示例#1
0
def check_script_water_sto3g(scheme, do_deriv=True):
    with tmpdir('horton.scripts.test.test_wpart.test_script_water_sto3g_%s' %
                scheme) as dn:
        fn_fchk = 'water_sto3g_hf_g03.fchk'
        copy_files(dn, [fn_fchk])
        if scheme == 'b':
            check_script(
                'horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart %s --debug'
                % (fn_fchk, scheme), dn)
        else:
            write_atomdb_sto3g(dn, do_deriv)
            check_script(
                'horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart %s atoms.h5 --slow'
                % (fn_fchk, scheme), dn)
        fn_h5 = 'water_sto3g_hf_g03_wpart.h5'
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'wpart' in f
            assert abs(f['wpart/charges'][:].sum()) < 1e-2
            assert 'wpart/spin_charges' not in f
            assert 'atom_00000' in f['wpart']
            for s in 'density_decomposition', 'hartree_decomposition':
                assert s in f['wpart']['atom_00000']
                assert 'spline_00000' in f['wpart']['atom_00000'][s]
                assert 'rtransform' in f['wpart']['atom_00000'][s][
                    'spline_00000'].attrs
                assert 'extrapolation' in f['wpart']['atom_00000'][s][
                    'spline_00000'].attrs
                assert 'y' in f['wpart']['atom_00000'][s]['spline_00000']
                assert 'd' in f['wpart']['atom_00000'][s]['spline_00000']
            if scheme != 'b':
                assert 'spline_prodensity' in f['wpart']['atom_00000']
                assert 'spline_prohartree' in f['wpart']['atom_00000']
示例#2
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def check_script_lta(fn_sym, suffix):
    with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' % suffix) as dn:
        # prepare files
        if fn_sym is not None:
            copy_files(dn, [fn_sym])
        write_atomdb_refatoms(dn)

        # write a random cube file
        fn_cube = 'dens.cube'
        sys = write_random_lta_cube(dn, fn_cube)

        # run the script
        fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
        if fn_sym is None:
            check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5' % (fn_cube, fn_h5), dn)
        else:
            check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 --symmetry=%s' % (fn_cube, fn_h5, fn_sym), dn)

        # check the output
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'cpart' in f
            assert 'h_r1' in f['cpart']
            if fn_sym is not None:
                assert 'symmetry' in f['cpart/h_r1']
                assert 'charges' in f['cpart/h_r1/symmetry']
                assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
                for name, ds in f['cpart/h_r1/symmetry'].iteritems():
                    assert ds.shape[0] == sys.extra['symmetry'].natom
                    assert ds.shape[1] == 2
示例#3
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def test_script_input_orca():
    with tmpdir("horton.scripts.test.test_atomdb.test_script_input_orca") as dn:
        fn_template = "template_atomdb_orca.in"
        copy_files(dn, [fn_template])
        check_script("horton-atomdb.py input orca H,13 %s --no-hund" % fn_template, dn)
        fns = [
            "001__h_003_q-02/mult02/atom.in",
            "001__h_003_q-02/mult04/atom.in",
            "001__h_002_q-01/mult01/atom.in",
            "001__h_002_q-01/mult03/atom.in",
            "001__h_001_q+00/mult02/atom.in",
            "013_al_015_q-02/mult04/atom.in",
            "013_al_015_q-02/mult02/atom.in",
            "013_al_014_q-01/mult03/atom.in",
            "013_al_014_q-01/mult05/atom.in",
            "013_al_014_q-01/mult01/atom.in",
            "013_al_013_q+00/mult02/atom.in",
            "013_al_013_q+00/mult04/atom.in",
            "013_al_012_q+01/mult01/atom.in",
            "013_al_012_q+01/mult03/atom.in",
            "013_al_011_q+02/mult02/atom.in",
            "013_al_010_q+03/mult01/atom.in",
            "run_orca.sh",
        ]
        check_files(dn, fns)
示例#4
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def check_script_water_sto3g(scheme, do_deriv=True):
    with tmpdir('horton.scripts.test.test_wpart.test_script_water_sto3g_%s' % scheme) as dn:
        fn_fchk = 'water_sto3g_hf_g03.fchk'
        copy_files(dn, [fn_fchk])
        if scheme == 'b':
            check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart %s --debug' % (fn_fchk, scheme), dn)
        else:
            write_atomdb_sto3g(dn, do_deriv)
            check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart %s atoms.h5 --slow' % (fn_fchk, scheme), dn)
        fn_h5 = 'water_sto3g_hf_g03_wpart.h5'
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'wpart' in f
            assert abs(f['wpart/charges'][:].sum()) < 1e-2
            assert 'wpart/spin_charges' not in f
            assert 'atom_00000' in f['wpart']
            for s in 'density_decomposition', 'hartree_decomposition':
                assert s in f['wpart']['atom_00000']
                assert 'spline_00000' in f['wpart']['atom_00000'][s]
                assert 'rtransform' in f['wpart']['atom_00000'][s]['spline_00000'].attrs
                assert 'extrapolation' in f['wpart']['atom_00000'][s]['spline_00000'].attrs
                assert 'y' in f['wpart']['atom_00000'][s]['spline_00000']
                assert 'd' in f['wpart']['atom_00000'][s]['spline_00000']
            if scheme != 'b':
                assert 'spline_prodensity' in f['wpart']['atom_00000']
                assert 'spline_prohartree' in f['wpart']['atom_00000']
示例#5
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def test_script_input_orca():
    with tmpdir(
            'horton.scripts.test.test_atomdb.test_script_input_orca') as dn:
        fn_template = 'template_atomdb_orca.in'
        copy_files(dn, [fn_template])
        check_script(
            'horton-atomdb.py input orca H,13 %s --no-hund' % fn_template, dn)
        fns = [
            '001__h_003_q-02/mult02/atom.in',
            '001__h_003_q-02/mult04/atom.in',
            '001__h_002_q-01/mult01/atom.in',
            '001__h_002_q-01/mult03/atom.in',
            '001__h_001_q+00/mult02/atom.in',
            '013_al_015_q-02/mult04/atom.in',
            '013_al_015_q-02/mult02/atom.in',
            '013_al_014_q-01/mult03/atom.in',
            '013_al_014_q-01/mult05/atom.in',
            '013_al_014_q-01/mult01/atom.in',
            '013_al_013_q+00/mult02/atom.in',
            '013_al_013_q+00/mult04/atom.in',
            '013_al_012_q+01/mult01/atom.in',
            '013_al_012_q+01/mult03/atom.in',
            '013_al_011_q+02/mult02/atom.in',
            '013_al_010_q+03/mult01/atom.in',
            'run_orca.sh',
        ]
        check_files(dn, fns)
示例#6
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def check_script_lta(fn_sym, suffix):
    with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' % suffix) as dn:
        # prepare files
        if fn_sym is not None:
            copy_files(dn, [fn_sym])
        write_atomdb_refatoms(dn)

        # write a random cube file
        fn_cube = 'dens.cube'
        sys = write_random_lta_cube(dn, fn_cube)

        # run the script
        fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
        if fn_sym is None:
            check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5' % (fn_cube, fn_h5), dn)
        else:
            check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 --symmetry=%s' % (fn_cube, fn_h5, fn_sym), dn)

        # check the output
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'cpart' in f
            assert 'h_r1' in f['cpart']
            if fn_sym is not None:
                assert 'symmetry' in f['cpart/h_r1']
                assert 'charges' in f['cpart/h_r1/symmetry']
                assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
                for name, ds in f['cpart/h_r1/symmetry'].iteritems():
                    assert ds.shape[0] == sys.extra['symmetry'].natom
                    assert ds.shape[1] == 2
示例#7
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def check_script_jbw_coarse(scheme):
    with tmpdir("horton.scripts.test.test_cpart.test_script_jbw_coarse_%s" % scheme) as dn:
        fn_cube = "jbw_coarse_aedens.cube"
        copy_files(dn, [fn_cube])
        write_atomdb_refatoms(dn)
        fn_h5 = "foobar.h5"
        check_script("horton-cpart.py %s foobar.h5:cpart/%s_r1 %s atoms.h5" % (fn_cube, scheme, scheme), dn)
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert "cpart" in f
            assert scheme + "_r1" in f["cpart"]
示例#8
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def check_script_jbw_coarse(scheme):
    with tmpdir('horton.scripts.test.test_cpart.test_script_jbw_coarse_%s' % scheme) as dn:
        fn_cube = 'jbw_coarse_aedens.cube'
        copy_files(dn, [fn_cube])
        write_atomdb_refatoms(dn)
        fn_h5 = 'foobar.h5'
        check_script('horton-cpart.py %s foobar.h5:cpart/%s_r1 %s atoms.h5' % (fn_cube, scheme, scheme), dn)
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'cpart' in f
            assert scheme + '_r1' in f['cpart']
示例#9
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def check_script_jbw_coarse(scheme):
    with tmpdir('horton.scripts.test.test_cpart.test_script_jbw_coarse_%s' % scheme) as dn:
        fn_cube = 'jbw_coarse_aedens.cube'
        copy_files(dn, [fn_cube])
        write_atomdb_refatoms(dn)
        fn_h5 = 'foobar.h5'
        check_script('horton-cpart.py %s foobar.h5:cpart/%s_r1 %s atoms.h5' % (fn_cube, scheme, scheme), dn)
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'cpart' in f
            assert scheme + '_r1' in f['cpart']
示例#10
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def test_scripts_symmetry():
    # Write the cube file to the tmpdir and run scripts
    with tmpdir('horton.scripts.test.test_espfit.test_scripts_symmetry') as dn:
        # prepare files
        sys = write_random_lta_cube(dn, 'esp.cube')
        copy_files(dn, ['lta_gulp.cif'])
        # run scripts
        check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5 --rcut=4 --alpha-scale=0.1', dn)
        check_files(dn, ['esp.h5'])
        check_script('horton-esp-fit.py esp.h5 other.h5 --symmetry esp.cube lta_gulp.cif', dn)
        sys_sym = System.from_file('%s/lta_gulp.cif' % dn)
        with h5.File(os.path.join(dn, 'other.h5')) as f:
            assert 'symmetry' in f
            assert f['symmetry/charges'].shape == (sys_sym.extra['symmetry'].natom, 2)
示例#11
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def check_script_water_sto3g(scheme, do_deriv=True):
    with tmpdir('horton.scripts.test.test_wpart.test_script_water_sto3g_%s' % scheme) as dn:
        fn_fchk = 'water_sto3g_hf_g03.fchk'
        copy_files(dn, [fn_fchk])
        if scheme == 'b':
            check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s --debug' % (fn_fchk, scheme, scheme), dn)
        else:
            write_atomdb_sto3g(dn, do_deriv)
            check_script('horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s atoms.h5' % (fn_fchk, scheme, scheme), dn)
        fn_h5 = 'water_sto3g_hf_g03_wpart.h5'
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'wpart' in f
            assert scheme in f['wpart']
示例#12
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def test_scripts_symmetry():
    # Write the cube file to the tmpdir and run scripts
    with tmpdir('horton.scripts.test.test_espfit.test_scripts_symmetry') as dn:
        # prepare files
        write_random_lta_cube(dn, 'esp.cube')
        copy_files(dn, ['lta_gulp.cif'])
        # run scripts
        check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5 --rcut=4 --alpha-scale=0.1', dn)
        check_files(dn, ['esp.h5'])
        check_script('horton-esp-fit.py esp.h5 other.h5 --symmetry esp.cube lta_gulp.cif', dn)
        mol_sym = IOData.from_file('%s/lta_gulp.cif' % dn)
        with h5.File(os.path.join(dn, 'other.h5')) as f:
            assert 'symmetry' in f
            assert f['symmetry/charges'].shape == (mol_sym.symmetry.natom, 2)
示例#13
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def check_script_ch3_rohf_sto3g(scheme, do_deriv=True):
    with tmpdir('horton.scripts.test.test_wpart.test_script_ch3_rohf_sto3g_%s' % scheme) as dn:
        fn_fchk = 'ch3_rohf_sto3g_g03.fchk'
        copy_files(dn, [fn_fchk])
        if scheme == 'b':
            check_script('horton-wpart.py %s foo.h5:wpart %s --debug' % (fn_fchk, scheme), dn)
        else:
            write_atomdb_sto3g(dn, do_deriv)
            check_script('horton-wpart.py %s foo.h5:wpart %s atoms.h5' % (fn_fchk, scheme), dn)
        fn_h5 = 'foo.h5'
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'wpart' in f
            assert abs(f['wpart/charges'][:].sum()) < 1e-2
            assert abs(f['wpart/spin_charges'][:].sum() - 1) < 1e-2
示例#14
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def check_script_input_gaussian(binary):
    with tmpdir('horton.scripts.test.test_atomdb.test_script_input_%s' % binary) as dn:
        fn_template = 'template_atomdb_gaussian.in'
        fn_basis1 = 'include_atomdb_gaussian_basis.001_000_00'
        fn_basis8 = 'include_atomdb_gaussian_basis.008_000_00'
        copy_files(dn, [fn_template, fn_basis1, fn_basis8])
        check_script('horton-atomdb.py input %s 1,O %s' % (binary, fn_template), dn)
        fns = [
            '001__h_003_q-02/mult02/atom.in', '001__h_002_q-01/mult01/atom.in',
            '001__h_001_q+00/mult02/atom.in', '008__o_010_q-02/mult01/atom.in',
            '008__o_009_q-01/mult02/atom.in', '008__o_008_q+00/mult03/atom.in',
            '008__o_007_q+01/mult04/atom.in', '008__o_006_q+02/mult03/atom.in',
            '008__o_005_q+03/mult02/atom.in',
            'run_%s.sh' % binary,
        ]
        check_files(dn, fns)
示例#15
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def test_script_input_cp2k():
    with tmpdir('horton.scripts.test.test_atomdb.test_script_input_cp2k') as dn:
        fn_template = 'template_atomdb_cp2k.in'
        fn_valence = 'include_atomdb_cp2k_valence.inc'
        fn_ppot = 'include_atomdb_cp2k_ppot.inc'
        copy_files(dn, [fn_template, fn_valence, fn_ppot])
        check_script('horton-atomdb.py input cp2k Ca,F %s' % fn_template, dn)
        fns = [
            '020_ca_021_q-01/mult02/atom.in', '020_ca_020_q+00/mult01/atom.in',
            '020_ca_019_q+01/mult02/atom.in', '020_ca_018_q+02/mult01/atom.in',
            '020_ca_017_q+03/mult02/atom.in', '009__f_010_q-01/mult01/atom.in',
            '009__f_009_q+00/mult02/atom.in', '009__f_008_q+01/mult03/atom.in',
            '009__f_007_q+02/mult04/atom.in',
            'run_cp2k.sh',
        ]
        check_files(dn, fns)
示例#16
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def check_script_input_gaussian(binary):
    with tmpdir('horton.scripts.test.test_atomdb.test_script_input_%s' % binary) as dn:
        fn_template = 'template_atomdb_gaussian.in'
        fn_basis1 = 'include_atomdb_gaussian_basis.001_000_00'
        fn_basis8 = 'include_atomdb_gaussian_basis.008_000_00'
        copy_files(dn, [fn_template, fn_basis1, fn_basis8])
        check_script('horton-atomdb.py input %s 1,O %s' % (binary, fn_template), dn)
        fns = [
            '001__h_003_q-02/mult02/atom.in', '001__h_002_q-01/mult01/atom.in',
            '001__h_001_q+00/mult02/atom.in', '008__o_010_q-02/mult01/atom.in',
            '008__o_009_q-01/mult02/atom.in', '008__o_008_q+00/mult03/atom.in',
            '008__o_007_q+01/mult04/atom.in', '008__o_006_q+02/mult03/atom.in',
            '008__o_005_q+03/mult02/atom.in',
            'run_%s.sh' % binary,
        ]
        check_files(dn, fns)
示例#17
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def test_script_input_cp2k():
    with tmpdir('horton.scripts.test.test_atomdb.test_script_input_cp2k') as dn:
        fn_template = 'template_atomdb_cp2k.in'
        fn_valence = 'include_atomdb_cp2k_valence.inc'
        fn_ppot = 'include_atomdb_cp2k_ppot.inc'
        copy_files(dn, [fn_template, fn_valence, fn_ppot])
        check_script('horton-atomdb.py input cp2k Ca,F %s' % fn_template, dn)
        fns = [
            '020_ca_021_q-01/mult02/atom.in', '020_ca_020_q+00/mult01/atom.in',
            '020_ca_019_q+01/mult02/atom.in', '020_ca_018_q+02/mult01/atom.in',
            '020_ca_017_q+03/mult02/atom.in', '009__f_010_q-01/mult01/atom.in',
            '009__f_009_q+00/mult02/atom.in', '009__f_008_q+01/mult03/atom.in',
            '009__f_007_q+02/mult04/atom.in',
            'run_cp2k.sh',
        ]
        check_files(dn, fns)
示例#18
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def test_script_input_orca():
    with tmpdir('horton.scripts.test.test_atomdb.test_script_input_orca') as dn:
        fn_template = 'template_atomdb_orca.in'
        copy_files(dn, [fn_template])
        check_script('horton-atomdb.py input orca H,13 %s --no-hund' % fn_template, dn)
        fns = [
            '001__h_003_q-02/mult02/atom.in', '001__h_003_q-02/mult04/atom.in',
            '001__h_002_q-01/mult01/atom.in', '001__h_002_q-01/mult03/atom.in',
            '001__h_001_q+00/mult02/atom.in', '013_al_015_q-02/mult04/atom.in',
            '013_al_015_q-02/mult02/atom.in', '013_al_014_q-01/mult03/atom.in',
            '013_al_014_q-01/mult05/atom.in', '013_al_014_q-01/mult01/atom.in',
            '013_al_013_q+00/mult02/atom.in', '013_al_013_q+00/mult04/atom.in',
            '013_al_012_q+01/mult01/atom.in', '013_al_012_q+01/mult03/atom.in',
            '013_al_011_q+02/mult02/atom.in', '013_al_010_q+03/mult01/atom.in',
            'run_orca.sh',
        ]
        check_files(dn, fns)
示例#19
0
def check_script_lta(fn_sym, suffix, do_spin=False):
    with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' %
                suffix) as dn:
        # prepare files
        if fn_sym is not None:
            copy_files(dn, [fn_sym])
        write_atomdb_refatoms(dn)

        # write a random cube file
        fn_cube = 'dens.cube'
        mol = write_random_lta_cube(dn, fn_cube)

        # if needed, write a random spin cube file
        if do_spin:
            fn_spin = 'spin.cube'
            molspin = write_random_lta_cube(dn, fn_spin)

        # run the script
        fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
        opts = ''
        if not (fn_sym is None):
            opts += ' --symmetry=%s' % fn_sym
        if do_spin:
            opts += ' --spindens=%s' % fn_spin
        check_script(
            'horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 %s' %
            (fn_cube, fn_h5, opts), dn)

        # check the output
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'cpart' in f
            assert 'h_r1' in f['cpart']
            assert 'charges' in f['cpart/h_r1']
            if do_spin:
                assert 'spin_charges' in f['cpart/h_r1']
            if fn_sym is not None:
                assert 'symmetry' in f['cpart/h_r1']
                assert 'charges' in f['cpart/h_r1/symmetry']
                if do_spin:
                    assert 'spin_charges' in f['cpart/h_r1/symmetry']
                assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
                for name, ds in f['cpart/h_r1/symmetry'].iteritems():
                    assert ds.shape[0] == mol.symmetry.natom
                    assert ds.shape[1] == 2
示例#20
0
def check_script_water_sto3g(scheme, do_deriv=True):
    with tmpdir('horton.scripts.test.test_wpart.test_script_water_sto3g_%s' %
                scheme) as dn:
        fn_fchk = 'water_sto3g_hf_g03.fchk'
        copy_files(dn, [fn_fchk])
        if scheme == 'b':
            check_script(
                'horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s --debug'
                % (fn_fchk, scheme, scheme), dn)
        else:
            write_atomdb_sto3g(dn, do_deriv)
            check_script(
                'horton-wpart.py %s water_sto3g_hf_g03_wpart.h5:wpart/%s %s atoms.h5'
                % (fn_fchk, scheme, scheme), dn)
        fn_h5 = 'water_sto3g_hf_g03_wpart.h5'
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'wpart' in f
            assert scheme in f['wpart']
示例#21
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def check_script_lta(fn_sym, suffix, do_spin=False):
    with tmpdir('horton.scripts.test.test_cpart.test_script_lta_coarse_h_%s' % suffix) as dn:
        # prepare files
        if fn_sym is not None:
            copy_files(dn, [fn_sym])
        write_atomdb_refatoms(dn)

        # write a random cube file
        fn_cube = 'dens.cube'
        mol = write_random_lta_cube(dn, fn_cube)

        # if needed, write a random spin cube file
        if do_spin:
            fn_spin = 'spin.cube'
            molspin = write_random_lta_cube(dn, fn_spin)

        # run the script
        fn_h5 = '%s_cpart.h5' % fn_cube[:-5]
        opts = ''
        if not (fn_sym is None):
            opts += ' --symmetry=%s' % fn_sym
        if do_spin:
            opts += ' --spindens=%s' % fn_spin
        check_script('horton-cpart.py %s %s:cpart/h_r1 h atoms.h5 %s' % (fn_cube, fn_h5, opts), dn)

        # check the output
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'cpart' in f
            assert 'h_r1' in f['cpart']
            assert 'charges' in f['cpart/h_r1']
            if do_spin:
                assert 'spin_charges' in f['cpart/h_r1']
            if fn_sym is not None:
                assert 'symmetry' in f['cpart/h_r1']
                assert 'charges' in f['cpart/h_r1/symmetry']
                if do_spin:
                    assert 'spin_charges' in f['cpart/h_r1/symmetry']
                assert 'cartesian_multipoles' in f['cpart/h_r1/symmetry']
                for name, ds in f['cpart/h_r1/symmetry'].iteritems():
                    assert ds.shape[0] == mol.symmetry.natom
                    assert ds.shape[1] == 2
示例#22
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def test_script_input_cp2k():
    with tmpdir("horton.scripts.test.test_atomdb.test_script_input_cp2k") as dn:
        fn_template = "template_atomdb_cp2k.in"
        fn_valence = "include_atomdb_cp2k_valence.inc"
        fn_ppot = "include_atomdb_cp2k_ppot.inc"
        copy_files(dn, [fn_template, fn_valence, fn_ppot])
        check_script("horton-atomdb.py input cp2k Ca,F %s" % fn_template, dn)
        fns = [
            "020_ca_021_q-01/mult02/atom.in",
            "020_ca_020_q+00/mult01/atom.in",
            "020_ca_019_q+01/mult02/atom.in",
            "020_ca_018_q+02/mult01/atom.in",
            "020_ca_017_q+03/mult02/atom.in",
            "009__f_010_q-01/mult01/atom.in",
            "009__f_009_q+00/mult02/atom.in",
            "009__f_008_q+01/mult03/atom.in",
            "009__f_007_q+02/mult04/atom.in",
            "run_cp2k.sh",
        ]
        check_files(dn, fns)
示例#23
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def check_script_ch3_rohf_sto3g(scheme, do_deriv=True):
    with tmpdir(
            'horton.scripts.test.test_wpart.test_script_ch3_rohf_sto3g_%s' %
            scheme) as dn:
        fn_fchk = 'ch3_rohf_sto3g_g03.fchk'
        copy_files(dn, [fn_fchk])
        if scheme == 'b':
            check_script(
                'horton-wpart.py %s foo.h5:wpart %s --debug' %
                (fn_fchk, scheme), dn)
        else:
            write_atomdb_sto3g(dn, do_deriv)
            check_script(
                'horton-wpart.py %s foo.h5:wpart %s atoms.h5' %
                (fn_fchk, scheme), dn)
        fn_h5 = 'foo.h5'
        check_files(dn, [fn_h5])
        with h5.File(os.path.join(dn, fn_h5)) as f:
            assert 'wpart' in f
            assert abs(f['wpart/charges'][:].sum()) < 1e-2
            assert abs(f['wpart/spin_charges'][:].sum() - 1) < 1e-2
示例#24
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def test_scripts():
    with tmpdir("horton.scripts.test.test_convert.test_scripts") as dn:
        fn_fchk = "water_sto3g_hf_g03.fchk"
        copy_files(dn, [fn_fchk])
        check_script("horton-convert.py %s test.xyz" % fn_fchk, dn)
示例#25
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def test_script():
    with tmpdir('horton.scripts.test.test_cubehead.test_script') as dn:
        fn_fchk = 'water_sto3g_hf_g03.fchk'
        copy_files(dn, [fn_fchk])
        check_script('horton-cubehead.py %s cubehead.txt' % fn_fchk, dn)
        check_files(dn, ['cubehead.txt'])
示例#26
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def test_scripts():
    with tmpdir('horton.scripts.test.test_convert.test_scripts') as dn:
        fn_fchk = 'water_sto3g_hf_g03.fchk'
        copy_files(dn, [fn_fchk])
        check_script('horton-convert.py %s test.xyz' % fn_fchk, dn)
示例#27
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def test_scripts():
    with tmpdir('horton.scripts.test.test_convert.test_scripts') as dn:
        fn_fchk = 'water_sto3g_hf_g03.fchk'
        copy_files(dn, [fn_fchk])
        check_script('horton-convert.py %s test.xyz' % fn_fchk, dn)