Python AbiFiles Examples

Example #1

def test_abinit_abifiles():
    """
    Tests (pychemia.code.abinit) [abifiles]                      :
    """
    if pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC:
        from pychemia.code.abinit import AbiFiles

        filename = "pychemia/test/data/abinit_01/abinit.files"
        abf = AbiFiles(filename)
        assert abf.filename == "abinit.files"
        assert abf.get_input_filename() == 'pychemia/test/data/abinit_01/abinit.in'

Example #2

File: test_code_abinit.py Project: wwmeng/PyChemia

def test_abinit_abifiles():
    """
    Test (pychemia.code.abinit) [abifiles]                      :
    """

    from pychemia.code.abinit import AbiFiles

    filename = "tests/data/abinit_01/abinit.files"
    abf = AbiFiles(filename)
    assert abf.filename == "abinit.files"
    assert abf.get_input_filename() == 'tests/data/abinit_01/abinit.in'

Example #3

File: test_code_abinit.py Project: MaterialsDiscovery/PyChemia

def test_abinit_abifiles():
    """
    Tests (pychemia.code.abinit) [abifiles]                      :
    """

    from pychemia.code.abinit import AbiFiles

    filename = "tests/data/abinit_01/abinit.files"
    abf = AbiFiles(filename)
    assert abf.filename == "abinit.files"
    assert abf.get_input_filename() == 'tests/data/abinit_01/abinit.in'

Example #4

File: test_code_abinit.py Project: wwmeng/PyChemia

def test_abinit_input():
    """
    Test (pychemia.code.abinit) [input]                         :
    """
    from pychemia.code.abinit import AbiFiles, AbinitInput

    filename = "tests/data/abinit_01/abinit.files"
    abf = AbiFiles(filename)
    inp = AbinitInput(abf.get_input_filename())
    print(inp)
    print(len(inp))
    assert len(inp) == 31
    assert inp.get_value('ecut') == 10
    assert len(inp.get_dtsets_keys()) == 12
    assert inp.get_value('ntime', 41) == 10
    assert inp.get_value('acell', 41)[0] == 14

Example #5

File: test_code_abinit.py Project: MaterialsDiscovery/PyChemia

def test_abinit_input():
    """
    Tests (pychemia.code.abinit) [input]                         :
    """
    from pychemia.code.abinit import AbiFiles, AbinitInput

    filename = "tests/data/abinit_01/abinit.files"
    abf = AbiFiles(filename)
    inp = AbinitInput(abf.get_input_filename())
    print(inp)
    print(len(inp))
    assert len(inp) == 31
    assert inp.get_value('ecut') == 10
    assert len(inp.get_dtsets_keys()) == 12
    assert inp.get_value('ntime', 41) == 10
    assert inp.get_value('acell', 41)[0] == 14

Example #6

def test_abinit_input():
    """
    Tests (pychemia.code.abinit) [input]                         :
    """
    if pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC:
        from pychemia.code.abinit import AbiFiles, InputVariables

        filename = "pychemia/test/data/abinit_01/abinit.files"
        abf = AbiFiles(filename)
        inp = InputVariables(abf)
        print(inp)
        print(len(inp))
        assert len(inp) == 31
        assert inp.get_value('ecut') == 10
        assert len(inp.get_dtsets_keys()) == 12
        assert inp.get_value('ntime', 41) == 10
        assert inp.get_value('acell', 41)[0] == 14

Example #7

File: abi_plot_bonds.py Project: zeledon14/PyChemia

if __name__ == '__main__':

    narg = len(sys.argv) - 1

    list_abifile = []
    list_idtset = []
    dtsetall = False
    for i in range(narg):
        filename = sys.argv[i + 1]
        if ':' in filename:
            idtset = filename.split(':')[1]
            if idtset == 'all':
                dtsetall = True
            else:
                list_idtset.append(idtset)
            filename = filename.split(':')[0]

        abifile = AbiFiles(filename)
        if dtsetall:
            av = InputVariables(abifile.get_input_filename())
            keys = av.get_dtsets_keys()
            for j in keys:
                list_abifile.append(abifile)
                list_idtset.append(str(j))

        else:
            list_abifile.append(abifile)

    plot_bonds(list_abifile, list_idtset)

Example #8

File: abi_plot_bonds.py Project: wwmeng/PyChemia

if __name__ == '__main__':

    narg = len(sys.argv) - 1

    list_abifile = []
    list_idtset = []
    dtsetall = False
    for i in range(narg):
        filename = sys.argv[i + 1]
        if ':' in filename:
            idtset = filename.split(':')[1]
            if idtset == 'all':
                dtsetall = True
            else:
                list_idtset.append(idtset)
            filename = filename.split(':')[0]

        abifile = AbiFiles(filename)
        if dtsetall:
            av = AbinitInput(abifile.get_input_filename())
            keys = av.get_dtsets_keys()
            #            print(keys)
            for j in keys:
                list_abifile.append(abifile)
                list_idtset.append(str(j))

        else:
            list_abifile.append(abifile)

    plot_bonds(list_abifile, list_idtset)

Example #9

    else:
        ekin = None

    # Getting Labels of atoms
    labels = [av.atom_name(i) for i in range(av.get_value('natom', dataset))]
    znucl = av.get_value('znucl', idtset=dataset)
    typat = av.get_value('typat', idtset=dataset)

    bonds = compute_bonds(typat, xcart, znucl)
    # natom = len(xcart[0])
    # ComputeAngles(bonds,natom)

    plot_history_energy(etotal, ekin, fcart, labels, bonds, filep)


if __name__ == '__main__':

    # Script starts from here
    if len(sys.argv) < 2:
        print('No option specified.')
        sys.exit()

    filename = sys.argv[1]
    if len(sys.argv) == 3:
        idtset = int(sys.argv[2])
    else:
        idtset = ""

    abifile = AbiFiles(filename)
    plot_history(abifile, idtset)

Example #10

File: abi_plot_bonds.py Project: MaterialsDiscovery/PyChemia

if __name__ == '__main__':

    narg = len(sys.argv) - 1

    list_abifile = []
    list_idtset = []
    dtsetall = False
    for i in range(narg):
        filename = sys.argv[i + 1]
        if ':' in filename:
            idtset = filename.split(':')[1]
            if idtset == 'all':
                dtsetall = True
            else:
                list_idtset.append(idtset)
            filename = filename.split(':')[0]

        abifile = AbiFiles(filename)
        if dtsetall:
            av = AbinitInput(abifile.get_input_filename())
            keys = av.get_dtsets_keys()
#            print(keys)
            for j in keys:
                list_abifile.append(abifile)
                list_idtset.append(str(j))

        else:
            list_abifile.append(abifile)

    plot_bonds(list_abifile, list_idtset)