1), txt=name + '.exx') pbe0.calculate() deps0_kn = pbe0.get_eigenvalue_contributions()[0] eps0_kn = eps_kn - deps_kn + deps0_kn data = {} for k, point in enumerate('GXL'): data[point] = [eps_kn[k][1] - eps_kn[0][0], eps0_kn[k, 1] - eps0_kn[0, 0]] data[point] += bfb[name][2 + k * 4:6 + k * 4] if name == 'Ar': break c.write(atoms, name=name, data=data) del c[id]
mode = PW(pwcutoff), kpts={'size': (k, k, k), 'gamma': True}, dtype=complex, xc='PBE', txt='si.pbe+exx.pbe_output.txt', parallel={'band':1} ) bulk_crystal.set_calculator(bulk_calc) e0_bulk_pbe = bulk_crystal.get_potential_energy() # Write to file bulk_calc.write('bulk.gpw',mode='all') # Now the exact exchange exx_bulk = EXX('bulk.gpw', txt='si.pbe+exx.exx_output.txt') exx_bulk.calculate() e0_bulk_exx = exx_bulk.get_total_energy() s = str(alat) s += ' ' s += str(k) s += ' ' s += str(pwcutoff) s += ' ' s += str(e0_bulk_pbe) s += ' ' s += str(e0_bulk_exx) s += '\n' resultfile.write(s)
def hse(base_dir="./", kdens=6.0): emptybands = 20 convbands = 10 # If pbc in z direction, use vdW for relaxation as default! # if atoms.pbc[-1]: # Do not compare with np.bool_ ! # use_vdW = True # else: # use_vdW = False curr_dir = os.path.dirname(os.path.abspath(__file__)) param_file = os.path.join(curr_dir, "../parameters.json") gpw_file = os.path.join(base_dir, "gs.gpw") hse_file = os.path.join(base_dir, "hse.gpw") hse_nowfs_file = os.path.join(base_dir, "hse_nowfs.gpw") hse_eigen_file = os.path.join(base_dir, "hse_eigenvalues.npz") if not os.path.exists(gpw_file): parprint("No ground state calculation? Exit...") return 0 if os.path.exists(param_file): params = json.load(open(param_file, "r")) else: raise FileNotFoundError("no parameter file!") if not os.path.exists(hse_file): calc = GPAW(gpw_file) # reload the calculation atoms = calc.get_atoms() kpts = get_kpts_size(atoms, kdens) calc.set(nbands=-emptybands, fixdensity=True, kpts=kpts, convergence={'bands': -convbands}) calc.get_potential_energy() calc.write(hse_file, 'all') calc.write(hse_nowfs_file) # no wavefunction mpi.world.barrier() time.sleep(10) # is this needed? calc = GPAW(hse_file, txt=None) ns = calc.get_number_of_spins() nk = len(calc.get_ibz_k_points()) nb = calc.get_number_of_bands() vxc_pbe_skn = vxc(calc, 'PBE') vxc_pbe_nsk = numpy.ascontiguousarray(vxc_pbe_skn.transpose(2, 0, 1)) vxc_pbe_nsk = calc.wfs.bd.collect(vxc_pbe_nsk, broadcast=True) vxc_pbe_skn = vxc_pbe_nsk.transpose(1, 2, 0)[:, :, :-convbands] e_pbe_skn = np.zeros((ns, nk, nb)) for s in range(ns): for k in range(nk): e_pbe_skn[s, k, :] = calc.get_eigenvalues(spin=s, kpt=k) e_pbe_skn = e_pbe_skn[:, :, :-convbands] hse_calc = EXX(hse_file, xc='HSE06', bands=[0, nb - convbands]) hse_calc.calculate() vxc_hse_skn = hse_calc.get_eigenvalue_contributions() e_hse_skn = e_pbe_skn - vxc_pbe_skn + vxc_hse_skn ranks = [0] if mpi.world.rank in ranks: dct = dict(vxc_hse_skn=vxc_hse_skn, e_pbe_skn=e_pbe_skn, vxc_pbe_skn=vxc_pbe_skn, e_hse_skn=e_hse_skn) with open(hse_eigen_file, 'wb') as f: numpy.savez(f, **dct) parprint("Single HSE06 finished!")