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# Source code for ase.io.dacapo

    import numpy as np

    from ase.calculators.singlepoint import SinglePointCalculator
    from ase.atom import Atom
    from ase.atoms import Atoms
    from ase.utils import basestring

    def read_dacapo_text(fileobj):
        if isinstance(fileobj, basestring):
            fileobj = open(fileobj)

        lines = fileobj.readlines()
        i = lines.index(' Structure:             A1           A2            A3\n')
        cell = np.array([[float(w) for w in line.split()[2:5]]
                         for line in lines[i + 1:i + 4]]).transpose()
        i = lines.index(' Structure:  >>         Ionic positions/velocities ' +
                        'in cartesian coordinates       <<\n')
        atoms = []
        for line in lines[i + 4:]:
            words = line.split()
            if len(words) != 9:
                break
            Z, x, y, z = words[2:6]
            atoms.append(Atom(int(Z), [float(x), float(y), float(z)]))

        atoms = Atoms(atoms, cell=cell.tolist())

        try:
            i = lines.index(
                ' DFT:  CPU time                           Total energy\n')
        except ValueError:
            pass
        else:
            column = lines[i + 3].split().index('selfcons') - 1
            try:
                i2 = lines.index(' ANALYSIS PART OF CODE\n', i)
            except ValueError:
                pass
            else:
                while i2 > i:
                    if lines[i2].startswith(' DFT:'):
                        break
                    i2 -= 1
                energy = float(lines[i2].split()[column])
                atoms.set_calculator(SinglePointCalculator(atoms, energy=energy))

        return atoms

    def read_dacapo(filename):
        from ase.io.pupynere import NetCDFFile

        nc = NetCDFFile(filename)
        vars = nc.variables

        cell = vars['UnitCell'][-1]
        try:
            magmoms = vars['InitialAtomicMagneticMoment'][:]
        except KeyError:
            magmoms = None
        try:
            tags = vars['AtomTags'][:]
        except KeyError:
            tags = None
        atoms = Atoms(scaled_positions=vars['DynamicAtomPositions'][-1],
                      symbols=[(a + b).strip()
                               for a, b in vars['DynamicAtomSpecies'][:]],
                      cell=cell,
                      magmoms=magmoms,
                      tags=tags,
                      pbc=True)

        try:
            energy = vars['TotalEnergy'][-1]
            force = vars['DynamicAtomForces'][-1]
        except KeyError:
            energy = None
            force = None
        calc = SinglePointCalculator(atoms, energy=energy, forces=force)  ### Fixme magmoms
        atoms.set_calculator(calc)

        return atoms

Documentation v: 3.19.0

Versions
  3.20.0b1 (development)
  3.19.0 (latest stable)