Esempio n. 1
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 def estimate_memory(self, mem):
     RealSpaceHamiltonian.estimate_memory(self, mem)
     solvation = mem.subnode('Solvation')
     for name, obj in [
         ('Cavity', self.cavity),
         ('Dielectric', self.dielectric),
     ] + [('Interaction: ' + ia.subscript, ia) for ia in self.interactions]:
         obj.estimate_memory(solvation.subnode(name))
Esempio n. 2
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    def __init__(
            self,
            # solvation related arguments:
            cavity,
            dielectric,
            interactions,
            # RealSpaceHamiltonian arguments:
            gd,
            finegd,
            nspins,
            collinear,
            setups,
            timer,
            xc,
            world,
            redistributor,
            vext=None,
            psolver=None,
            stencil=3):
        """Constructor of SolvationRealSpaceHamiltonian class.

        Additional arguments not present in RealSpaceHamiltonian:
        cavity       -- A Cavity instance.
        dielectric   -- A Dielectric instance.
        interactions -- A list of Interaction instances.
        """
        self.cavity = cavity
        self.dielectric = dielectric
        self.interactions = interactions
        cavity.set_grid_descriptor(finegd)
        dielectric.set_grid_descriptor(finegd)
        for ia in interactions:
            ia.set_grid_descriptor(finegd)
        if psolver is None:
            psolver = WeightedFDPoissonSolver()
        psolver.set_dielectric(self.dielectric)
        self.gradient = None
        RealSpaceHamiltonian.__init__(self,
                                      gd,
                                      finegd,
                                      nspins,
                                      collinear,
                                      setups,
                                      timer,
                                      xc,
                                      world,
                                      vext=vext,
                                      psolver=psolver,
                                      stencil=stencil,
                                      redistributor=redistributor)

        for ia in interactions:
            setattr(self, 'e_' + ia.subscript, None)
        self.new_atoms = None
        self.vt_ia_g = None
        self.e_el_free = None
        self.e_el_extrapolated = None
Esempio n. 3
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 def initialize(self):
     self.gradient = [
         Gradient(self.finegd, i, 1.0, self.poisson.nn) for i in (0, 1, 2)
     ]
     self.vt_ia_g = self.finegd.zeros()
     self.cavity.allocate()
     self.dielectric.allocate()
     for ia in self.interactions:
         ia.allocate()
     RealSpaceHamiltonian.initialize(self)
Esempio n. 4
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 def summary(self, fermilevel, log):
     self.cavity.summary(log)
     log()
     log('Solvation Energy Contributions:')
     for ia in self.interactions:
         E = Hartree * getattr(self, 'e_' + ia.subscript)
         log('%-14s %+11.6f' % (ia.subscript + ':', E))
     E_el_free = Hartree * self.e_el_free
     E_el_extrapolated = Hartree * self.e_el_extrapolated
     log('%-14s %+11.6f' % ('el (free):', E_el_free))
     log('%-14s %+11.6f' % ('el (extrpol.):', E_el_extrapolated))
     log('el (free) is composed of:')
     RealSpaceHamiltonian.summary(self, fermilevel, log)
Esempio n. 5
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class UTHamiltonianFunctionSetup(UTLocalizedFunctionSetup):
    __doc__ = UTLocalizedFunctionSetup.__doc__ + """
    Atomic hamiltonian matrices are distributed over domains."""

    def setUp(self):
        UTLocalizedFunctionSetup.setUp(self)

        self.finegd = self.gd.refine()
        self.hamiltonian = RealSpaceHamiltonian(
            self.gd, self.finegd, self.nspins,
            self.setups, self.timer,
            xc, p.external, True,
            p.poissonsolver, p.stencils[1])
        self.hamiltonian.dH_asp = {}
        self.hamiltonian.rank_a = self.rank0_a
        self.allocate(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)
        assert self.allocated

        for a, dH_sp in self.hamiltonian.dH_asp.items():
            ni = self.setups[a].ni
            for s, dH_p in enumerate(dH_sp):
                dH_p[:] = 1e9 * self.kd_old.comm.rank + 1e6 * self.bd.comm.rank \
                    + 1e3 * s + np.arange(ni * (ni + 1) // 2, dtype=float)    

    def tearDown(self):
        del self.hamiltonian
        UTLocalizedFunctionSetup.tearDown(self)

    # =================================

    def test_initial_consistency(self):
        self.update_references(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)
        self.check_values(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)

    def test_redistribution_to_domains(self):
        self.update_references(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)
        spos_ac = self.atoms.get_scaled_positions() % 1.0
        rank_a = self.gd.get_ranks_from_positions(spos_ac)
        self.hamiltonian.set_positions(spos_ac, rank_a)
        self.check_values(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)

    def test_redistribution_to_same(self):
        self.update_references(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)
        spos_ac = self.atoms.get_scaled_positions() % 1.0
        rank_a = self.gd.get_ranks_from_positions(spos_ac)
        self.hamiltonian.set_positions(spos_ac, rank_a)
        self.hamiltonian.set_positions(spos_ac, rank_a)
        self.check_values(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)
Esempio n. 6
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 def update_pseudo_potential(self, density):
     ret = RealSpaceHamiltonian.update_pseudo_potential(self, density)
     if not self.cavity.depends_on_el_density:
         return ret
     del_g_del_n_g = self.cavity.del_g_del_n_g
     # XXX optimize numerics
     del_eps_del_g_g = self.dielectric.del_eps_del_g_g
     Veps = -1. / (8. * np.pi) * del_eps_del_g_g * del_g_del_n_g
     Veps *= self.grad_squared(self.vHt_g)
     for vt_g in self.vt_sg:
         vt_g += Veps
     return ret
Esempio n. 7
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    def create_hamiltonian(self, realspace, mode, xc):
        dens = self.density
        kwargs = dict(gd=dens.gd,
                      finegd=dens.finegd,
                      nspins=dens.nspins,
                      collinear=dens.collinear,
                      setups=dens.setups,
                      timer=self.timer,
                      xc=xc,
                      world=self.world,
                      redistributor=dens.redistributor,
                      vext=self.parameters.external,
                      psolver=self.parameters.poissonsolver)
        if realspace:
            self.hamiltonian = RealSpaceHamiltonian(stencil=mode.interpolation,
                                                    **kwargs)
            xc.set_grid_descriptor(self.hamiltonian.finegd)
        else:
            # This code will work if dens.redistributor uses
            # ordinary density.gd as aux_gd
            gd = dens.finegd

            xc_redist = None
            if self.parallel['augment_grids']:
                from gpaw.grid_descriptor import BadGridError
                try:
                    aux_gd = gd.new_descriptor(comm=self.world)
                except BadGridError as err:
                    import warnings
                    warnings.warn('Ignoring augment_grids: {}'.format(err))
                else:
                    bcast_comm = dens.redistributor.broadcast_comm
                    xc_redist = GridRedistributor(self.world, bcast_comm, gd,
                                                  aux_gd)

            self.hamiltonian = pw.ReciprocalSpaceHamiltonian(
                pd2=dens.pd2,
                pd3=dens.pd3,
                realpbc_c=self.atoms.pbc,
                xc_redistributor=xc_redist,
                **kwargs)
            xc.set_grid_descriptor(self.hamiltonian.xc_gd)

        self.hamiltonian.soc = self.parameters.experimental.get('soc')
        self.log(self.hamiltonian, '\n')
Esempio n. 8
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 def calculate_forces(self, dens, F_av):
     # XXX reorganize
     self.el_force_correction(dens, F_av)
     for ia in self.interactions:
         if self.cavity.depends_on_atomic_positions:
             for a, F_v in enumerate(F_av):
                 del_g_del_r_vg = self.cavity.get_del_r_vg(a, dens)
                 for v in (0, 1, 2):
                     F_v[v] -= self.finegd.integrate(ia.delta_E_delta_g_g *
                                                     del_g_del_r_vg[v],
                                                     global_integral=False)
         if ia.depends_on_atomic_positions:
             for a, F_v in enumerate(F_av):
                 del_E_del_r_vg = ia.get_del_r_vg(a, dens)
                 for v in (0, 1, 2):
                     F_v[v] -= self.finegd.integrate(del_E_del_r_vg[v],
                                                     global_integral=False)
     return RealSpaceHamiltonian.calculate_forces(self, dens, F_av)
Esempio n. 9
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    def setUp(self):
        UTLocalizedFunctionSetup.setUp(self)

        self.finegd = self.gd.refine()
        self.hamiltonian = RealSpaceHamiltonian(
            self.gd, self.finegd, self.nspins,
            self.setups, self.timer,
            xc, p.external, True,
            p.poissonsolver, p.stencils[1])
        self.hamiltonian.dH_asp = {}
        self.hamiltonian.rank_a = self.rank0_a
        self.allocate(self.hamiltonian.dH_asp, self.hamiltonian.rank_a)
        assert self.allocated

        for a, dH_sp in self.hamiltonian.dH_asp.items():
            ni = self.setups[a].ni
            for s, dH_p in enumerate(dH_sp):
                dH_p[:] = 1e9 * self.kd_old.comm.rank + 1e6 * self.bd.comm.rank \
                    + 1e3 * s + np.arange(ni * (ni + 1) // 2, dtype=float)    
Esempio n. 10
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    def create_hamiltonian(self, realspace, mode, xc):
        dens = self.density
        kwargs = dict(gd=dens.gd,
                      finegd=dens.finegd,
                      nspins=dens.nspins,
                      setups=dens.setups,
                      timer=self.timer,
                      xc=xc,
                      world=self.world,
                      redistributor=dens.redistributor,
                      vext=self.parameters.external,
                      psolver=self.parameters.poissonsolver)
        if realspace:
            self.hamiltonian = RealSpaceHamiltonian(stencil=mode.interpolation,
                                                    **kwargs)
            xc.set_grid_descriptor(self.hamiltonian.finegd)  # XXX
        else:
            self.hamiltonian = pw.ReciprocalSpaceHamiltonian(
                pd2=dens.pd2, pd3=dens.pd3, realpbc_c=self.atoms.pbc, **kwargs)
            xc.set_grid_descriptor(dens.xc_redistributor.aux_gd)  # XXX

        self.log(self.hamiltonian, '\n')
Esempio n. 11
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 def __str__(self):
     s = RealSpaceHamiltonian.__str__(self) + '\n'
     s += '  Solvation:\n'
     components = [self.cavity, self.dielectric] + self.interactions
     s += ''.join([indent(str(c), 2) for c in components])
     return s
Esempio n. 12
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class PAW(PAWTextOutput):
    """This is the main calculation object for doing a PAW calculation."""
    def __init__(self,
                 filename=None,
                 timer=None,
                 read_projections=True,
                 **kwargs):
        """ASE-calculator interface.

        The following parameters can be used: nbands, xc, kpts,
        spinpol, gpts, h, charge, symmetry, width, mixer,
        hund, lmax, fixdensity, convergence, txt, parallel,
        communicator, dtype, softgauss and stencils.

        If you don't specify any parameters, you will get:

        Defaults: neutrally charged, LDA, gamma-point calculation, a
        reasonable grid-spacing, zero Kelvin electronic temperature,
        and the number of bands will be equal to the number of atomic
        orbitals present in the setups. Only occupied bands are used
        in the convergence decision. The calculation will be
        spin-polarized if and only if one or more of the atoms have
        non-zero magnetic moments. Text output will be written to
        standard output.

        For a non-gamma point calculation, the electronic temperature
        will be 0.1 eV (energies are extrapolated to zero Kelvin) and
        all symmetries will be used to reduce the number of
        **k**-points."""

        PAWTextOutput.__init__(self)
        self.grid_descriptor_class = GridDescriptor
        self.input_parameters = InputParameters()

        if timer is None:
            self.timer = Timer()
        else:
            self.timer = timer

        self.scf = None
        self.forces = ForceCalculator(self.timer)
        self.stress_vv = None
        self.dipole_v = None
        self.magmom_av = None
        self.wfs = EmptyWaveFunctions()
        self.occupations = None
        self.density = None
        self.hamiltonian = None
        self.atoms = None
        self.iter = 0

        self.initialized = False
        self.nbands_parallelization_adjustment = None  # Somehow avoid this?

        # Possibly read GPAW keyword arguments from file:
        if filename is not None and filename.endswith('.gkw'):
            from gpaw.utilities.kwargs import load
            parameters = load(filename)
            parameters.update(kwargs)
            kwargs = parameters
            filename = None  # XXX

        if filename is not None:
            comm = kwargs.get('communicator', mpi.world)
            reader = gpaw.io.open(filename, 'r', comm)
            self.atoms = gpaw.io.read_atoms(reader)
            par = self.input_parameters
            par.read(reader)

        # _changed_keywords contains those keywords that have been
        # changed by set() since last time initialize() was called.
        self._changed_keywords = set()
        self.set(**kwargs)
        # Here in the beginning, effectively every keyword has been changed.
        self._changed_keywords.update(self.input_parameters)

        if filename is not None:
            # Setups are not saved in the file if the setups were not loaded
            # *from* files in the first place
            if par.setups is None:
                if par.idiotproof:
                    raise RuntimeError('Setups not specified in file. Use '
                                       'idiotproof=False to proceed anyway.')
                else:
                    par.setups = {None: 'paw'}
            if par.basis is None:
                if par.idiotproof:
                    raise RuntimeError('Basis not specified in file. Use '
                                       'idiotproof=False to proceed anyway.')
                else:
                    par.basis = {}

            self.initialize()
            self.read(reader, read_projections)
            if self.hamiltonian.xc.type == 'GLLB':
                self.occupations.calculate(self.wfs)

            self.print_cell_and_parameters()

        self.observers = []

    def read(self, reader, read_projections=True):
        gpaw.io.read(self, reader, read_projections)

    def set(self, **kwargs):
        """Change parameters for calculator.

        Examples::

            calc.set(xc='PBE')
            calc.set(nbands=20, kpts=(4, 1, 1))
        """
        p = self.input_parameters
        self._changed_keywords.update(kwargs)

        if (kwargs.get('h') is not None) and (kwargs.get('gpts') is not None):
            raise TypeError("""You can't use both "gpts" and "h"!""")
        if 'h' in kwargs:
            p['gpts'] = None
        if 'gpts' in kwargs:
            p['h'] = None

        # Special treatment for dictionary parameters:
        for name in ['convergence', 'parallel']:
            if kwargs.get(name) is not None:
                tmp = p[name]
                for key in kwargs[name]:
                    if key not in tmp:
                        raise KeyError('Unknown subparameter "%s" in '
                                       'dictionary parameter "%s"' %
                                       (key, name))
                tmp.update(kwargs[name])
                kwargs[name] = tmp

        self.initialized = False

        for key in kwargs:
            if key == 'basis' and str(p['mode']) == 'fd':  # umm what about PW?
                # The second criterion seems buggy, will not touch it.  -Ask
                continue

            if key == 'eigensolver':
                self.wfs.set_eigensolver(None)

            if key in [
                    'fixmom', 'mixer', 'verbose', 'txt', 'hund', 'random',
                    'eigensolver', 'idiotproof', 'notify'
            ]:
                continue

            if key in ['convergence', 'fixdensity', 'maxiter']:
                self.scf = None
                continue

            # More drastic changes:
            self.scf = None
            self.wfs.set_orthonormalized(False)
            if key in [
                    'lmax', 'width', 'stencils', 'external', 'xc',
                    'poissonsolver'
            ]:
                self.hamiltonian = None
                self.occupations = None
            elif key in ['occupations']:
                self.occupations = None
            elif key in ['charge']:
                self.hamiltonian = None
                self.density = None
                self.wfs = EmptyWaveFunctions()
                self.occupations = None
            elif key in ['kpts', 'nbands', 'usesymm', 'symmetry']:
                self.wfs = EmptyWaveFunctions()
                self.occupations = None
            elif key in [
                    'h', 'gpts', 'setups', 'spinpol', 'realspace', 'parallel',
                    'communicator', 'dtype', 'mode'
            ]:
                self.density = None
                self.occupations = None
                self.hamiltonian = None
                self.wfs = EmptyWaveFunctions()
            elif key in ['basis']:
                self.wfs = EmptyWaveFunctions()
            elif key in ['parsize', 'parsize_bands', 'parstride_bands']:
                name = {
                    'parsize': 'domain',
                    'parsize_bands': 'band',
                    'parstride_bands': 'stridebands'
                }[key]
                raise DeprecationWarning(
                    'Keyword argument has been moved ' +
                    "to the 'parallel' dictionary keyword under '%s'." % name)
            else:
                raise TypeError("Unknown keyword argument: '%s'" % key)

        p.update(kwargs)

    def calculate(self,
                  atoms=None,
                  converge=False,
                  force_call_to_set_positions=False):
        """Update PAW calculaton if needed.

        Returns True/False whether a calculation was performed or not."""

        self.timer.start('Initialization')
        if atoms is None:
            atoms = self.atoms

        if self.atoms is None:
            # First time:
            self.initialize(atoms)
            self.set_positions(atoms)
        elif (len(atoms) != len(self.atoms)
              or (atoms.get_atomic_numbers() !=
                  self.atoms.get_atomic_numbers()).any()
              or (atoms.get_initial_magnetic_moments() !=
                  self.atoms.get_initial_magnetic_moments()).any()
              or (atoms.get_cell() != self.atoms.get_cell()).any()
              or (atoms.get_pbc() != self.atoms.get_pbc()).any()):
            # Drastic changes:
            self.wfs = EmptyWaveFunctions()
            self.occupations = None
            self.density = None
            self.hamiltonian = None
            self.scf = None
            self.initialize(atoms)
            self.set_positions(atoms)
        elif not self.initialized:
            self.initialize(atoms)
            self.set_positions(atoms)
        elif (atoms.get_positions() != self.atoms.get_positions()).any():
            self.density.reset()
            self.set_positions(atoms)
        elif not self.scf.converged:
            # Do not call scf.check_convergence() here as it overwrites
            # scf.converged, and setting scf.converged is the only
            # 'practical' way for a user to force the calculation to proceed
            self.set_positions(atoms)
        elif force_call_to_set_positions:
            self.set_positions(atoms)

        self.timer.stop('Initialization')

        if self.scf.converged:
            return False
        else:
            self.print_cell_and_parameters()

        self.timer.start('SCF-cycle')
        for iter in self.scf.run(self.wfs, self.hamiltonian, self.density,
                                 self.occupations, self.forces):
            self.iter = iter
            self.call_observers(iter)
            self.print_iteration(iter)
        self.timer.stop('SCF-cycle')

        if self.scf.converged:
            self.call_observers(iter, final=True)
            self.print_converged(iter)
        elif converge:
            self.txt.write(oops)
            raise KohnShamConvergenceError(
                'Did not converge!  See text output for help.')

        return True

    def initialize_positions(self, atoms=None):
        """Update the positions of the atoms."""
        if atoms is None:
            atoms = self.atoms
        else:
            # Save the state of the atoms:
            self.atoms = atoms.copy()

        self.check_atoms()

        spos_ac = atoms.get_scaled_positions() % 1.0

        self.wfs.set_positions(spos_ac)
        self.density.set_positions(spos_ac, self.wfs.rank_a)
        self.hamiltonian.set_positions(spos_ac, self.wfs.rank_a)

        return spos_ac

    def set_positions(self, atoms=None):
        """Update the positions of the atoms and initialize wave functions."""
        spos_ac = self.initialize_positions(atoms)
        self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
        self.wfs.eigensolver.reset()
        self.scf.reset()
        self.forces.reset()
        self.stress_vv = None
        self.dipole_v = None
        self.magmom_av = None
        self.print_positions()

    def initialize(self, atoms=None):
        """Inexpensive initialization."""

        if atoms is None:
            atoms = self.atoms
        else:
            # Save the state of the atoms:
            self.atoms = atoms.copy()

        par = self.input_parameters

        world = par.communicator
        if world is None:
            world = mpi.world
        elif hasattr(world, 'new_communicator'):
            # Check for whether object has correct type already
            #
            # Using isinstance() is complicated because of all the
            # combinations, serial/parallel/debug...
            pass
        else:
            # world should be a list of ranks:
            world = mpi.world.new_communicator(np.asarray(world))
        self.wfs.world = world

        if 'txt' in self._changed_keywords:
            self.set_txt(par.txt)
        self.verbose = par.verbose

        natoms = len(atoms)

        cell_cv = atoms.get_cell() / Bohr
        pbc_c = atoms.get_pbc()
        Z_a = atoms.get_atomic_numbers()
        magmom_av = atoms.get_initial_magnetic_moments()

        self.check_atoms()

        # Generate new xc functional only when it is reset by set
        # XXX sounds like this should use the _changed_keywords dictionary.
        if self.hamiltonian is None or self.hamiltonian.xc is None:
            if isinstance(par.xc, str):
                xc = XC(par.xc)
            else:
                xc = par.xc
        else:
            xc = self.hamiltonian.xc

        mode = par.mode

        if mode == 'fd':
            mode = FD()
        elif mode == 'pw':
            mode = pw.PW()
        elif mode == 'lcao':
            mode = LCAO()
        else:
            assert hasattr(mode, 'name'), str(mode)

        if xc.orbital_dependent and mode.name == 'lcao':
            raise NotImplementedError('LCAO mode does not support '
                                      'orbital-dependent XC functionals.')

        if par.realspace is None:
            realspace = (mode.name != 'pw')
        else:
            realspace = par.realspace
            if mode.name == 'pw':
                assert not realspace

        if par.filter is None and mode.name != 'pw':
            gamma = 1.6
            if par.gpts is not None:
                h = ((np.linalg.inv(cell_cv)**2).sum(0)**-0.5 / par.gpts).max()
            else:
                h = (par.h or 0.2) / Bohr

            def filter(rgd, rcut, f_r, l=0):
                gcut = np.pi / h - 2 / rcut / gamma
                f_r[:] = rgd.filter(f_r, rcut * gamma, gcut, l)
        else:
            filter = par.filter

        setups = Setups(Z_a, par.setups, par.basis, par.lmax, xc, filter,
                        world)

        if magmom_av.ndim == 1:
            collinear = True
            magmom_av, magmom_a = np.zeros((natoms, 3)), magmom_av
            magmom_av[:, 2] = magmom_a
        else:
            collinear = False

        magnetic = magmom_av.any()

        spinpol = par.spinpol
        if par.hund:
            if natoms != 1:
                raise ValueError('hund=True arg only valid for single atoms!')
            spinpol = True
            magmom_av[0] = (0, 0, setups[0].get_hunds_rule_moment(par.charge))

        if spinpol is None:
            spinpol = magnetic
        elif magnetic and not spinpol:
            raise ValueError('Non-zero initial magnetic moment for a ' +
                             'spin-paired calculation!')

        if collinear:
            nspins = 1 + int(spinpol)
            ncomp = 1
        else:
            nspins = 1
            ncomp = 2

        if par.usesymm != 'default':
            warnings.warn('Use "symmetry" keyword instead of ' +
                          '"usesymm" keyword')
            par.symmetry = usesymm2symmetry(par.usesymm)

        symm = par.symmetry
        if symm == 'off':
            symm = {'point_group': False, 'time_reversal': False}

        bzkpts_kc = kpts2ndarray(par.kpts, self.atoms)
        kd = KPointDescriptor(bzkpts_kc, nspins, collinear)
        m_av = magmom_av.round(decimals=3)  # round off
        id_a = zip(setups.id_a, *m_av.T)
        symmetry = Symmetry(id_a, cell_cv, atoms.pbc, **symm)
        kd.set_symmetry(atoms, symmetry, comm=world)
        setups.set_symmetry(symmetry)

        if par.gpts is not None:
            N_c = np.array(par.gpts)
        else:
            h = par.h
            if h is not None:
                h /= Bohr
            N_c = get_number_of_grid_points(cell_cv, h, mode, realspace,
                                            kd.symmetry)

        symmetry.check_grid(N_c)

        width = par.width
        if width is None:
            if pbc_c.any():
                width = 0.1  # eV
            else:
                width = 0.0
        else:
            assert par.occupations is None

        if hasattr(self, 'time') or par.dtype == complex:
            dtype = complex
        else:
            if kd.gamma:
                dtype = float
            else:
                dtype = complex

        nao = setups.nao
        nvalence = setups.nvalence - par.charge
        M_v = magmom_av.sum(0)
        M = np.dot(M_v, M_v)**0.5

        nbands = par.nbands

        orbital_free = any(setup.orbital_free for setup in setups)
        if orbital_free:
            nbands = 1

        if isinstance(nbands, basestring):
            if nbands[-1] == '%':
                basebands = int(nvalence + M + 0.5) // 2
                nbands = int((float(nbands[:-1]) / 100) * basebands)
            else:
                raise ValueError('Integer Expected: Only use a string '
                                 'if giving a percentage of occupied bands')

        if nbands is None:
            nbands = 0
            for setup in setups:
                nbands_from_atom = setup.get_default_nbands()

                # Any obscure setup errors?
                if nbands_from_atom < -(-setup.Nv // 2):
                    raise ValueError('Bad setup: This setup requests %d'
                                     ' bands but has %d electrons.' %
                                     (nbands_from_atom, setup.Nv))
                nbands += nbands_from_atom
            nbands = min(nao, nbands)
        elif nbands > nao and mode.name == 'lcao':
            raise ValueError('Too many bands for LCAO calculation: '
                             '%d bands and only %d atomic orbitals!' %
                             (nbands, nao))

        if nvalence < 0:
            raise ValueError(
                'Charge %f is not possible - not enough valence electrons' %
                par.charge)

        if nbands <= 0:
            nbands = int(nvalence + M + 0.5) // 2 + (-nbands)

        if nvalence > 2 * nbands and not orbital_free:
            raise ValueError('Too few bands!  Electrons: %f, bands: %d' %
                             (nvalence, nbands))

        nbands *= ncomp

        if par.width is not None:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width).')
        if par.fixmom:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width, fixmagmom=True).')

        if self.occupations is None:
            if par.occupations is None:
                # Create object for occupation numbers:
                if orbital_free:
                    width = 0.0  # even for PBC
                    self.occupations = occupations.TFOccupations(
                        width, par.fixmom)
                else:
                    self.occupations = occupations.FermiDirac(
                        width, par.fixmom)
            else:
                self.occupations = par.occupations

            # If occupation numbers are changed, and we have wave functions,
            # recalculate the occupation numbers
            if self.wfs is not None and not isinstance(self.wfs,
                                                       EmptyWaveFunctions):
                self.occupations.calculate(self.wfs)

        self.occupations.magmom = M_v[2]

        cc = par.convergence

        if mode.name == 'lcao':
            niter_fixdensity = 0
        else:
            niter_fixdensity = None

        if self.scf is None:
            force_crit = cc['forces']
            if force_crit is not None:
                force_crit /= Hartree / Bohr
            self.scf = SCFLoop(cc['eigenstates'] / Hartree**2 * nvalence,
                               cc['energy'] / Hartree * max(nvalence, 1),
                               cc['density'] * nvalence, par.maxiter,
                               par.fixdensity, niter_fixdensity, force_crit)

        parsize_kpt = par.parallel['kpt']
        parsize_domain = par.parallel['domain']
        parsize_bands = par.parallel['band']

        if not realspace:
            pbc_c = np.ones(3, bool)

        if not self.wfs:
            if parsize_domain == 'domain only':  # XXX this was silly!
                parsize_domain = world.size

            parallelization = mpi.Parallelization(world, nspins * kd.nibzkpts)
            ndomains = None
            if parsize_domain is not None:
                ndomains = np.prod(parsize_domain)
            if mode.name == 'pw':
                if ndomains > 1:
                    raise ValueError('Planewave mode does not support '
                                     'domain decomposition.')
                ndomains = 1
            parallelization.set(kpt=parsize_kpt,
                                domain=ndomains,
                                band=parsize_bands)
            comms = parallelization.build_communicators()
            domain_comm = comms['d']
            kpt_comm = comms['k']
            band_comm = comms['b']
            kptband_comm = comms['D']
            domainband_comm = comms['K']

            self.comms = comms
            kd.set_communicator(kpt_comm)

            parstride_bands = par.parallel['stridebands']

            # Unfortunately we need to remember that we adjusted the
            # number of bands so we can print a warning if it differs
            # from the number specified by the user.  (The number can
            # be inferred from the input parameters, but it's tricky
            # because we allow negative numbers)
            self.nbands_parallelization_adjustment = -nbands % band_comm.size
            nbands += self.nbands_parallelization_adjustment

            # I would like to give the following error message, but apparently
            # there are cases, e.g. gpaw/test/gw_ppa.py, which involve
            # nbands > nao and are supposed to work that way.
            #if nbands > nao:
            #    raise ValueError('Number of bands %d adjusted for band '
            #                     'parallelization %d exceeds number of atomic '
            #                     'orbitals %d.  This problem can be fixed '
            #                     'by reducing the number of bands a bit.'
            #                     % (nbands, band_comm.size, nao))
            bd = BandDescriptor(nbands, band_comm, parstride_bands)

            if (self.density is not None
                    and self.density.gd.comm.size != domain_comm.size):
                # Domain decomposition has changed, so we need to
                # reinitialize density and hamiltonian:
                if par.fixdensity:
                    raise RuntimeError(
                        'Density reinitialization conflict ' +
                        'with "fixdensity" - specify domain decomposition.')
                self.density = None
                self.hamiltonian = None

            # Construct grid descriptor for coarse grids for wave functions:
            gd = self.grid_descriptor_class(N_c, cell_cv, pbc_c, domain_comm,
                                            parsize_domain)

            # do k-point analysis here? XXX
            args = (gd, nvalence, setups, bd, dtype, world, kd, kptband_comm,
                    self.timer)

            if par.parallel['sl_auto']:
                # Choose scalapack parallelization automatically

                for key, val in par.parallel.items():
                    if (key.startswith('sl_') and key != 'sl_auto'
                            and val is not None):
                        raise ValueError("Cannot use 'sl_auto' together "
                                         "with '%s'" % key)
                max_scalapack_cpus = bd.comm.size * gd.comm.size
                nprow = max_scalapack_cpus
                npcol = 1

                # Get a sort of reasonable number of columns/rows
                while npcol < nprow and nprow % 2 == 0:
                    npcol *= 2
                    nprow //= 2
                assert npcol * nprow == max_scalapack_cpus

                # ScaLAPACK creates trouble if there aren't at least a few
                # whole blocks; choose block size so there will always be
                # several blocks.  This will crash for small test systems,
                # but so will ScaLAPACK in any case
                blocksize = min(-(-nbands // 4), 64)
                sl_default = (nprow, npcol, blocksize)
            else:
                sl_default = par.parallel['sl_default']

            if mode.name == 'lcao':
                # Layouts used for general diagonalizer
                sl_lcao = par.parallel['sl_lcao']
                if sl_lcao is None:
                    sl_lcao = sl_default
                lcaoksl = get_KohnSham_layouts(sl_lcao,
                                               'lcao',
                                               gd,
                                               bd,
                                               domainband_comm,
                                               dtype,
                                               nao=nao,
                                               timer=self.timer)

                self.wfs = mode(collinear, lcaoksl, *args)

            elif mode.name == 'fd' or mode.name == 'pw':
                # buffer_size keyword only relevant for fdpw
                buffer_size = par.parallel['buffer_size']
                # Layouts used for diagonalizer
                sl_diagonalize = par.parallel['sl_diagonalize']
                if sl_diagonalize is None:
                    sl_diagonalize = sl_default
                diagksl = get_KohnSham_layouts(
                    sl_diagonalize,
                    'fd',  # XXX
                    # choice of key 'fd' not so nice
                    gd,
                    bd,
                    domainband_comm,
                    dtype,
                    buffer_size=buffer_size,
                    timer=self.timer)

                # Layouts used for orthonormalizer
                sl_inverse_cholesky = par.parallel['sl_inverse_cholesky']
                if sl_inverse_cholesky is None:
                    sl_inverse_cholesky = sl_default
                if sl_inverse_cholesky != sl_diagonalize:
                    message = 'sl_inverse_cholesky != sl_diagonalize ' \
                        'is not implemented.'
                    raise NotImplementedError(message)
                orthoksl = get_KohnSham_layouts(sl_inverse_cholesky,
                                                'fd',
                                                gd,
                                                bd,
                                                domainband_comm,
                                                dtype,
                                                buffer_size=buffer_size,
                                                timer=self.timer)

                # Use (at most) all available LCAO for initialization
                lcaonbands = min(nbands, nao)

                try:
                    lcaobd = BandDescriptor(lcaonbands, band_comm,
                                            parstride_bands)
                except RuntimeError:
                    initksl = None
                else:
                    # Layouts used for general diagonalizer
                    # (LCAO initialization)
                    sl_lcao = par.parallel['sl_lcao']
                    if sl_lcao is None:
                        sl_lcao = sl_default
                    initksl = get_KohnSham_layouts(sl_lcao,
                                                   'lcao',
                                                   gd,
                                                   lcaobd,
                                                   domainband_comm,
                                                   dtype,
                                                   nao=nao,
                                                   timer=self.timer)

                if hasattr(self, 'time'):
                    assert mode.name == 'fd'
                    from gpaw.tddft import TimeDependentWaveFunctions
                    self.wfs = TimeDependentWaveFunctions(
                        par.stencils[0], diagksl, orthoksl, initksl, gd,
                        nvalence, setups, bd, world, kd, kptband_comm,
                        self.timer)
                elif mode.name == 'fd':
                    self.wfs = mode(par.stencils[0], diagksl, orthoksl,
                                    initksl, *args)
                else:
                    assert mode.name == 'pw'
                    self.wfs = mode(diagksl, orthoksl, initksl, *args)
            else:
                self.wfs = mode(self, *args)
        else:
            self.wfs.set_setups(setups)

        if not self.wfs.eigensolver:
            # Number of bands to converge:
            nbands_converge = cc['bands']
            if nbands_converge == 'all':
                nbands_converge = nbands
            elif nbands_converge != 'occupied':
                assert isinstance(nbands_converge, int)
                if nbands_converge < 0:
                    nbands_converge += nbands
            eigensolver = get_eigensolver(par.eigensolver, mode,
                                          par.convergence)
            eigensolver.nbands_converge = nbands_converge
            # XXX Eigensolver class doesn't define an nbands_converge property

            if isinstance(xc, SIC):
                eigensolver.blocksize = 1
            self.wfs.set_eigensolver(eigensolver)

        if self.density is None:
            gd = self.wfs.gd
            if par.stencils[1] != 9:
                # Construct grid descriptor for fine grids for densities
                # and potentials:
                finegd = gd.refine()
            else:
                # Special case (use only coarse grid):
                finegd = gd

            if realspace:
                self.density = RealSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear, par.stencils[1])
            else:
                self.density = pw.ReciprocalSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear)

        self.density.initialize(setups, self.timer, magmom_av, par.hund)
        self.density.set_mixer(par.mixer)

        if self.hamiltonian is None:
            gd, finegd = self.density.gd, self.density.finegd
            if realspace:
                self.hamiltonian = RealSpaceHamiltonian(
                    gd, finegd, nspins, setups, self.timer, xc, world,
                    self.wfs.kptband_comm, par.external, collinear,
                    par.poissonsolver, par.stencils[1])
            else:
                self.hamiltonian = pw.ReciprocalSpaceHamiltonian(
                    gd, finegd, self.density.pd2, self.density.pd3, nspins,
                    setups, self.timer, xc, world, self.wfs.kptband_comm,
                    par.external, collinear)

        xc.initialize(self.density, self.hamiltonian, self.wfs,
                      self.occupations)

        self.text()
        self.print_memory_estimate(self.txt, maxdepth=memory_estimate_depth)
        self.txt.flush()

        self.timer.print_info(self)

        if dry_run:
            self.dry_run()

        if realspace and \
                self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
            self.hamiltonian.poisson.set_density(self.density)
            self.hamiltonian.poisson.print_messages(self.text)
            self.txt.flush()

        self.initialized = True
        self._changed_keywords.clear()

    def dry_run(self):
        # Can be overridden like in gpaw.atom.atompaw
        self.print_cell_and_parameters()
        self.print_positions()
        self.txt.flush()
        raise SystemExit

    def linearize_to_xc(self, newxc):
        """Linearize Hamiltonian to difference XC functional.
        
        Used in real time TDDFT to perform calculations with various kernels.
        """
        if isinstance(newxc, str):
            newxc = XC(newxc)
        self.txt.write('Linearizing xc-hamiltonian to ' + str(newxc))
        newxc.initialize(self.density, self.hamiltonian, self.wfs,
                         self.occupations)
        self.hamiltonian.linearize_to_xc(newxc, self.density)

    def restore_state(self):
        """After restart, calculate fine density and poisson solution.

        These are not initialized by default.
        TODO: Is this really the most efficient way?
        """
        spos_ac = self.atoms.get_scaled_positions() % 1.0
        self.density.set_positions(spos_ac, self.wfs.rank_a)
        self.density.interpolate_pseudo_density()
        self.density.calculate_pseudo_charge()
        self.hamiltonian.set_positions(spos_ac, self.wfs.rank_a)
        self.hamiltonian.update(self.density)

    def attach(self, function, n=1, *args, **kwargs):
        """Register observer function.

        Call *function* using *args* and
        *kwargs* as arguments.
        
        If *n* is positive, then
        *function* will be called every *n* iterations + the
        final iteration if it would not be otherwise
        
        If *n* is negative, then *function* will only be
        called on iteration *abs(n)*.
        
        If *n* is 0, then *function* will only be called
        on convergence"""

        try:
            slf = function.im_self
        except AttributeError:
            pass
        else:
            if slf is self:
                # function is a bound method of self.  Store the name
                # of the method and avoid circular reference:
                function = function.im_func.func_name

        self.observers.append((function, n, args, kwargs))

    def call_observers(self, iter, final=False):
        """Call all registered callback functions."""
        for function, n, args, kwargs in self.observers:
            call = False
            # Call every n iterations, including the last
            if n > 0:
                if ((iter % n) == 0) != final:
                    call = True
            # Call only on iteration n
            elif n < 0 and not final:
                if iter == abs(n):
                    call = True
            # Call only on convergence
            elif n == 0 and final:
                call = True
            if call:
                if isinstance(function, str):
                    function = getattr(self, function)
                function(*args, **kwargs)

    def get_reference_energy(self):
        return self.wfs.setups.Eref * Hartree

    def write(self, filename, mode='', cmr_params={}, **kwargs):
        """Write state to file.

        use mode='all' to write the wave functions.  cmr_params is a
        dictionary that allows you to specify parameters for CMR
        (Computational Materials Repository).
        """

        self.timer.start('IO')
        gpaw.io.write(self, filename, mode, cmr_params=cmr_params, **kwargs)
        self.timer.stop('IO')

    def get_myu(self, k, s):
        """Return my u corresponding to a certain kpoint and spin - or None"""
        # very slow, but we are sure that we have it
        for u in range(len(self.wfs.kpt_u)):
            if self.wfs.kpt_u[u].k == k and self.wfs.kpt_u[u].s == s:
                return u
        return None

    def get_homo_lumo(self):
        """Return H**O and LUMO eigenvalues."""
        return self.occupations.get_homo_lumo(self.wfs) * Hartree

    def estimate_memory(self, mem):
        """Estimate memory use of this object."""
        for name, obj in [
            ('Density', self.density),
            ('Hamiltonian', self.hamiltonian),
            ('Wavefunctions', self.wfs),
        ]:
            obj.estimate_memory(mem.subnode(name))

    def print_memory_estimate(self, txt=None, maxdepth=-1):
        """Print estimated memory usage for PAW object and components.

        maxdepth is the maximum nesting level of displayed components.

        The PAW object must be initialize()'d, but needs not have large
        arrays allocated."""
        # NOTE.  This should work with --dry-run=N
        #
        # However, the initial overhead estimate is wrong if this method
        # is called within a real mpirun/gpaw-python context.
        if txt is None:
            txt = self.txt
        txt.write('Memory estimate\n')
        txt.write('---------------\n')

        mem_init = maxrss()  # initial overhead includes part of Hamiltonian!
        txt.write('Process memory now: %.2f MiB\n' % (mem_init / 1024.0**2))

        mem = MemNode('Calculator', 0)
        try:
            self.estimate_memory(mem)
        except AttributeError as m:
            txt.write('Attribute error: %r' % m)
            txt.write('Some object probably lacks estimate_memory() method')
            txt.write('Memory breakdown may be incomplete')
        mem.calculate_size()
        mem.write(txt, maxdepth=maxdepth)

    def converge_wave_functions(self):
        """Converge the wave-functions if not present."""

        if not self.wfs or not self.scf:
            self.initialize()
        else:
            self.wfs.initialize_wave_functions_from_restart_file()
            spos_ac = self.atoms.get_scaled_positions() % 1.0
            self.wfs.set_positions(spos_ac)

        no_wave_functions = (self.wfs.kpt_u[0].psit_nG is None)
        converged = self.scf.check_convergence(self.density,
                                               self.wfs.eigensolver, self.wfs,
                                               self.hamiltonian, self.forces)
        if no_wave_functions or not converged:
            self.wfs.eigensolver.error = np.inf
            self.scf.converged = False

            # is the density ok ?
            error = self.density.mixer.get_charge_sloshing()
            criterion = (self.input_parameters['convergence']['density'] *
                         self.wfs.nvalence)
            if error < criterion and not self.hamiltonian.xc.orbital_dependent:
                self.scf.fix_density()

            self.calculate()

    def diagonalize_full_hamiltonian(self,
                                     nbands=None,
                                     scalapack=None,
                                     expert=False):
        self.wfs.diagonalize_full_hamiltonian(self.hamiltonian, self.atoms,
                                              self.occupations, self.txt,
                                              nbands, scalapack, expert)

    def check_atoms(self):
        """Check that atoms objects are identical on all processors."""
        if not mpi.compare_atoms(self.atoms, comm=self.wfs.world):
            raise RuntimeError('Atoms objects on different processors ' +
                               'are not identical!')
Esempio n. 13
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    def initialize(self, atoms=None):
        """Inexpensive initialization."""

        if atoms is None:
            atoms = self.atoms
        else:
            # Save the state of the atoms:
            self.atoms = atoms.copy()

        par = self.input_parameters

        world = par.communicator
        if world is None:
            world = mpi.world
        elif hasattr(world, 'new_communicator'):
            # Check for whether object has correct type already
            #
            # Using isinstance() is complicated because of all the
            # combinations, serial/parallel/debug...
            pass
        else:
            # world should be a list of ranks:
            world = mpi.world.new_communicator(np.asarray(world))
        self.wfs.world = world

        if 'txt' in self._changed_keywords:
            self.set_txt(par.txt)
        self.verbose = par.verbose

        natoms = len(atoms)

        cell_cv = atoms.get_cell() / Bohr
        pbc_c = atoms.get_pbc()
        Z_a = atoms.get_atomic_numbers()
        magmom_av = atoms.get_initial_magnetic_moments()

        self.check_atoms()

        # Generate new xc functional only when it is reset by set
        # XXX sounds like this should use the _changed_keywords dictionary.
        if self.hamiltonian is None or self.hamiltonian.xc is None:
            if isinstance(par.xc, str):
                xc = XC(par.xc)
            else:
                xc = par.xc
        else:
            xc = self.hamiltonian.xc

        mode = par.mode

        if mode == 'fd':
            mode = FD()
        elif mode == 'pw':
            mode = pw.PW()
        elif mode == 'lcao':
            mode = LCAO()
        else:
            assert hasattr(mode, 'name'), str(mode)

        if xc.orbital_dependent and mode.name == 'lcao':
            raise NotImplementedError('LCAO mode does not support '
                                      'orbital-dependent XC functionals.')

        if par.realspace is None:
            realspace = (mode.name != 'pw')
        else:
            realspace = par.realspace
            if mode.name == 'pw':
                assert not realspace

        if par.filter is None and mode.name != 'pw':
            gamma = 1.6
            if par.gpts is not None:
                h = ((np.linalg.inv(cell_cv)**2).sum(0)**-0.5 / par.gpts).max()
            else:
                h = (par.h or 0.2) / Bohr

            def filter(rgd, rcut, f_r, l=0):
                gcut = np.pi / h - 2 / rcut / gamma
                f_r[:] = rgd.filter(f_r, rcut * gamma, gcut, l)
        else:
            filter = par.filter

        setups = Setups(Z_a, par.setups, par.basis, par.lmax, xc, filter,
                        world)

        if magmom_av.ndim == 1:
            collinear = True
            magmom_av, magmom_a = np.zeros((natoms, 3)), magmom_av
            magmom_av[:, 2] = magmom_a
        else:
            collinear = False

        magnetic = magmom_av.any()

        spinpol = par.spinpol
        if par.hund:
            if natoms != 1:
                raise ValueError('hund=True arg only valid for single atoms!')
            spinpol = True
            magmom_av[0] = (0, 0, setups[0].get_hunds_rule_moment(par.charge))

        if spinpol is None:
            spinpol = magnetic
        elif magnetic and not spinpol:
            raise ValueError('Non-zero initial magnetic moment for a ' +
                             'spin-paired calculation!')

        if collinear:
            nspins = 1 + int(spinpol)
            ncomp = 1
        else:
            nspins = 1
            ncomp = 2

        if par.usesymm != 'default':
            warnings.warn('Use "symmetry" keyword instead of ' +
                          '"usesymm" keyword')
            par.symmetry = usesymm2symmetry(par.usesymm)

        symm = par.symmetry
        if symm == 'off':
            symm = {'point_group': False, 'time_reversal': False}

        bzkpts_kc = kpts2ndarray(par.kpts, self.atoms)
        kd = KPointDescriptor(bzkpts_kc, nspins, collinear)
        m_av = magmom_av.round(decimals=3)  # round off
        id_a = zip(setups.id_a, *m_av.T)
        symmetry = Symmetry(id_a, cell_cv, atoms.pbc, **symm)
        kd.set_symmetry(atoms, symmetry, comm=world)
        setups.set_symmetry(symmetry)

        if par.gpts is not None:
            N_c = np.array(par.gpts)
        else:
            h = par.h
            if h is not None:
                h /= Bohr
            N_c = get_number_of_grid_points(cell_cv, h, mode, realspace,
                                            kd.symmetry)

        symmetry.check_grid(N_c)

        width = par.width
        if width is None:
            if pbc_c.any():
                width = 0.1  # eV
            else:
                width = 0.0
        else:
            assert par.occupations is None

        if hasattr(self, 'time') or par.dtype == complex:
            dtype = complex
        else:
            if kd.gamma:
                dtype = float
            else:
                dtype = complex

        nao = setups.nao
        nvalence = setups.nvalence - par.charge
        M_v = magmom_av.sum(0)
        M = np.dot(M_v, M_v)**0.5

        nbands = par.nbands

        orbital_free = any(setup.orbital_free for setup in setups)
        if orbital_free:
            nbands = 1

        if isinstance(nbands, basestring):
            if nbands[-1] == '%':
                basebands = int(nvalence + M + 0.5) // 2
                nbands = int((float(nbands[:-1]) / 100) * basebands)
            else:
                raise ValueError('Integer Expected: Only use a string '
                                 'if giving a percentage of occupied bands')

        if nbands is None:
            nbands = 0
            for setup in setups:
                nbands_from_atom = setup.get_default_nbands()

                # Any obscure setup errors?
                if nbands_from_atom < -(-setup.Nv // 2):
                    raise ValueError('Bad setup: This setup requests %d'
                                     ' bands but has %d electrons.' %
                                     (nbands_from_atom, setup.Nv))
                nbands += nbands_from_atom
            nbands = min(nao, nbands)
        elif nbands > nao and mode.name == 'lcao':
            raise ValueError('Too many bands for LCAO calculation: '
                             '%d bands and only %d atomic orbitals!' %
                             (nbands, nao))

        if nvalence < 0:
            raise ValueError(
                'Charge %f is not possible - not enough valence electrons' %
                par.charge)

        if nbands <= 0:
            nbands = int(nvalence + M + 0.5) // 2 + (-nbands)

        if nvalence > 2 * nbands and not orbital_free:
            raise ValueError('Too few bands!  Electrons: %f, bands: %d' %
                             (nvalence, nbands))

        nbands *= ncomp

        if par.width is not None:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width).')
        if par.fixmom:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width, fixmagmom=True).')

        if self.occupations is None:
            if par.occupations is None:
                # Create object for occupation numbers:
                if orbital_free:
                    width = 0.0  # even for PBC
                    self.occupations = occupations.TFOccupations(
                        width, par.fixmom)
                else:
                    self.occupations = occupations.FermiDirac(
                        width, par.fixmom)
            else:
                self.occupations = par.occupations

            # If occupation numbers are changed, and we have wave functions,
            # recalculate the occupation numbers
            if self.wfs is not None and not isinstance(self.wfs,
                                                       EmptyWaveFunctions):
                self.occupations.calculate(self.wfs)

        self.occupations.magmom = M_v[2]

        cc = par.convergence

        if mode.name == 'lcao':
            niter_fixdensity = 0
        else:
            niter_fixdensity = None

        if self.scf is None:
            force_crit = cc['forces']
            if force_crit is not None:
                force_crit /= Hartree / Bohr
            self.scf = SCFLoop(cc['eigenstates'] / Hartree**2 * nvalence,
                               cc['energy'] / Hartree * max(nvalence, 1),
                               cc['density'] * nvalence, par.maxiter,
                               par.fixdensity, niter_fixdensity, force_crit)

        parsize_kpt = par.parallel['kpt']
        parsize_domain = par.parallel['domain']
        parsize_bands = par.parallel['band']

        if not realspace:
            pbc_c = np.ones(3, bool)

        if not self.wfs:
            if parsize_domain == 'domain only':  # XXX this was silly!
                parsize_domain = world.size

            parallelization = mpi.Parallelization(world, nspins * kd.nibzkpts)
            ndomains = None
            if parsize_domain is not None:
                ndomains = np.prod(parsize_domain)
            if mode.name == 'pw':
                if ndomains > 1:
                    raise ValueError('Planewave mode does not support '
                                     'domain decomposition.')
                ndomains = 1
            parallelization.set(kpt=parsize_kpt,
                                domain=ndomains,
                                band=parsize_bands)
            comms = parallelization.build_communicators()
            domain_comm = comms['d']
            kpt_comm = comms['k']
            band_comm = comms['b']
            kptband_comm = comms['D']
            domainband_comm = comms['K']

            self.comms = comms
            kd.set_communicator(kpt_comm)

            parstride_bands = par.parallel['stridebands']

            # Unfortunately we need to remember that we adjusted the
            # number of bands so we can print a warning if it differs
            # from the number specified by the user.  (The number can
            # be inferred from the input parameters, but it's tricky
            # because we allow negative numbers)
            self.nbands_parallelization_adjustment = -nbands % band_comm.size
            nbands += self.nbands_parallelization_adjustment

            # I would like to give the following error message, but apparently
            # there are cases, e.g. gpaw/test/gw_ppa.py, which involve
            # nbands > nao and are supposed to work that way.
            #if nbands > nao:
            #    raise ValueError('Number of bands %d adjusted for band '
            #                     'parallelization %d exceeds number of atomic '
            #                     'orbitals %d.  This problem can be fixed '
            #                     'by reducing the number of bands a bit.'
            #                     % (nbands, band_comm.size, nao))
            bd = BandDescriptor(nbands, band_comm, parstride_bands)

            if (self.density is not None
                    and self.density.gd.comm.size != domain_comm.size):
                # Domain decomposition has changed, so we need to
                # reinitialize density and hamiltonian:
                if par.fixdensity:
                    raise RuntimeError(
                        'Density reinitialization conflict ' +
                        'with "fixdensity" - specify domain decomposition.')
                self.density = None
                self.hamiltonian = None

            # Construct grid descriptor for coarse grids for wave functions:
            gd = self.grid_descriptor_class(N_c, cell_cv, pbc_c, domain_comm,
                                            parsize_domain)

            # do k-point analysis here? XXX
            args = (gd, nvalence, setups, bd, dtype, world, kd, kptband_comm,
                    self.timer)

            if par.parallel['sl_auto']:
                # Choose scalapack parallelization automatically

                for key, val in par.parallel.items():
                    if (key.startswith('sl_') and key != 'sl_auto'
                            and val is not None):
                        raise ValueError("Cannot use 'sl_auto' together "
                                         "with '%s'" % key)
                max_scalapack_cpus = bd.comm.size * gd.comm.size
                nprow = max_scalapack_cpus
                npcol = 1

                # Get a sort of reasonable number of columns/rows
                while npcol < nprow and nprow % 2 == 0:
                    npcol *= 2
                    nprow //= 2
                assert npcol * nprow == max_scalapack_cpus

                # ScaLAPACK creates trouble if there aren't at least a few
                # whole blocks; choose block size so there will always be
                # several blocks.  This will crash for small test systems,
                # but so will ScaLAPACK in any case
                blocksize = min(-(-nbands // 4), 64)
                sl_default = (nprow, npcol, blocksize)
            else:
                sl_default = par.parallel['sl_default']

            if mode.name == 'lcao':
                # Layouts used for general diagonalizer
                sl_lcao = par.parallel['sl_lcao']
                if sl_lcao is None:
                    sl_lcao = sl_default
                lcaoksl = get_KohnSham_layouts(sl_lcao,
                                               'lcao',
                                               gd,
                                               bd,
                                               domainband_comm,
                                               dtype,
                                               nao=nao,
                                               timer=self.timer)

                self.wfs = mode(collinear, lcaoksl, *args)

            elif mode.name == 'fd' or mode.name == 'pw':
                # buffer_size keyword only relevant for fdpw
                buffer_size = par.parallel['buffer_size']
                # Layouts used for diagonalizer
                sl_diagonalize = par.parallel['sl_diagonalize']
                if sl_diagonalize is None:
                    sl_diagonalize = sl_default
                diagksl = get_KohnSham_layouts(
                    sl_diagonalize,
                    'fd',  # XXX
                    # choice of key 'fd' not so nice
                    gd,
                    bd,
                    domainband_comm,
                    dtype,
                    buffer_size=buffer_size,
                    timer=self.timer)

                # Layouts used for orthonormalizer
                sl_inverse_cholesky = par.parallel['sl_inverse_cholesky']
                if sl_inverse_cholesky is None:
                    sl_inverse_cholesky = sl_default
                if sl_inverse_cholesky != sl_diagonalize:
                    message = 'sl_inverse_cholesky != sl_diagonalize ' \
                        'is not implemented.'
                    raise NotImplementedError(message)
                orthoksl = get_KohnSham_layouts(sl_inverse_cholesky,
                                                'fd',
                                                gd,
                                                bd,
                                                domainband_comm,
                                                dtype,
                                                buffer_size=buffer_size,
                                                timer=self.timer)

                # Use (at most) all available LCAO for initialization
                lcaonbands = min(nbands, nao)

                try:
                    lcaobd = BandDescriptor(lcaonbands, band_comm,
                                            parstride_bands)
                except RuntimeError:
                    initksl = None
                else:
                    # Layouts used for general diagonalizer
                    # (LCAO initialization)
                    sl_lcao = par.parallel['sl_lcao']
                    if sl_lcao is None:
                        sl_lcao = sl_default
                    initksl = get_KohnSham_layouts(sl_lcao,
                                                   'lcao',
                                                   gd,
                                                   lcaobd,
                                                   domainband_comm,
                                                   dtype,
                                                   nao=nao,
                                                   timer=self.timer)

                if hasattr(self, 'time'):
                    assert mode.name == 'fd'
                    from gpaw.tddft import TimeDependentWaveFunctions
                    self.wfs = TimeDependentWaveFunctions(
                        par.stencils[0], diagksl, orthoksl, initksl, gd,
                        nvalence, setups, bd, world, kd, kptband_comm,
                        self.timer)
                elif mode.name == 'fd':
                    self.wfs = mode(par.stencils[0], diagksl, orthoksl,
                                    initksl, *args)
                else:
                    assert mode.name == 'pw'
                    self.wfs = mode(diagksl, orthoksl, initksl, *args)
            else:
                self.wfs = mode(self, *args)
        else:
            self.wfs.set_setups(setups)

        if not self.wfs.eigensolver:
            # Number of bands to converge:
            nbands_converge = cc['bands']
            if nbands_converge == 'all':
                nbands_converge = nbands
            elif nbands_converge != 'occupied':
                assert isinstance(nbands_converge, int)
                if nbands_converge < 0:
                    nbands_converge += nbands
            eigensolver = get_eigensolver(par.eigensolver, mode,
                                          par.convergence)
            eigensolver.nbands_converge = nbands_converge
            # XXX Eigensolver class doesn't define an nbands_converge property

            if isinstance(xc, SIC):
                eigensolver.blocksize = 1
            self.wfs.set_eigensolver(eigensolver)

        if self.density is None:
            gd = self.wfs.gd
            if par.stencils[1] != 9:
                # Construct grid descriptor for fine grids for densities
                # and potentials:
                finegd = gd.refine()
            else:
                # Special case (use only coarse grid):
                finegd = gd

            if realspace:
                self.density = RealSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear, par.stencils[1])
            else:
                self.density = pw.ReciprocalSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear)

        self.density.initialize(setups, self.timer, magmom_av, par.hund)
        self.density.set_mixer(par.mixer)

        if self.hamiltonian is None:
            gd, finegd = self.density.gd, self.density.finegd
            if realspace:
                self.hamiltonian = RealSpaceHamiltonian(
                    gd, finegd, nspins, setups, self.timer, xc, world,
                    self.wfs.kptband_comm, par.external, collinear,
                    par.poissonsolver, par.stencils[1])
            else:
                self.hamiltonian = pw.ReciprocalSpaceHamiltonian(
                    gd, finegd, self.density.pd2, self.density.pd3, nspins,
                    setups, self.timer, xc, world, self.wfs.kptband_comm,
                    par.external, collinear)

        xc.initialize(self.density, self.hamiltonian, self.wfs,
                      self.occupations)

        self.text()
        self.print_memory_estimate(self.txt, maxdepth=memory_estimate_depth)
        self.txt.flush()

        self.timer.print_info(self)

        if dry_run:
            self.dry_run()

        if realspace and \
                self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
            self.hamiltonian.poisson.set_density(self.density)
            self.hamiltonian.poisson.print_messages(self.text)
            self.txt.flush()

        self.initialized = True
        self._changed_keywords.clear()
Esempio n. 14
0
    def __init__(self,
                 cavity,
                 dielectric,
                 interactions,
                 gd,
                 finegd,
                 nspins,
                 setups,
                 timer,
                 xc,
                 world,
                 redistributor,
                 vext=None,
                 psolver=None,
                 stencil=3,
                 collinear=None):
        """Constructor of SJM_RealSpaceHamiltonian class.


        Notes
        -----
        The only difference to SolvationRealSpaceHamiltonian is the
        possibility to perform a dipole correction

        """

        self.cavity = cavity
        self.dielectric = dielectric
        self.interactions = interactions
        cavity.set_grid_descriptor(finegd)
        dielectric.set_grid_descriptor(finegd)
        for ia in interactions:
            ia.set_grid_descriptor(finegd)

        if psolver is None:
            psolver = WeightedFDPoissonSolver()
            self.dipcorr = False
        elif isinstance(psolver, dict):
            psolver = SJMDipoleCorrection(WeightedFDPoissonSolver(),
                                          psolver['dipolelayer'])
            self.dipcorr = True

        if self.dipcorr:
            psolver.poissonsolver.set_dielectric(self.dielectric)
        else:
            psolver.set_dielectric(self.dielectric)

        self.gradient = None

        RealSpaceHamiltonian.__init__(self,
                                      gd,
                                      finegd,
                                      nspins,
                                      collinear,
                                      setups,
                                      timer,
                                      xc,
                                      world,
                                      vext=vext,
                                      psolver=psolver,
                                      stencil=stencil,
                                      redistributor=redistributor)

        for ia in interactions:
            setattr(self, 'e_' + ia.subscript, None)
        self.new_atoms = None
        self.vt_ia_g = None
        self.e_el_free = None
        self.e_el_extrapolated = None
Esempio n. 15
0
class PAW(PAWTextOutput):

    """This is the main calculation object for doing a PAW calculation."""

    def __init__(self, filename=None, timer=None,
                 read_projections=True, **kwargs):
        """ASE-calculator interface.

        The following parameters can be used: nbands, xc, kpts,
        spinpol, gpts, h, charge, symmetry, width, mixer,
        hund, lmax, fixdensity, convergence, txt, parallel,
        communicator, dtype, softgauss and stencils.

        If you don't specify any parameters, you will get:

        Defaults: neutrally charged, LDA, gamma-point calculation, a
        reasonable grid-spacing, zero Kelvin electronic temperature,
        and the number of bands will be equal to the number of atomic
        orbitals present in the setups. Only occupied bands are used
        in the convergence decision. The calculation will be
        spin-polarized if and only if one or more of the atoms have
        non-zero magnetic moments. Text output will be written to
        standard output.

        For a non-gamma point calculation, the electronic temperature
        will be 0.1 eV (energies are extrapolated to zero Kelvin) and
        all symmetries will be used to reduce the number of
        **k**-points."""

        PAWTextOutput.__init__(self)
        self.grid_descriptor_class = GridDescriptor
        self.input_parameters = InputParameters()

        if timer is None:
            self.timer = Timer()
        else:
            self.timer = timer

        self.scf = None
        self.forces = ForceCalculator(self.timer)
        self.stress_vv = None
        self.dipole_v = None
        self.magmom_av = None
        self.wfs = EmptyWaveFunctions()
        self.occupations = None
        self.density = None
        self.hamiltonian = None
        self.atoms = None
        self.iter = 0

        self.initialized = False
        self.nbands_parallelization_adjustment = None  # Somehow avoid this?

        # Possibly read GPAW keyword arguments from file:
        if filename is not None and filename.endswith('.gkw'):
            from gpaw.utilities.kwargs import load
            parameters = load(filename)
            parameters.update(kwargs)
            kwargs = parameters
            filename = None  # XXX

        if filename is not None:
            comm = kwargs.get('communicator', mpi.world)
            reader = gpaw.io.open(filename, 'r', comm)
            self.atoms = gpaw.io.read_atoms(reader)
            par = self.input_parameters
            par.read(reader)

        # _changed_keywords contains those keywords that have been
        # changed by set() since last time initialize() was called.
        self._changed_keywords = set()
        self.set(**kwargs)
        # Here in the beginning, effectively every keyword has been changed.
        self._changed_keywords.update(self.input_parameters)

        if filename is not None:
            # Setups are not saved in the file if the setups were not loaded
            # *from* files in the first place
            if par.setups is None:
                if par.idiotproof:
                    raise RuntimeError('Setups not specified in file. Use '
                                       'idiotproof=False to proceed anyway.')
                else:
                    par.setups = {None: 'paw'}
            if par.basis is None:
                if par.idiotproof:
                    raise RuntimeError('Basis not specified in file. Use '
                                       'idiotproof=False to proceed anyway.')
                else:
                    par.basis = {}

            self.initialize()
            self.read(reader, read_projections)
            if self.hamiltonian.xc.type == 'GLLB':
                self.occupations.calculate(self.wfs)

            self.print_cell_and_parameters()

        self.observers = []

    def read(self, reader, read_projections=True):
        gpaw.io.read(self, reader, read_projections)

    def set(self, **kwargs):
        """Change parameters for calculator.

        Examples::

            calc.set(xc='PBE')
            calc.set(nbands=20, kpts=(4, 1, 1))
        """
        p = self.input_parameters
        self._changed_keywords.update(kwargs)

        if (kwargs.get('h') is not None) and (kwargs.get('gpts') is not None):
            raise TypeError("""You can't use both "gpts" and "h"!""")
        if 'h' in kwargs:
            p['gpts'] = None
        if 'gpts' in kwargs:
            p['h'] = None

        # Special treatment for dictionary parameters:
        for name in ['convergence', 'parallel']:
            if kwargs.get(name) is not None:
                tmp = p[name]
                for key in kwargs[name]:
                    if key not in tmp:
                        raise KeyError('Unknown subparameter "%s" in '
                                       'dictionary parameter "%s"' % (key,
                                                                      name))
                tmp.update(kwargs[name])
                kwargs[name] = tmp

        self.initialized = False

        for key in kwargs:
            if key == 'basis' and str(p['mode']) == 'fd':  # umm what about PW?
                # The second criterion seems buggy, will not touch it.  -Ask
                continue

            if key == 'eigensolver':
                self.wfs.set_eigensolver(None)

            if key in ['fixmom', 'mixer',
                       'verbose', 'txt', 'hund', 'random',
                       'eigensolver', 'idiotproof', 'notify']:
                continue

            if key in ['convergence', 'fixdensity', 'maxiter']:
                self.scf = None
                continue

            # More drastic changes:
            self.scf = None
            self.wfs.set_orthonormalized(False)
            if key in ['lmax', 'width', 'stencils', 'external', 'xc',
                       'poissonsolver']:
                self.hamiltonian = None
                self.occupations = None
            elif key in ['occupations']:
                self.occupations = None
            elif key in ['charge']:
                self.hamiltonian = None
                self.density = None
                self.wfs = EmptyWaveFunctions()
                self.occupations = None
            elif key in ['kpts', 'nbands', 'usesymm', 'symmetry']:
                self.wfs = EmptyWaveFunctions()
                self.occupations = None
            elif key in ['h', 'gpts', 'setups', 'spinpol', 'realspace',
                         'parallel', 'communicator', 'dtype', 'mode']:
                self.density = None
                self.occupations = None
                self.hamiltonian = None
                self.wfs = EmptyWaveFunctions()
            elif key in ['basis']:
                self.wfs = EmptyWaveFunctions()
            elif key in ['parsize', 'parsize_bands', 'parstride_bands']:
                name = {'parsize': 'domain',
                        'parsize_bands': 'band',
                        'parstride_bands': 'stridebands'}[key]
                raise DeprecationWarning(
                    'Keyword argument has been moved ' +
                    "to the 'parallel' dictionary keyword under '%s'." % name)
            else:
                raise TypeError("Unknown keyword argument: '%s'" % key)

        p.update(kwargs)

    def calculate(self, atoms=None, converge=False,
                  force_call_to_set_positions=False):
        """Update PAW calculaton if needed.

        Returns True/False whether a calculation was performed or not."""

        self.timer.start('Initialization')
        if atoms is None:
            atoms = self.atoms

        if self.atoms is None:
            # First time:
            self.initialize(atoms)
            self.set_positions(atoms)
        elif (len(atoms) != len(self.atoms) or
              (atoms.get_atomic_numbers() !=
               self.atoms.get_atomic_numbers()).any() or
              (atoms.get_initial_magnetic_moments() !=
               self.atoms.get_initial_magnetic_moments()).any() or
              (atoms.get_cell() != self.atoms.get_cell()).any() or
              (atoms.get_pbc() != self.atoms.get_pbc()).any()):
            # Drastic changes:
            self.wfs = EmptyWaveFunctions()
            self.occupations = None
            self.density = None
            self.hamiltonian = None
            self.scf = None
            self.initialize(atoms)
            self.set_positions(atoms)
        elif not self.initialized:
            self.initialize(atoms)
            self.set_positions(atoms)
        elif (atoms.get_positions() != self.atoms.get_positions()).any():
            self.density.reset()
            self.set_positions(atoms)
        elif not self.scf.converged:
            # Do not call scf.check_convergence() here as it overwrites
            # scf.converged, and setting scf.converged is the only
            # 'practical' way for a user to force the calculation to proceed
            self.set_positions(atoms)
        elif force_call_to_set_positions:
            self.set_positions(atoms)

        self.timer.stop('Initialization')

        if self.scf.converged:
            return False
        else:
            self.print_cell_and_parameters()

        self.timer.start('SCF-cycle')
        for iter in self.scf.run(self.wfs, self.hamiltonian, self.density,
                                 self.occupations, self.forces):
            self.iter = iter
            self.call_observers(iter)
            self.print_iteration(iter)
        self.timer.stop('SCF-cycle')

        if self.scf.converged:
            self.call_observers(iter, final=True)
            self.print_converged(iter)
        elif converge:
            self.txt.write(oops)
            raise KohnShamConvergenceError(
                'Did not converge!  See text output for help.')

        return True

    def initialize_positions(self, atoms=None):
        """Update the positions of the atoms."""
        if atoms is None:
            atoms = self.atoms
        else:
            # Save the state of the atoms:
            self.atoms = atoms.copy()

        self.check_atoms()

        spos_ac = atoms.get_scaled_positions() % 1.0

        self.wfs.set_positions(spos_ac)
        self.density.set_positions(spos_ac, self.wfs.rank_a)
        self.hamiltonian.set_positions(spos_ac, self.wfs.rank_a)

        return spos_ac

    def set_positions(self, atoms=None):
        """Update the positions of the atoms and initialize wave functions."""
        spos_ac = self.initialize_positions(atoms)
        self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
        self.wfs.eigensolver.reset()
        self.scf.reset()
        self.forces.reset()
        self.stress_vv = None
        self.dipole_v = None
        self.magmom_av = None
        self.print_positions()

    def initialize(self, atoms=None):
        """Inexpensive initialization."""

        if atoms is None:
            atoms = self.atoms
        else:
            # Save the state of the atoms:
            self.atoms = atoms.copy()

        par = self.input_parameters

        world = par.communicator
        if world is None:
            world = mpi.world
        elif hasattr(world, 'new_communicator'):
            # Check for whether object has correct type already
            #
            # Using isinstance() is complicated because of all the
            # combinations, serial/parallel/debug...
            pass
        else:
            # world should be a list of ranks:
            world = mpi.world.new_communicator(np.asarray(world))
        self.wfs.world = world

        if 'txt' in self._changed_keywords:
            self.set_txt(par.txt)
        self.verbose = par.verbose

        natoms = len(atoms)

        cell_cv = atoms.get_cell() / Bohr
        pbc_c = atoms.get_pbc()
        Z_a = atoms.get_atomic_numbers()
        magmom_av = atoms.get_initial_magnetic_moments()

        self.check_atoms()

        # Generate new xc functional only when it is reset by set
        # XXX sounds like this should use the _changed_keywords dictionary.
        if self.hamiltonian is None or self.hamiltonian.xc is None:
            if isinstance(par.xc, str):
                xc = XC(par.xc)
            else:
                xc = par.xc
        else:
            xc = self.hamiltonian.xc

        mode = par.mode

        if mode == 'fd':
            mode = FD()
        elif mode == 'pw':
            mode = pw.PW()
        elif mode == 'lcao':
            mode = LCAO()
        else:
            assert hasattr(mode, 'name'), str(mode)

        if xc.orbital_dependent and mode.name == 'lcao':
            raise NotImplementedError('LCAO mode does not support '
                                      'orbital-dependent XC functionals.')

        if par.realspace is None:
            realspace = (mode.name != 'pw')
        else:
            realspace = par.realspace
            if mode.name == 'pw':
                assert not realspace

        if par.filter is None and mode.name != 'pw':
            gamma = 1.6
            if par.gpts is not None:
                h = ((np.linalg.inv(cell_cv)**2).sum(0)**-0.5
                     / par.gpts).max()
            else:
                h = (par.h or 0.2) / Bohr

            def filter(rgd, rcut, f_r, l=0):
                gcut = np.pi / h - 2 / rcut / gamma
                f_r[:] = rgd.filter(f_r, rcut * gamma, gcut, l)
        else:
            filter = par.filter

        setups = Setups(Z_a, par.setups, par.basis, par.lmax, xc,
                        filter, world)

        if magmom_av.ndim == 1:
            collinear = True
            magmom_av, magmom_a = np.zeros((natoms, 3)), magmom_av
            magmom_av[:, 2] = magmom_a
        else:
            collinear = False

        magnetic = magmom_av.any()

        spinpol = par.spinpol
        if par.hund:
            if natoms != 1:
                raise ValueError('hund=True arg only valid for single atoms!')
            spinpol = True
            magmom_av[0] = (0, 0, setups[0].get_hunds_rule_moment(par.charge))

        if spinpol is None:
            spinpol = magnetic
        elif magnetic and not spinpol:
            raise ValueError('Non-zero initial magnetic moment for a ' +
                             'spin-paired calculation!')

        if collinear:
            nspins = 1 + int(spinpol)
            ncomp = 1
        else:
            nspins = 1
            ncomp = 2

        if par.usesymm != 'default':
            warnings.warn('Use "symmetry" keyword instead of ' +
                          '"usesymm" keyword')
            par.symmetry = usesymm2symmetry(par.usesymm)

        symm = par.symmetry
        if symm == 'off':
            symm = {'point_group': False, 'time_reversal': False}

        bzkpts_kc = kpts2ndarray(par.kpts, self.atoms)
        kd = KPointDescriptor(bzkpts_kc, nspins, collinear)
        m_av = magmom_av.round(decimals=3)  # round off
        id_a = zip(setups.id_a, *m_av.T)
        symmetry = Symmetry(id_a, cell_cv, atoms.pbc, **symm)
        kd.set_symmetry(atoms, symmetry, comm=world)
        setups.set_symmetry(symmetry)

        if par.gpts is not None:
            N_c = np.array(par.gpts)
        else:
            h = par.h
            if h is not None:
                h /= Bohr
            N_c = get_number_of_grid_points(cell_cv, h, mode, realspace,
                                            kd.symmetry)

        symmetry.check_grid(N_c)

        width = par.width
        if width is None:
            if pbc_c.any():
                width = 0.1  # eV
            else:
                width = 0.0
        else:
            assert par.occupations is None

        if hasattr(self, 'time') or par.dtype == complex:
            dtype = complex
        else:
            if kd.gamma:
                dtype = float
            else:
                dtype = complex

        nao = setups.nao
        nvalence = setups.nvalence - par.charge
        M_v = magmom_av.sum(0)
        M = np.dot(M_v, M_v) ** 0.5

        nbands = par.nbands
        
        orbital_free = any(setup.orbital_free for setup in setups)
        if orbital_free:
            nbands = 1

        if isinstance(nbands, basestring):
            if nbands[-1] == '%':
                basebands = int(nvalence + M + 0.5) // 2
                nbands = int((float(nbands[:-1]) / 100) * basebands)
            else:
                raise ValueError('Integer Expected: Only use a string '
                                 'if giving a percentage of occupied bands')

        if nbands is None:
            nbands = 0
            for setup in setups:
                nbands_from_atom = setup.get_default_nbands()

                # Any obscure setup errors?
                if nbands_from_atom < -(-setup.Nv // 2):
                    raise ValueError('Bad setup: This setup requests %d'
                                     ' bands but has %d electrons.'
                                     % (nbands_from_atom, setup.Nv))
                nbands += nbands_from_atom
            nbands = min(nao, nbands)
        elif nbands > nao and mode.name == 'lcao':
            raise ValueError('Too many bands for LCAO calculation: '
                             '%d bands and only %d atomic orbitals!' %
                             (nbands, nao))

        if nvalence < 0:
            raise ValueError(
                'Charge %f is not possible - not enough valence electrons' %
                par.charge)

        if nbands <= 0:
            nbands = int(nvalence + M + 0.5) // 2 + (-nbands)

        if nvalence > 2 * nbands and not orbital_free:
            raise ValueError('Too few bands!  Electrons: %f, bands: %d'
                             % (nvalence, nbands))

        nbands *= ncomp

        if par.width is not None:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width).')
        if par.fixmom:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width, fixmagmom=True).')

        if self.occupations is None:
            if par.occupations is None:
                # Create object for occupation numbers:
                if orbital_free:
                    width = 0.0  # even for PBC
                    self.occupations = occupations.TFOccupations(width,
                                                                 par.fixmom)
                else:
                    self.occupations = occupations.FermiDirac(width,
                                                              par.fixmom)
            else:
                self.occupations = par.occupations

            # If occupation numbers are changed, and we have wave functions,
            # recalculate the occupation numbers
            if self.wfs is not None and not isinstance(
                    self.wfs,
                    EmptyWaveFunctions):
                self.occupations.calculate(self.wfs)

        self.occupations.magmom = M_v[2]

        cc = par.convergence

        if mode.name == 'lcao':
            niter_fixdensity = 0
        else:
            niter_fixdensity = None

        if self.scf is None:
            force_crit = cc['forces']
            if force_crit is not None:
                force_crit /= Hartree / Bohr
            self.scf = SCFLoop(
                cc['eigenstates'] / Hartree**2 * nvalence,
                cc['energy'] / Hartree * max(nvalence, 1),
                cc['density'] * nvalence,
                par.maxiter, par.fixdensity,
                niter_fixdensity,
                force_crit)

        parsize_kpt = par.parallel['kpt']
        parsize_domain = par.parallel['domain']
        parsize_bands = par.parallel['band']

        if not realspace:
            pbc_c = np.ones(3, bool)

        if not self.wfs:
            if parsize_domain == 'domain only':  # XXX this was silly!
                parsize_domain = world.size

            parallelization = mpi.Parallelization(world,
                                                  nspins * kd.nibzkpts)
            ndomains = None
            if parsize_domain is not None:
                ndomains = np.prod(parsize_domain)
            if mode.name == 'pw':
                if ndomains > 1:
                    raise ValueError('Planewave mode does not support '
                                     'domain decomposition.')
                ndomains = 1
            parallelization.set(kpt=parsize_kpt,
                                domain=ndomains,
                                band=parsize_bands)
            comms = parallelization.build_communicators()
            domain_comm = comms['d']
            kpt_comm = comms['k']
            band_comm = comms['b']
            kptband_comm = comms['D']
            domainband_comm = comms['K']

            self.comms = comms
            kd.set_communicator(kpt_comm)

            parstride_bands = par.parallel['stridebands']

            # Unfortunately we need to remember that we adjusted the
            # number of bands so we can print a warning if it differs
            # from the number specified by the user.  (The number can
            # be inferred from the input parameters, but it's tricky
            # because we allow negative numbers)
            self.nbands_parallelization_adjustment = -nbands % band_comm.size
            nbands += self.nbands_parallelization_adjustment

            # I would like to give the following error message, but apparently
            # there are cases, e.g. gpaw/test/gw_ppa.py, which involve
            # nbands > nao and are supposed to work that way.
            #if nbands > nao:
            #    raise ValueError('Number of bands %d adjusted for band '
            #                     'parallelization %d exceeds number of atomic '
            #                     'orbitals %d.  This problem can be fixed '
            #                     'by reducing the number of bands a bit.'
            #                     % (nbands, band_comm.size, nao))
            bd = BandDescriptor(nbands, band_comm, parstride_bands)

            if (self.density is not None and
                    self.density.gd.comm.size != domain_comm.size):
                # Domain decomposition has changed, so we need to
                # reinitialize density and hamiltonian:
                if par.fixdensity:
                    raise RuntimeError(
                        'Density reinitialization conflict ' +
                        'with "fixdensity" - specify domain decomposition.')
                self.density = None
                self.hamiltonian = None

            # Construct grid descriptor for coarse grids for wave functions:
            gd = self.grid_descriptor_class(N_c, cell_cv, pbc_c,
                                            domain_comm, parsize_domain)

            # do k-point analysis here? XXX
            args = (gd, nvalence, setups, bd, dtype, world, kd,
                    kptband_comm, self.timer)

            if par.parallel['sl_auto']:
                # Choose scalapack parallelization automatically

                for key, val in par.parallel.items():
                    if (key.startswith('sl_') and key != 'sl_auto'
                            and val is not None):
                        raise ValueError("Cannot use 'sl_auto' together "
                                         "with '%s'" % key)
                max_scalapack_cpus = bd.comm.size * gd.comm.size
                nprow = max_scalapack_cpus
                npcol = 1

                # Get a sort of reasonable number of columns/rows
                while npcol < nprow and nprow % 2 == 0:
                    npcol *= 2
                    nprow //= 2
                assert npcol * nprow == max_scalapack_cpus

                # ScaLAPACK creates trouble if there aren't at least a few
                # whole blocks; choose block size so there will always be
                # several blocks.  This will crash for small test systems,
                # but so will ScaLAPACK in any case
                blocksize = min(-(-nbands // 4), 64)
                sl_default = (nprow, npcol, blocksize)
            else:
                sl_default = par.parallel['sl_default']

            if mode.name == 'lcao':
                # Layouts used for general diagonalizer
                sl_lcao = par.parallel['sl_lcao']
                if sl_lcao is None:
                    sl_lcao = sl_default
                lcaoksl = get_KohnSham_layouts(sl_lcao, 'lcao',
                                               gd, bd, domainband_comm, dtype,
                                               nao=nao, timer=self.timer)

                self.wfs = mode(collinear, lcaoksl, *args)

            elif mode.name == 'fd' or mode.name == 'pw':
                # buffer_size keyword only relevant for fdpw
                buffer_size = par.parallel['buffer_size']
                # Layouts used for diagonalizer
                sl_diagonalize = par.parallel['sl_diagonalize']
                if sl_diagonalize is None:
                    sl_diagonalize = sl_default
                diagksl = get_KohnSham_layouts(sl_diagonalize, 'fd',  # XXX
                                               # choice of key 'fd' not so nice
                                               gd, bd, domainband_comm, dtype,
                                               buffer_size=buffer_size,
                                               timer=self.timer)

                # Layouts used for orthonormalizer
                sl_inverse_cholesky = par.parallel['sl_inverse_cholesky']
                if sl_inverse_cholesky is None:
                    sl_inverse_cholesky = sl_default
                if sl_inverse_cholesky != sl_diagonalize:
                    message = 'sl_inverse_cholesky != sl_diagonalize ' \
                        'is not implemented.'
                    raise NotImplementedError(message)
                orthoksl = get_KohnSham_layouts(sl_inverse_cholesky, 'fd',
                                                gd, bd, domainband_comm, dtype,
                                                buffer_size=buffer_size,
                                                timer=self.timer)

                # Use (at most) all available LCAO for initialization
                lcaonbands = min(nbands, nao)

                try:
                    lcaobd = BandDescriptor(lcaonbands, band_comm,
                                            parstride_bands)
                except RuntimeError:
                    initksl = None
                else:
                    # Layouts used for general diagonalizer
                    # (LCAO initialization)
                    sl_lcao = par.parallel['sl_lcao']
                    if sl_lcao is None:
                        sl_lcao = sl_default
                    initksl = get_KohnSham_layouts(sl_lcao, 'lcao',
                                                   gd, lcaobd, domainband_comm,
                                                   dtype, nao=nao,
                                                   timer=self.timer)

                if hasattr(self, 'time'):
                    assert mode.name == 'fd'
                    from gpaw.tddft import TimeDependentWaveFunctions
                    self.wfs = TimeDependentWaveFunctions(
                        par.stencils[0],
                        diagksl,
                        orthoksl,
                        initksl,
                        gd,
                        nvalence,
                        setups,
                        bd,
                        world,
                        kd,
                        kptband_comm,
                        self.timer)
                elif mode.name == 'fd':
                    self.wfs = mode(par.stencils[0], diagksl,
                                    orthoksl, initksl, *args)
                else:
                    assert mode.name == 'pw'
                    self.wfs = mode(diagksl, orthoksl, initksl, *args)
            else:
                self.wfs = mode(self, *args)
        else:
            self.wfs.set_setups(setups)

        if not self.wfs.eigensolver:
            # Number of bands to converge:
            nbands_converge = cc['bands']
            if nbands_converge == 'all':
                nbands_converge = nbands
            elif nbands_converge != 'occupied':
                assert isinstance(nbands_converge, int)
                if nbands_converge < 0:
                    nbands_converge += nbands
            eigensolver = get_eigensolver(par.eigensolver, mode,
                                          par.convergence)
            eigensolver.nbands_converge = nbands_converge
            # XXX Eigensolver class doesn't define an nbands_converge property

            if isinstance(xc, SIC):
                eigensolver.blocksize = 1
            self.wfs.set_eigensolver(eigensolver)

        if self.density is None:
            gd = self.wfs.gd
            if par.stencils[1] != 9:
                # Construct grid descriptor for fine grids for densities
                # and potentials:
                finegd = gd.refine()
            else:
                # Special case (use only coarse grid):
                finegd = gd

            if realspace:
                self.density = RealSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear, par.stencils[1])
            else:
                self.density = pw.ReciprocalSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear)

        self.density.initialize(setups, self.timer, magmom_av, par.hund)
        self.density.set_mixer(par.mixer)

        if self.hamiltonian is None:
            gd, finegd = self.density.gd, self.density.finegd
            if realspace:
                self.hamiltonian = RealSpaceHamiltonian(
                    gd, finegd, nspins, setups, self.timer, xc,
                    world, self.wfs.kptband_comm, par.external,
                    collinear, par.poissonsolver, par.stencils[1])
            else:
                self.hamiltonian = pw.ReciprocalSpaceHamiltonian(
                    gd, finegd, self.density.pd2, self.density.pd3,
                    nspins, setups, self.timer, xc, world,
                    self.wfs.kptband_comm, par.external, collinear)

        xc.initialize(self.density, self.hamiltonian, self.wfs,
                      self.occupations)

        self.text()
        self.print_memory_estimate(self.txt, maxdepth=memory_estimate_depth)
        self.txt.flush()

        self.timer.print_info(self)

        if dry_run:
            self.dry_run()

        if realspace and \
                self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
            self.hamiltonian.poisson.set_density(self.density)
            self.hamiltonian.poisson.print_messages(self.text)
            self.txt.flush()

        self.initialized = True
        self._changed_keywords.clear()

    def dry_run(self):
        # Can be overridden like in gpaw.atom.atompaw
        self.print_cell_and_parameters()
        self.print_positions()
        self.txt.flush()
        raise SystemExit

    def linearize_to_xc(self, newxc):
        """Linearize Hamiltonian to difference XC functional.
        
        Used in real time TDDFT to perform calculations with various kernels.
        """
        if isinstance(newxc, str):
            newxc = XC(newxc)
        self.txt.write('Linearizing xc-hamiltonian to ' + str(newxc))
        newxc.initialize(self.density, self.hamiltonian, self.wfs,
                         self.occupations)
        self.hamiltonian.linearize_to_xc(newxc, self.density)

    def restore_state(self):
        """After restart, calculate fine density and poisson solution.

        These are not initialized by default.
        TODO: Is this really the most efficient way?
        """
        spos_ac = self.atoms.get_scaled_positions() % 1.0
        self.density.set_positions(spos_ac, self.wfs.rank_a)
        self.density.interpolate_pseudo_density()
        self.density.calculate_pseudo_charge()
        self.hamiltonian.set_positions(spos_ac, self.wfs.rank_a)
        self.hamiltonian.update(self.density)

    def attach(self, function, n=1, *args, **kwargs):
        """Register observer function.

        Call *function* using *args* and
        *kwargs* as arguments.
        
        If *n* is positive, then
        *function* will be called every *n* iterations + the
        final iteration if it would not be otherwise
        
        If *n* is negative, then *function* will only be
        called on iteration *abs(n)*.
        
        If *n* is 0, then *function* will only be called
        on convergence"""

        try:
            slf = function.im_self
        except AttributeError:
            pass
        else:
            if slf is self:
                # function is a bound method of self.  Store the name
                # of the method and avoid circular reference:
                function = function.im_func.func_name

        self.observers.append((function, n, args, kwargs))

    def call_observers(self, iter, final=False):
        """Call all registered callback functions."""
        for function, n, args, kwargs in self.observers:
            call = False
            # Call every n iterations, including the last
            if n > 0:
                if ((iter % n) == 0) != final:
                    call = True
            # Call only on iteration n
            elif n < 0 and not final:
                if iter == abs(n):
                    call = True
            # Call only on convergence
            elif n == 0 and final:
                call = True
            if call:
                if isinstance(function, str):
                    function = getattr(self, function)
                function(*args, **kwargs)

    def get_reference_energy(self):
        return self.wfs.setups.Eref * Hartree

    def write(self, filename, mode='', cmr_params={}, **kwargs):
        """Write state to file.

        use mode='all' to write the wave functions.  cmr_params is a
        dictionary that allows you to specify parameters for CMR
        (Computational Materials Repository).
        """

        self.timer.start('IO')
        gpaw.io.write(self, filename, mode, cmr_params=cmr_params, **kwargs)
        self.timer.stop('IO')

    def get_myu(self, k, s):
        """Return my u corresponding to a certain kpoint and spin - or None"""
        # very slow, but we are sure that we have it
        for u in range(len(self.wfs.kpt_u)):
            if self.wfs.kpt_u[u].k == k and self.wfs.kpt_u[u].s == s:
                return u
        return None

    def get_homo_lumo(self):
        """Return H**O and LUMO eigenvalues."""
        return self.occupations.get_homo_lumo(self.wfs) * Hartree

    def estimate_memory(self, mem):
        """Estimate memory use of this object."""
        for name, obj in [('Density', self.density),
                          ('Hamiltonian', self.hamiltonian),
                          ('Wavefunctions', self.wfs),
                          ]:
            obj.estimate_memory(mem.subnode(name))

    def print_memory_estimate(self, txt=None, maxdepth=-1):
        """Print estimated memory usage for PAW object and components.

        maxdepth is the maximum nesting level of displayed components.

        The PAW object must be initialize()'d, but needs not have large
        arrays allocated."""
        # NOTE.  This should work with --dry-run=N
        #
        # However, the initial overhead estimate is wrong if this method
        # is called within a real mpirun/gpaw-python context.
        if txt is None:
            txt = self.txt
        txt.write('Memory estimate\n')
        txt.write('---------------\n')

        mem_init = maxrss()  # initial overhead includes part of Hamiltonian!
        txt.write('Process memory now: %.2f MiB\n' % (mem_init / 1024.0**2))

        mem = MemNode('Calculator', 0)
        try:
            self.estimate_memory(mem)
        except AttributeError as m:
            txt.write('Attribute error: %r' % m)
            txt.write('Some object probably lacks estimate_memory() method')
            txt.write('Memory breakdown may be incomplete')
        mem.calculate_size()
        mem.write(txt, maxdepth=maxdepth)

    def converge_wave_functions(self):
        """Converge the wave-functions if not present."""

        if not self.wfs or not self.scf:
            self.initialize()
        else:
            self.wfs.initialize_wave_functions_from_restart_file()
            spos_ac = self.atoms.get_scaled_positions() % 1.0
            self.wfs.set_positions(spos_ac)

        no_wave_functions = (self.wfs.kpt_u[0].psit_nG is None)
        converged = self.scf.check_convergence(self.density,
                                               self.wfs.eigensolver, self.wfs,
                                               self.hamiltonian, self.forces)
        if no_wave_functions or not converged:
            self.wfs.eigensolver.error = np.inf
            self.scf.converged = False

            # is the density ok ?
            error = self.density.mixer.get_charge_sloshing()
            criterion = (self.input_parameters['convergence']['density']
                         * self.wfs.nvalence)
            if error < criterion and not self.hamiltonian.xc.orbital_dependent:
                self.scf.fix_density()

            self.calculate()

    def diagonalize_full_hamiltonian(self, nbands=None, scalapack=None, expert=False):
        self.wfs.diagonalize_full_hamiltonian(self.hamiltonian, self.atoms,
                                              self.occupations, self.txt,
                                              nbands, scalapack, expert)

    def check_atoms(self):
        """Check that atoms objects are identical on all processors."""
        if not mpi.compare_atoms(self.atoms, comm=self.wfs.world):
            raise RuntimeError('Atoms objects on different processors ' +
                               'are not identical!')
Esempio n. 16
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    def initialize(self, atoms=None):
        """Inexpensive initialization."""

        if atoms is None:
            atoms = self.atoms
        else:
            # Save the state of the atoms:
            self.atoms = atoms.copy()

        par = self.input_parameters

        world = par.communicator
        if world is None:
            world = mpi.world
        elif hasattr(world, 'new_communicator'):
            # Check for whether object has correct type already
            #
            # Using isinstance() is complicated because of all the
            # combinations, serial/parallel/debug...
            pass
        else:
            # world should be a list of ranks:
            world = mpi.world.new_communicator(np.asarray(world))
        self.wfs.world = world

        if 'txt' in self._changed_keywords:
            self.set_txt(par.txt)
        self.verbose = par.verbose

        natoms = len(atoms)

        cell_cv = atoms.get_cell() / Bohr
        pbc_c = atoms.get_pbc()
        Z_a = atoms.get_atomic_numbers()
        magmom_av = atoms.get_initial_magnetic_moments()

        self.check_atoms()

        # Generate new xc functional only when it is reset by set
        # XXX sounds like this should use the _changed_keywords dictionary.
        if self.hamiltonian is None or self.hamiltonian.xc is None:
            if isinstance(par.xc, str):
                xc = XC(par.xc)
            else:
                xc = par.xc
        else:
            xc = self.hamiltonian.xc

        mode = par.mode

        if mode == 'fd':
            mode = FD()
        elif mode == 'pw':
            mode = pw.PW()
        elif mode == 'lcao':
            mode = LCAO()
        else:
            assert hasattr(mode, 'name'), str(mode)

        if xc.orbital_dependent and mode.name == 'lcao':
            raise NotImplementedError('LCAO mode does not support '
                                      'orbital-dependent XC functionals.')

        if par.realspace is None:
            realspace = (mode.name != 'pw')
        else:
            realspace = par.realspace
            if mode.name == 'pw':
                assert not realspace

        if par.filter is None and mode.name != 'pw':
            gamma = 1.6
            if par.gpts is not None:
                h = ((np.linalg.inv(cell_cv)**2).sum(0)**-0.5
                     / par.gpts).max()
            else:
                h = (par.h or 0.2) / Bohr

            def filter(rgd, rcut, f_r, l=0):
                gcut = np.pi / h - 2 / rcut / gamma
                f_r[:] = rgd.filter(f_r, rcut * gamma, gcut, l)
        else:
            filter = par.filter

        setups = Setups(Z_a, par.setups, par.basis, par.lmax, xc,
                        filter, world)

        if magmom_av.ndim == 1:
            collinear = True
            magmom_av, magmom_a = np.zeros((natoms, 3)), magmom_av
            magmom_av[:, 2] = magmom_a
        else:
            collinear = False

        magnetic = magmom_av.any()

        spinpol = par.spinpol
        if par.hund:
            if natoms != 1:
                raise ValueError('hund=True arg only valid for single atoms!')
            spinpol = True
            magmom_av[0] = (0, 0, setups[0].get_hunds_rule_moment(par.charge))

        if spinpol is None:
            spinpol = magnetic
        elif magnetic and not spinpol:
            raise ValueError('Non-zero initial magnetic moment for a ' +
                             'spin-paired calculation!')

        if collinear:
            nspins = 1 + int(spinpol)
            ncomp = 1
        else:
            nspins = 1
            ncomp = 2

        if par.usesymm != 'default':
            warnings.warn('Use "symmetry" keyword instead of ' +
                          '"usesymm" keyword')
            par.symmetry = usesymm2symmetry(par.usesymm)

        symm = par.symmetry
        if symm == 'off':
            symm = {'point_group': False, 'time_reversal': False}

        bzkpts_kc = kpts2ndarray(par.kpts, self.atoms)
        kd = KPointDescriptor(bzkpts_kc, nspins, collinear)
        m_av = magmom_av.round(decimals=3)  # round off
        id_a = zip(setups.id_a, *m_av.T)
        symmetry = Symmetry(id_a, cell_cv, atoms.pbc, **symm)
        kd.set_symmetry(atoms, symmetry, comm=world)
        setups.set_symmetry(symmetry)

        if par.gpts is not None:
            N_c = np.array(par.gpts)
        else:
            h = par.h
            if h is not None:
                h /= Bohr
            N_c = get_number_of_grid_points(cell_cv, h, mode, realspace,
                                            kd.symmetry)

        symmetry.check_grid(N_c)

        width = par.width
        if width is None:
            if pbc_c.any():
                width = 0.1  # eV
            else:
                width = 0.0
        else:
            assert par.occupations is None

        if hasattr(self, 'time') or par.dtype == complex:
            dtype = complex
        else:
            if kd.gamma:
                dtype = float
            else:
                dtype = complex

        nao = setups.nao
        nvalence = setups.nvalence - par.charge
        M_v = magmom_av.sum(0)
        M = np.dot(M_v, M_v) ** 0.5

        nbands = par.nbands
        
        orbital_free = any(setup.orbital_free for setup in setups)
        if orbital_free:
            nbands = 1

        if isinstance(nbands, basestring):
            if nbands[-1] == '%':
                basebands = int(nvalence + M + 0.5) // 2
                nbands = int((float(nbands[:-1]) / 100) * basebands)
            else:
                raise ValueError('Integer Expected: Only use a string '
                                 'if giving a percentage of occupied bands')

        if nbands is None:
            nbands = 0
            for setup in setups:
                nbands_from_atom = setup.get_default_nbands()

                # Any obscure setup errors?
                if nbands_from_atom < -(-setup.Nv // 2):
                    raise ValueError('Bad setup: This setup requests %d'
                                     ' bands but has %d electrons.'
                                     % (nbands_from_atom, setup.Nv))
                nbands += nbands_from_atom
            nbands = min(nao, nbands)
        elif nbands > nao and mode.name == 'lcao':
            raise ValueError('Too many bands for LCAO calculation: '
                             '%d bands and only %d atomic orbitals!' %
                             (nbands, nao))

        if nvalence < 0:
            raise ValueError(
                'Charge %f is not possible - not enough valence electrons' %
                par.charge)

        if nbands <= 0:
            nbands = int(nvalence + M + 0.5) // 2 + (-nbands)

        if nvalence > 2 * nbands and not orbital_free:
            raise ValueError('Too few bands!  Electrons: %f, bands: %d'
                             % (nvalence, nbands))

        nbands *= ncomp

        if par.width is not None:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width).')
        if par.fixmom:
            self.text('**NOTE**: please start using '
                      'occupations=FermiDirac(width, fixmagmom=True).')

        if self.occupations is None:
            if par.occupations is None:
                # Create object for occupation numbers:
                if orbital_free:
                    width = 0.0  # even for PBC
                    self.occupations = occupations.TFOccupations(width,
                                                                 par.fixmom)
                else:
                    self.occupations = occupations.FermiDirac(width,
                                                              par.fixmom)
            else:
                self.occupations = par.occupations

            # If occupation numbers are changed, and we have wave functions,
            # recalculate the occupation numbers
            if self.wfs is not None and not isinstance(
                    self.wfs,
                    EmptyWaveFunctions):
                self.occupations.calculate(self.wfs)

        self.occupations.magmom = M_v[2]

        cc = par.convergence

        if mode.name == 'lcao':
            niter_fixdensity = 0
        else:
            niter_fixdensity = None

        if self.scf is None:
            force_crit = cc['forces']
            if force_crit is not None:
                force_crit /= Hartree / Bohr
            self.scf = SCFLoop(
                cc['eigenstates'] / Hartree**2 * nvalence,
                cc['energy'] / Hartree * max(nvalence, 1),
                cc['density'] * nvalence,
                par.maxiter, par.fixdensity,
                niter_fixdensity,
                force_crit)

        parsize_kpt = par.parallel['kpt']
        parsize_domain = par.parallel['domain']
        parsize_bands = par.parallel['band']

        if not realspace:
            pbc_c = np.ones(3, bool)

        if not self.wfs:
            if parsize_domain == 'domain only':  # XXX this was silly!
                parsize_domain = world.size

            parallelization = mpi.Parallelization(world,
                                                  nspins * kd.nibzkpts)
            ndomains = None
            if parsize_domain is not None:
                ndomains = np.prod(parsize_domain)
            if mode.name == 'pw':
                if ndomains > 1:
                    raise ValueError('Planewave mode does not support '
                                     'domain decomposition.')
                ndomains = 1
            parallelization.set(kpt=parsize_kpt,
                                domain=ndomains,
                                band=parsize_bands)
            comms = parallelization.build_communicators()
            domain_comm = comms['d']
            kpt_comm = comms['k']
            band_comm = comms['b']
            kptband_comm = comms['D']
            domainband_comm = comms['K']

            self.comms = comms
            kd.set_communicator(kpt_comm)

            parstride_bands = par.parallel['stridebands']

            # Unfortunately we need to remember that we adjusted the
            # number of bands so we can print a warning if it differs
            # from the number specified by the user.  (The number can
            # be inferred from the input parameters, but it's tricky
            # because we allow negative numbers)
            self.nbands_parallelization_adjustment = -nbands % band_comm.size
            nbands += self.nbands_parallelization_adjustment

            # I would like to give the following error message, but apparently
            # there are cases, e.g. gpaw/test/gw_ppa.py, which involve
            # nbands > nao and are supposed to work that way.
            #if nbands > nao:
            #    raise ValueError('Number of bands %d adjusted for band '
            #                     'parallelization %d exceeds number of atomic '
            #                     'orbitals %d.  This problem can be fixed '
            #                     'by reducing the number of bands a bit.'
            #                     % (nbands, band_comm.size, nao))
            bd = BandDescriptor(nbands, band_comm, parstride_bands)

            if (self.density is not None and
                    self.density.gd.comm.size != domain_comm.size):
                # Domain decomposition has changed, so we need to
                # reinitialize density and hamiltonian:
                if par.fixdensity:
                    raise RuntimeError(
                        'Density reinitialization conflict ' +
                        'with "fixdensity" - specify domain decomposition.')
                self.density = None
                self.hamiltonian = None

            # Construct grid descriptor for coarse grids for wave functions:
            gd = self.grid_descriptor_class(N_c, cell_cv, pbc_c,
                                            domain_comm, parsize_domain)

            # do k-point analysis here? XXX
            args = (gd, nvalence, setups, bd, dtype, world, kd,
                    kptband_comm, self.timer)

            if par.parallel['sl_auto']:
                # Choose scalapack parallelization automatically

                for key, val in par.parallel.items():
                    if (key.startswith('sl_') and key != 'sl_auto'
                            and val is not None):
                        raise ValueError("Cannot use 'sl_auto' together "
                                         "with '%s'" % key)
                max_scalapack_cpus = bd.comm.size * gd.comm.size
                nprow = max_scalapack_cpus
                npcol = 1

                # Get a sort of reasonable number of columns/rows
                while npcol < nprow and nprow % 2 == 0:
                    npcol *= 2
                    nprow //= 2
                assert npcol * nprow == max_scalapack_cpus

                # ScaLAPACK creates trouble if there aren't at least a few
                # whole blocks; choose block size so there will always be
                # several blocks.  This will crash for small test systems,
                # but so will ScaLAPACK in any case
                blocksize = min(-(-nbands // 4), 64)
                sl_default = (nprow, npcol, blocksize)
            else:
                sl_default = par.parallel['sl_default']

            if mode.name == 'lcao':
                # Layouts used for general diagonalizer
                sl_lcao = par.parallel['sl_lcao']
                if sl_lcao is None:
                    sl_lcao = sl_default
                lcaoksl = get_KohnSham_layouts(sl_lcao, 'lcao',
                                               gd, bd, domainband_comm, dtype,
                                               nao=nao, timer=self.timer)

                self.wfs = mode(collinear, lcaoksl, *args)

            elif mode.name == 'fd' or mode.name == 'pw':
                # buffer_size keyword only relevant for fdpw
                buffer_size = par.parallel['buffer_size']
                # Layouts used for diagonalizer
                sl_diagonalize = par.parallel['sl_diagonalize']
                if sl_diagonalize is None:
                    sl_diagonalize = sl_default
                diagksl = get_KohnSham_layouts(sl_diagonalize, 'fd',  # XXX
                                               # choice of key 'fd' not so nice
                                               gd, bd, domainband_comm, dtype,
                                               buffer_size=buffer_size,
                                               timer=self.timer)

                # Layouts used for orthonormalizer
                sl_inverse_cholesky = par.parallel['sl_inverse_cholesky']
                if sl_inverse_cholesky is None:
                    sl_inverse_cholesky = sl_default
                if sl_inverse_cholesky != sl_diagonalize:
                    message = 'sl_inverse_cholesky != sl_diagonalize ' \
                        'is not implemented.'
                    raise NotImplementedError(message)
                orthoksl = get_KohnSham_layouts(sl_inverse_cholesky, 'fd',
                                                gd, bd, domainband_comm, dtype,
                                                buffer_size=buffer_size,
                                                timer=self.timer)

                # Use (at most) all available LCAO for initialization
                lcaonbands = min(nbands, nao)

                try:
                    lcaobd = BandDescriptor(lcaonbands, band_comm,
                                            parstride_bands)
                except RuntimeError:
                    initksl = None
                else:
                    # Layouts used for general diagonalizer
                    # (LCAO initialization)
                    sl_lcao = par.parallel['sl_lcao']
                    if sl_lcao is None:
                        sl_lcao = sl_default
                    initksl = get_KohnSham_layouts(sl_lcao, 'lcao',
                                                   gd, lcaobd, domainband_comm,
                                                   dtype, nao=nao,
                                                   timer=self.timer)

                if hasattr(self, 'time'):
                    assert mode.name == 'fd'
                    from gpaw.tddft import TimeDependentWaveFunctions
                    self.wfs = TimeDependentWaveFunctions(
                        par.stencils[0],
                        diagksl,
                        orthoksl,
                        initksl,
                        gd,
                        nvalence,
                        setups,
                        bd,
                        world,
                        kd,
                        kptband_comm,
                        self.timer)
                elif mode.name == 'fd':
                    self.wfs = mode(par.stencils[0], diagksl,
                                    orthoksl, initksl, *args)
                else:
                    assert mode.name == 'pw'
                    self.wfs = mode(diagksl, orthoksl, initksl, *args)
            else:
                self.wfs = mode(self, *args)
        else:
            self.wfs.set_setups(setups)

        if not self.wfs.eigensolver:
            # Number of bands to converge:
            nbands_converge = cc['bands']
            if nbands_converge == 'all':
                nbands_converge = nbands
            elif nbands_converge != 'occupied':
                assert isinstance(nbands_converge, int)
                if nbands_converge < 0:
                    nbands_converge += nbands
            eigensolver = get_eigensolver(par.eigensolver, mode,
                                          par.convergence)
            eigensolver.nbands_converge = nbands_converge
            # XXX Eigensolver class doesn't define an nbands_converge property

            if isinstance(xc, SIC):
                eigensolver.blocksize = 1
            self.wfs.set_eigensolver(eigensolver)

        if self.density is None:
            gd = self.wfs.gd
            if par.stencils[1] != 9:
                # Construct grid descriptor for fine grids for densities
                # and potentials:
                finegd = gd.refine()
            else:
                # Special case (use only coarse grid):
                finegd = gd

            if realspace:
                self.density = RealSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear, par.stencils[1])
            else:
                self.density = pw.ReciprocalSpaceDensity(
                    gd, finegd, nspins, par.charge + setups.core_charge,
                    collinear)

        self.density.initialize(setups, self.timer, magmom_av, par.hund)
        self.density.set_mixer(par.mixer)

        if self.hamiltonian is None:
            gd, finegd = self.density.gd, self.density.finegd
            if realspace:
                self.hamiltonian = RealSpaceHamiltonian(
                    gd, finegd, nspins, setups, self.timer, xc,
                    world, self.wfs.kptband_comm, par.external,
                    collinear, par.poissonsolver, par.stencils[1])
            else:
                self.hamiltonian = pw.ReciprocalSpaceHamiltonian(
                    gd, finegd, self.density.pd2, self.density.pd3,
                    nspins, setups, self.timer, xc, world,
                    self.wfs.kptband_comm, par.external, collinear)

        xc.initialize(self.density, self.hamiltonian, self.wfs,
                      self.occupations)

        self.text()
        self.print_memory_estimate(self.txt, maxdepth=memory_estimate_depth)
        self.txt.flush()

        self.timer.print_info(self)

        if dry_run:
            self.dry_run()

        if realspace and \
                self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
            self.hamiltonian.poisson.set_density(self.density)
            self.hamiltonian.poisson.print_messages(self.text)
            self.txt.flush()

        self.initialized = True
        self._changed_keywords.clear()