"""This module defines an ASE interface to SIESTA.

http://www.uam.es/departamentos/ciencias/fismateriac/siesta
"""

import os
from os.path import join, isfile, islink, getmtime
from cmath import exp
import array

import numpy as np

from ase.data import chemical_symbols
from ase.units import Rydberg, fs
from ase.io.siesta import read_rho, read_fdf, read_struct
from ase.io.cube import read_cube_data

class Siesta:
    """Class for doing SIESTA calculations.

    The default parameters are very close to those that the SIESTA
    Fortran code would use.  These are the exceptions::

      calc = Siesta(label='siesta', xc='LDA', pulay=5, mix=0.1)

    Use the set_fdf method to set extra FDF parameters::

      calc.set_fdf('PAO.EnergyShift', 0.01 * Rydberg)

    """
    def __init__(self, label='siesta', xc='LDA', kpts=None, nbands=None,
                 width=None, meshcutoff=None, charge=None,
                 pulay=5, mix=0.1, maxiter=120,
                 basis=None, ghosts=[],
                 write_fdf=True):
        """Construct SIESTA-calculator object.

        Parameters
        ==========
        label: str
            Prefix to use for filenames (label.fdf, label.txt, ...).
            Default is 'siesta'.
        xc: str
            Exchange-correlation functional.  Must be one of LDA, PBE,
            revPBE, RPBE.
        kpts: list of three int
            Monkhost-Pack sampling.
        nbands: int
            Number of bands.
        width: float
            Fermi-distribution width in eV.
        meshcutoff: float
            Cutoff energy in eV for grid.
        charge: float
            Total charge of the system.
        pulay: int
            Number of old densities to use for Pulay mixing.
        mix: float
            Mixing parameter between zero and one for density mixing.
        write_fdf: bool
            Use write_fdf=False to use your own fdf-file.

        Examples
        ========
        Use default values:

        >>> h = Atoms('H', calculator=Siesta())
        >>> h.center(vacuum=3.0)
        >>> e = h.get_potential_energy()

        """

        self.name = 'Siesta'
        self.label = label#################### != out
        self.xc = xc
        self.kpts = kpts
        self.nbands = nbands
        self.width = width
        self.meshcutoff = meshcutoff
        self.charge = charge
        self.pulay = pulay
        self.mix = mix
        self.maxiter = maxiter
        self.basis = basis
        self.ghosts = ghosts
        self.write_fdf_file = write_fdf

        self.converged = False
        self.fdf = {}
        self.e_fermi = None

    def update(self, atoms):
        if (not self.converged or
            len(self.numbers) != len(atoms) or
            (self.numbers != atoms.get_atomic_numbers()).any()):
            self.initialize(atoms)
            self.calculate(atoms)
        elif ((self.positions != atoms.get_positions()).any() or
              (self.pbc != atoms.get_pbc()).any() or
              (self.cell != atoms.get_cell()).any()):
            self.calculate(atoms)

    def initialize(self, atoms):
        self.numbers = atoms.get_atomic_numbers().copy()
        self.species = []
        for a, Z in enumerate(self.numbers):
            if a in self.ghosts:
                Z = -Z
            if Z not in self.species:
                self.species.append(Z)

        if 'SIESTA_PP_PATH' in os.environ:
            pppaths = os.environ['SIESTA_PP_PATH'].split(':')
        else:
            pppaths = []

        for Z in self.species:
            symbol = chemical_symbols[abs(Z)]
            name = symbol + '.vps'
            name1 = symbol + '.psf'
            found = False
            for path in pppaths:
                filename = join(path, name)
                filename1 = join(path, name1)
                if isfile(filename) or islink(filename):
                    found = True
                    if path != '.':
                        if islink(name) or isfile(name):
                            os.remove(name)
                        os.symlink(filename, name)

                elif isfile(filename1) or islink(filename1):
                    found = True
                    if path != '.':
                        if islink(name1) or isfile(name1):
                            os.remove(name1)
                        os.symlink(filename1, name1)
            if not found:
                raise RuntimeError('No pseudopotential for %s!' % symbol)

        self.converged = False

    def get_potential_energy(self, atoms, force_consistent=False):
        self.update(atoms)

        if force_consistent:
            return self.efree
        else:
            # Energy extrapolated to zero Kelvin:
            return  (self.etotal + self.efree) / 2

    def get_forces(self, atoms):
        self.update(atoms)
        return self.forces.copy()

    def get_stress(self, atoms):
        self.update(atoms)
        return self.stress.copy()

    def get_dipole_moment(self, atoms):
        """Returns total dipole moment of the system."""
        self.update(atoms)
        return self.dipole

    def read_dipole(self):
        dipolemoment = np.zeros([1, 3])
        for line in open(self.label + '.txt', 'r'):
            if line.rfind('Electric dipole (Debye)') > -1:
                dipolemoment = np.array([float(f) for f in line.split()[5:8]])
        #debye to e*Ang (the units of VASP)
        dipolemoment = dipolemoment*0.2081943482534
        return dipolemoment

    def get_pseudo_density(self, spin=None, pad=True):
        """Return pseudo-density array.

        If *spin* is not given, then the total density is returned.
        Otherwise, the spin up or down density is returned (spin=0 or 1).
        """
        filename = self.label + '.RHO'
        if not isfile(filename):
            raise RuntimeError('Could not find rho-file (make sure to add fdf-option '
                               '"SaveRho=True" to your calculation)')

        rho = read_rho(filename)

        if spin is None:
            return rho.sum(axis=3)
        elif rho.shape[3] != 2:
            raise RuntimeError('Explicit spin-value requested. '
                               'Only total density is available.')
        elif spin == 0 or spin == 1:
            return rho[:, :, :, spin]
        else:
            raise RuntimeError('Invalid spin-value requested. '
                               'Expected 0 or 1, got %s' % spin)


    def get_pseudo_wave_function(self, band=0, kpt=0, spin=None):
        """Return pseudo-wave-function array.

        The method is limited to the gamma point, and is implemented
        as a wrapper to denchar (a tool shipped with siesta);
        denchar must be available in the command path.

        When retrieving a p_w_f from a non-spin-polarized calculation,
        spin must be None (default), and for spin-polarized
        calculations, spin must be set to either 0 (up) or 1 (down).

        As long as the necessary files are present and named
        correctly, old p_w_fs can be read as long as the
        calculator label is set. E.g.

        >>> c = Siesta(label='name_of_old_calculation')
        >>> pwf = c.get_pseudo_wave_function()

        The broadcast and pad options are not implemented.
        """

        # Not implemented: kpt=0, broadcast=True, pad=True
        # kpoint must be Gamma
        assert kpt == 0, \
            "siesta.get_pseudo_wave_function is unfortunately limited " \
            "to the gamma point only. kpt must be 0."

        # In denchar, band numbering starts from 1
        assert type(band) is int and band >= 0
        band = band+1

        if spin is None:
            spin_name = ""
        elif spin == 0:
            spin_name = ".UP"
        elif spin == 1:
            spin_name = ".DOWN"

        label = self.label
        # If <label>.WF<band>.cube already exist and is newer than <label>.fdf,
        # just return it
        fn_wf = label+('.WF%i%s.cube'%(band,spin_name))
        fn_fdf = label+'.fdf'
        if isfile(fn_wf) and isfile(fn_fdf) and (getmtime(fn_wf) > getmtime(fn_fdf)):
            x, _ = read_cube_data(fn_wf)
            return x

        if not isfile(fn_fdf):
            raise RuntimeError('Could not find the fdf-file. It is required as '
                               'part of the input for denchar.')

        fdf_mtime = getmtime(fn_fdf)
        for suf in ['.WFS', '.PLD', '.DM', '.DIM']:
            if not isfile(label+suf):
                raise RuntimeError('Could not find file "%s%s" which is required '
                                   'when extracting wave functions '
                                   '(make sure the fdf options "WriteDenchar" is '
                                   'True, and WaveFuncKpoints is [0.0 0.0 0.0]")' %
                                   (label, suf))
            if not getmtime(label+suf) > fdf_mtime:
                # This should be handled in a better way, e.g. by implementing
                # a "calculation_required() and calculate()"
                raise RuntimeError('The calculation is not up to date.')

        # Simply read the old fdf-file and pick some meta info from there.
        # However, strictly it's not always neccesary
        fdf = read_fdf(fn_fdf)
        if 'latticeconstant' in fdf:
            const = float(fdf['latticeconstant'][0])
            unit =  fdf['latticeconstant'][1]
        else:
            const = 1.0
            unit = 'Ang'

        if 'latticevectors' in fdf:
            cell = np.array(fdf['latticevectors'], dtype='d')
        else:
            raise RuntimeError('Failed to find the lattice vectors in the fdf-file.')

        if 'spinpolarized' in fdf and \
                fdf['spinpolarized'][0].lower() in ['yes', 'true', '.true.', 'T', '']:
            if spin is None:
                raise RuntimeError('The calculation was spin polarized, pick either '
                                   'spin=0 or 1.')
        else:
            if not spin is None:
                raise RuntimeError('The calculation was not spin polarized, '
                                   'spin argument must be None.')

        denc_fdf = open(fn_fdf).readlines()
        denc_fdf.append('Denchar.TypeOfRun 3D\n')
        denc_fdf.append('Denchar.PlotWaveFunctions T\n')
        for dim, dir in zip(cell.transpose(), ['X', 'Y', 'Z']):
            # Naive square box limits to denchar
            denc_fdf.append('Denchar.Min%s %f %s\n' % (dir, const*dim.min(), unit))
            denc_fdf.append('Denchar.Max%s %f %s\n' % (dir, const*dim.max(), unit))

        # denchar rewinds stdin and fails if stdin is a pipe
        denc_fdf_file = open(label+'.denchar.fdf', 'w')
        denc_fdf_file.write(''.join(denc_fdf))
        denc_fdf_file.close()

        try:
            from subprocess import Popen, PIPE
            p = Popen('denchar', shell=True, stdin=open(label+'.denchar.fdf'),
                      stdout=PIPE, stderr=PIPE, close_fds=True)
            exitcode = p.wait()
        except ImportError:
            raise RuntimeError('get_pseudo_wave_function implemented only with subprocess.')

        if exitcode == 0:
            if not isfile(fn_wf):
                raise RuntimeError('Could not find the requested file (%s)'%fn_wf)
            x, _ = read_cube_data(fn_wf)
            return x
        elif exitcode == 127:
            raise RuntimeError('No denchar executable found. Make sure it is in the path.')
        else:
            import sys
            print >>sys.stderr, ''.join(p.stderr.readlines())
            raise RuntimeError('Execution of denchar failed!')


    def calculate(self, atoms):
        self.positions = atoms.get_positions().copy()
        self.cell = atoms.get_cell().copy()
        self.pbc = atoms.get_pbc().copy()

        if self.write_fdf_file:
            self.write_fdf(atoms)

        siesta = os.environ['SIESTA_SCRIPT']
        locals = {'label': self.label}
        execfile(siesta, {}, locals)
        exitcode = locals['exitcode']
        if exitcode != 0:
            raise RuntimeError(('Siesta exited with exit code: %d.  ' +
                                'Check %s.txt for more information.') %
                               (exitcode, self.label))

        self.dipole = self.read_dipole()
        self.read()

        atoms_structout = read_struct('%s.STRUCT_OUT' % self.label)
        atoms.cell = atoms_structout.cell
        atoms.positions = atoms_structout.positions

        self.converged = True

    def set_fdf(self, key, value):
        """Set FDF parameter."""
        self.fdf[key] = value

    def write_fdf(self, atoms):
        """Write input parameters to fdf-file."""
        fh = open(self.label + '.fdf', 'w')

        fdf = {
            'SystemLabel': self.label,
            'AtomicCoordinatesFormat': 'Ang',
            'LatticeConstant': 1.0,
            'NumberOfAtoms': len(atoms),
            'MeshCutoff': self.meshcutoff,
            'NetCharge': self.charge,
            'ElectronicTemperature': self.width,
            'NumberOfEigenStates': self.nbands,
            'DM.UseSaveDM': self.converged,
            'PAO.BasisSize': self.basis,
            'SolutionMethod': 'diagon',
            'DM.NumberPulay': self.pulay,
            'DM.MixingWeight': self.mix,
            'MaxSCFIterations': self.maxiter
            }

        if self.xc != 'LDA':
            fdf['xc.functional'] = 'GGA'
            fdf['xc.authors'] = self.xc

        magmoms = atoms.get_initial_magnetic_moments()
        if magmoms.any():
            fdf['SpinPolarized'] = True
            fh.write('%block InitSpin\n')
            for n, M in enumerate(magmoms):
                if M != 0:
                    fh.write('%d %.14f\n' % (n + 1, M))
            fh.write('%endblock InitSpin\n')

        fdf['Number_of_species'] = len(self.species)

        fdf.update(self.fdf)

        for key, value in fdf.items():
            if value is None:
                continue

            if isinstance(value, list):
                fh.write('%%block %s\n' % key)
                for line in value:
                    fh.write(line + '\n')
                fh.write('%%endblock %s\n' % key)
            else:
                unit = keys_with_units.get(fdfify(key))
                if unit is None:
                    fh.write('%s %s\n' % (key, value))
                else:
                    if 'fs**2' in unit:
                        value /= fs**2
                    elif 'fs' in unit:
                        value /= fs
                    fh.write('%s %f %s\n' % (key, value, unit))

        fh.write('%block LatticeVectors\n')
        for v in self.cell:
            fh.write('%.14f %.14f %.14f\n' % tuple(v))
        fh.write('%endblock LatticeVectors\n')

        fh.write('%block Chemical_Species_label\n')
        for n, Z in enumerate(self.species):
            fh.write('%d %s %s\n' % (n + 1, Z, chemical_symbols[abs(Z)]))
        fh.write('%endblock Chemical_Species_label\n')

        fh.write('%block AtomicCoordinatesAndAtomicSpecies\n')
        a = 0
        for pos, Z in zip(self.positions, self.numbers):
            if a in self.ghosts:
                Z = -Z
            a += 1
            fh.write('%.14f %.14f %.14f' %  tuple(pos))
            fh.write(' %d\n' % (self.species.index(Z) + 1))
        fh.write('%endblock AtomicCoordinatesAndAtomicSpecies\n')

        if self.kpts is not None:
            fh.write('%block kgrid_Monkhorst_Pack\n')
            for i in range(3):
                for j in range(3):
                    if i == j:
                        fh.write('%d ' % self.kpts[i])
                    else:
                        fh.write('0 ')
                fh.write('%.1f\n' % (((self.kpts[i] + 1) % 2) * 0.5))
            fh.write('%endblock kgrid_Monkhorst_Pack\n')

        fh.close()

    def read(self):
        """Read results from SIESTA's text-output file."""
        text = open(self.label + '.txt', 'r').read().lower()
        assert 'error' not in text
        lines = iter(text.split('\n'))

        # Get the number of grid points used:
        for line in lines:
            if line.startswith('initmesh: mesh ='):
                self.grid = [int(word) for word in line.split()[3:8:2]]
                break

        # Stress (fixed so it's compatible with a MD run from siesta):
        for line in lines:
            if line.startswith('siesta: stress tensor '):
                stress = np.empty((3, 3))
                for i in range(3):
                    tmp = lines.next().split()
                    if len(tmp) == 4:
                        stress[i] = [float(word) for word in tmp[1:]]
                    else:
                        stress[i] = [float(word) for word in tmp]
                self.stress = np.array(
                    [stress[0, 0], stress[1, 1], stress[2, 2],
                     stress[1, 2], stress[0, 2], stress[0, 1]])
                break
        else:
            raise RuntimeError

        text = open(self.label + '.txt', 'r').read().lower()
        lines = iter(text.split('\n'))
        # Energy (again a fix to make it compatible with a MD run from siesta):
        counter = 0
        for line in lines:
            if line.startswith('siesta: etot    =') and counter == 0:
                counter += 1
            elif line.startswith('siesta: etot    ='):
                self.etotal = float(line.split()[-1])
                self.efree = float(lines.next().split()[-1])
                break
        else:
            raise RuntimeError

        # Forces (changed so forces smaller than -999eV/A can be fetched):
        lines = open(self.label + '.FA', 'r').readlines()
        assert int(lines[0]) == len(self.numbers)
        assert len(lines) == len(self.numbers) + 1
        lines = lines[1:]
        self.forces = np.zeros((len(lines), 3))
        for i in range(len(lines)):
            self.forces[i, 0] = float(lines[i][6:18].strip())
            self.forces[i, 1] = float(lines[i][18:30].strip())
            self.forces[i, 2] = float(lines[i][30:42].strip())

    def read_eig(self):
        if self.e_fermi is not None:
            return

        assert os.access(self.label + '.EIG', os.F_OK)
        assert os.access(self.label + '.KP', os.F_OK)

        # Read k point weights
        text = open(self.label + '.KP', 'r').read()
        lines = text.split('\n')
        n_kpts = int(lines[0].strip())
        self.weights = np.zeros((n_kpts,))
        for i in range(n_kpts):
            l = lines[i + 1].split()
            self.weights[i] = float(l[4])

        # Read eigenvalues and fermi-level
        text = open(self.label+'.EIG','r').read()
        lines = text.split('\n')
        self.e_fermi = float(lines[0].split()[0])
        tmp = lines[1].split()
        self.n_bands = int(tmp[0])
        n_spin_bands = int(tmp[1])
        self.spin_pol = n_spin_bands == 2
        lines = lines[2:-1]
        lines_per_kpt = (self.n_bands * n_spin_bands / 10 +
                         int((self.n_bands * n_spin_bands) % 10 != 0))
        self.eig = dict()
        for i in range(len(self.weights)):
            tmp = lines[i * lines_per_kpt:(i + 1) * lines_per_kpt]
            v = [float(v) for v in tmp[0].split()[1:]]
            for l in tmp[1:]:
                v.extend([float(t) for t in l.split()])
            if self.spin_pol:
                self.eig[(i, 0)] = np.array(v[0:self.n_bands])
                self.eig[(i, 1)] = np.array(v[self.n_bands:])
            else:
                self.eig[(i, 0)] = np.array(v)

    def get_k_point_weights(self):
        self.read_eig()
        return self.weights

    def get_fermi_level(self):
        self.read_eig()
        return self.e_fermi

    def get_eigenvalues(self, kpt=0, spin=0):
        self.read_eig()
        return self.eig[(kpt, spin)]

    def get_number_of_spins(self):
        self.read_eig()
        if self.spin_pol:
            return 2
        else:
            return 1

    def read_hs(self, filename, is_gamma_only=False, magnus=False):
        """Read the Hamiltonian and overlap matrix from a Siesta
           calculation in sparse format.

        Parameters
        ==========
        filename: str
            The filename should be on the form jobname.HS
        is_gamma_only: {False, True), optional
            Is it a gamma point calculation?
        magnus: bool
            The fileformat was changed by Magnus in Siesta at some
            point around version 2.xxx.
            Use mangus=False, to use the old file format.

        Note
        ====
        Data read in is put in self._dat.

        Examples
        ========
            >>> calc = Siesta()
            >>> calc.read_hs('jobname.HS')
            >>> print calc._dat.fermi_level
            >>> print 'Number of orbitals: %i' % calc._dat.nuotot
        """
        assert not magnus, 'Not implemented; changes by Magnus to file io'
        assert not is_gamma_only, 'Not implemented. Only works for k-points.'
        class Dummy:
            pass
        self._dat = dat = Dummy()
        # Try to read supercell and atom data from a jobname.XV file
        filename_xv = filename[:-2] + 'XV'
        #assert isfile(filename_xv), 'Missing jobname.XV file'
        if isfile(filename_xv):
            print 'Reading supercell and atom data from ' + filename_xv
            fd = open(filename_xv, 'r')
            dat.cell = np.zeros((3, 3)) # Supercell
            for a_vec in dat.cell:
                a_vec[:] = np.array(fd.readline().split()[:3], float)
            dat.rcell = 2 * np.pi * np.linalg.inv(dat.cell.T)
            dat.natoms = int(fd.readline().split()[0])
            dat.symbols = []
            dat.pos_ac = np.zeros((dat.natoms, 3))
            for a in range(dat.natoms):
                line = fd.readline().split()
                dat.symbols.append(chemical_symbols[int(line[1])])
                dat.pos_ac[a, :] = [float(line[i]) for i in range(2, 2 + 3)]
        # Read in the jobname.HS file
        fileobj = file(filename, 'rb')
        fileobj.seek(0)
        dat.fermi_level = float(open(filename[:-3] + '.EIG', 'r').readline())
        dat.is_gammay_only = is_gamma_only
        dat.nuotot, dat.ns, dat.mnh = getrecord(fileobj, 'l')
        nuotot, ns, mnh = dat.nuotot, dat.ns, dat.mnh
        print 'Number of orbitals found: %i' % nuotot
        dat.numh = numh = np.array([getrecord(fileobj, 'l')
                                    for i in range(nuotot)], 'l')
        dat.maxval = max(numh)
        dat.listhptr = listhptr = np.zeros(nuotot, 'l')
        listhptr[0] = 0
        for oi in xrange(1, nuotot):
            listhptr[oi] = listhptr[oi - 1] + numh[oi - 1]
        dat.listh = listh = np.zeros(mnh, 'l')

        print 'Reading sparse info'
        for oi in xrange(nuotot):
            for mi in xrange(numh[oi]):
                listh[listhptr[oi] + mi] = getrecord(fileobj, 'l')

        dat.nuotot_sc = max(listh)
        dat.h_sparse = h_sparse = np.zeros((mnh, ns), float)
        dat.s_sparse = s_sparse = np.zeros(mnh, float)
        print 'Reading H'
        for si in xrange(ns):
            for oi in xrange(nuotot):
                for mi in xrange(numh[oi]):
                    h_sparse[listhptr[oi] + mi, si] = getrecord(fileobj, 'd')
        print 'Reading S'
        for oi in xrange(nuotot):
            for mi in xrange(numh[oi]):
                s_sparse[listhptr[oi] + mi] = getrecord(fileobj, 'd')

        dat.qtot, dat.temperature = getrecord(fileobj, 'd')
        if not is_gamma_only:
            print 'Reading X'
            dat.xij_sparse = xij_sparse = np.zeros([3, mnh], float)
            for oi in xrange(nuotot):
                for mi in xrange(numh[oi]):
                    xij_sparse[:, listhptr[oi] + mi] = getrecord(fileobj, 'd')
        fileobj.close()

    def get_hs(self, kpt=(0, 0, 0), spin=0, remove_pbc=None, kpt_scaled=True):
        """Hamiltonian and overlap matrices for an arbitrary k-point.

        The default values corresponds to the Gamma point for
        spin 0 and periodic boundary conditions.

        Parameters
        ==========
        kpt : {(0, 0, 0), (3,) array_like}, optional
            k-point in scaled or absolute coordinates.
            For the latter the units should be Bohr^-1.
        spin : {0, 1}, optional
            Spin index
        remove_pbc : {None, ({'x', 'y', 'z'}, basis)}, optional
            Use remove_pbc to truncate h and s along a cartesian
            axis.
        basis: {str, dict}
            The basis specification as either a string or a dictionary.
        kpt_scaled : {True, bool}, optional
            Use kpt_scaled=False if `kpt` is in absolute units (Bohr^-1).

        Note
        ====
        read_hs should be called before get_hs gets called.

        Examples
        ========
        >>> calc = Siesta()
        >>> calc.read_hs('jobname.HS')
        >>> h, s = calc.get_hs((0.0, 0.375, 0.375))
        >>> h -= s * calc._dat.fermi_level # fermi level is now at 0.0
        >>> basis = 'szp'
        >>> h, s = calc.get_hs((0.0, 0.375, 0.375), remove_pbc=('x', basis))
        >>> basis = {'Au:'sz}', 'C':'dzp', None:'szp'}
        >>> h, s = calc.get_hs((0.0, 0.375, 0.375), remove_pbc=('x', basis))

        """
        if not hasattr(self, '_dat'):# XXX Crude check if data is avail.
            print 'Please read in data first by calling the method read_hs.'
            return None, None
        dot = np.dot
        dat = self._dat
        kpt_c = np.array(kpt, float)
        if kpt_scaled:
            kpt_c = dot(kpt_c, dat.rcell)

        h_MM = np.zeros((dat.nuotot, dat.nuotot), complex)
        s_MM = np.zeros((dat.nuotot, dat.nuotot), complex)
        h_sparse, s_sparse = dat.h_sparse, dat.s_sparse
        x_sparse = dat.xij_sparse
        numh, listhptr, listh = dat.numh, dat.listhptr, dat.listh
        indxuo = np.mod(np.arange(dat.nuotot_sc), dat.nuotot)

        for iuo in xrange(dat.nuotot):
            for j in range(numh[iuo]):
                ind =  listhptr[iuo] + j
                jo = listh[ind] - 1
                juo = indxuo[jo]
                kx = dot(kpt_c, x_sparse[:, ind])
                phasef = exp(1.0j * kx)
                h_MM[iuo, juo] += phasef * h_sparse[ind, spin]
                s_MM[iuo, juo] += phasef * s_sparse[ind]

        if remove_pbc is not None:
            direction, basis = remove_pbc
            centers_ic = get_bf_centers(dat.symbols, dat.pos_ac, basis)
            d = 'xyz'.index(direction)
            cutoff = dat.cell[d, d] * 0.5
            truncate_along_axis(h_MM, s_MM, direction, centers_ic, cutoff)

        h_MM *= complex(Rydberg)
        return h_MM, s_MM


def getrecord(fileobj, dtype):
    """Used to read in binary files.
    """
    typetosize = {'l':4, 'f':4, 'd':8}# XXX np.int, np.float32, np.float64
    assert dtype in typetosize # XXX
    size = typetosize[dtype]
    record = array.array('l')
    trunk = array.array(dtype)
    record.fromfile(fileobj, 1)
    nofelements = int(record[-1]) / size
    trunk.fromfile(fileobj, nofelements)
    record.fromfile(fileobj, 1)
    data = np.array(trunk, dtype=dtype)
    if len(data)==1:
        data = data[0]
    return data

def truncate_along_axis(h, s, direction, centers_ic, cutoff):
    """Truncate h and s such along a cartesian axis.

    Parameters:

    h: (N, N) ndarray
        Hamiltonian matrix.
    s: (N, N) ndarray
        Overlap matrix.
    direction: {'x', 'y', 'z'}
        Truncate allong a cartesian axis.
    centers_ic: (N, 3) ndarray
        Centers of the basis functions.
    cutoff: float
        The (direction-axis projected) cutoff distance.
    """
    dtype = h.dtype
    ni = len(centers_ic)
    d = 'xyz'.index(direction)
    pos_i = centers_ic[:, d]
    for i in range(ni):
        dpos_i = abs(pos_i - pos_i[i])
        mask_i = (dpos_i < cutoff).astype(dtype)
        h[i, :] *= mask_i
        h[:, i] *= mask_i
        s[i, :] *= mask_i
        s[:, i] *= mask_i

def get_nao(symbol, basis):
    """Number of basis functions.

    Parameters
    ==========
    symbol: str
        The chemical symbol.
    basis: str
        Basis function type.
    """
    ls = valence_config[symbol]
    nao = 0
    zeta = {'s':1, 'd':2, 't':3, 'q':4}
    nzeta = zeta[basis[0]]
    is_pol = 'p' in basis
    for l in ls:
        nao += (2 * l + 1) * nzeta
    if is_pol:
        l_pol = None
        l = -1
        while l_pol is None:
            l += 1
            if not l in ls:
                l_pol = l
        nao += 2 * l_pol + 1
    return nao

def get_bf_centers(symbols, positions, basis):
    """Centers of basis functions.

    Parameters
    ==========
    symbols: str, (N, ) array_like
        chemical symbol for each atom.
    positions: float, (N, 3) array_like
        Positions of the atoms.
    basis: {str,  dict}
        Basis set specification as either a string or a dictionary

    Examples
    ========
    >>> symbols = ['O', 'H']
    >>> positions = [(0, 0, 0), (0, 0, 1)]
    >>> basis = 'sz'
    >>> print get_bf_centers(symbols, positions, basis)
    [[0 0 0]
     [0 0 0]
     [0 0 0]
     [0 0 0]
     [0 0 1]]
    >>> basis = {'H':'dz', None:'sz'}
    >>> print get_bf_centers(symbols, positions, basis)
    [[0 0 0]
     [0 0 0]
     [0 0 0]
     [0 0 0]
     [0 0 1]
     [0 0 1]]

    """
    centers_ic = []
    dict_basis = False
    if type(basis)==dict:
        dict_basis = True
    for symbol, pos in zip(symbols, positions):
        if dict_basis:
            if symbol not in basis:
                bas = basis[None]
            else:
                bas = basis[symbol]
        else:
            bas = basis
        for i in range(get_nao(symbol, bas)):
            centers_ic.append(pos)
    return np.asarray(centers_ic)

def fdfify(key):
    return key.lower().replace('_', '').replace('.', '').replace('-', '')

valence_config = {
    'H': (0,),
    'C': (0, 1),
    'N': (0, 1),
    'O': (0, 1),
    'S': (0, 1),
    'Li': (0,),
    'Na': (0,),
    'Ni': (0, 2),
    'Cu': (0, 2),
    'Pd': (0, 2),
    'Ag': (0, 2),
    'Pt': (0, 2),
    'Au': (0, 2)}

keys_with_units = {
    'paoenergyshift': 'eV',
    'zmunitslength': 'Bohr',
    'zmunitsangle': 'rad',
    'zmforcetollength': 'eV/Ang',
    'zmforcetolangle': 'eV/rad',
    'zmmaxdispllength': 'Ang',
    'zmmaxdisplangle': 'rad',
    'meshcutoff': 'eV',
    'dmenergytolerance': 'eV',
    'electronictemperature': 'eV',
    'oneta': 'eV',
    'onetaalpha': 'eV',
    'onetabeta': 'eV',
    'onrclwf': 'Ang',
    'onchemicalpotentialrc': 'Ang',
    'onchemicalpotentialtemperature': 'eV',
    'mdmaxcgdispl': 'Ang',
    'mdmaxforcetol': 'eV/Ang',
    'mdmaxstresstol': 'eV/Ang**3',
    'mdlengthtimestep': 'fs',
    'mdinitialtemperature': 'eV',
    'mdtargettemperature': 'eV',
    'mdtargetpressure': 'eV/Ang**3',
    'mdnosemass': 'eV*fs**2',
    'mdparrinellorahmanmass': 'eV*fs**2',
    'mdtaurelax': 'fs',
    'mdbulkmodulus': 'eV/Ang**3',
    'mdfcdispl': 'Ang',
    'warningminimumatomicdistance': 'Ang',
    'rcspatial': 'Ang',
    'kgridcutoff': 'Ang',
    'latticeconstant': 'Ang'}
