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
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
def test_script_convert_g03():
with tmpdir("horton.scripts.test.test_atomdb.test_script_convert_g03") as dn:
copy_atom_output("atom_001_001_hf_sto3g.fchk", 1, 0, 2, dn, "atom.fchk")
copy_atom_output("atom_001_002_hf_sto3g.fchk", 1, -1, 1, dn, "atom.fchk")
copy_atom_output("atom_008_007_hf_sto3g.fchk", 8, +1, 4, dn, "atom.fchk")
copy_atom_output("atom_008_008_hf_sto3g.fchk", 8, 0, 3, dn, "atom.fchk")
copy_atom_output("atom_008_009_hf_sto3g.fchk", 8, -1, 2, dn, "atom.fchk")
make_fake_run_script("g03", dn)
check_script("horton-atomdb.py convert", dn)
# check presence of files
fns = [
"atoms.h5",
"dens_001__h.png",
"rdens_001__h.png",
"fukui_001__h.png",
"rfukui_001__h.png",
"dens_008__o.png",
"rdens_008__o.png",
"fukui_008__o.png",
"rfukui_008__o.png",
]
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, "atoms.h5"))
assert padb.get_numbers() == [1, 8]
assert padb.get_charges(1) == [0, -1]
assert padb.get_charges(8) == [+1, 0, -1]
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']
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']
def test_script_convert_g03():
with tmpdir(
'horton.scripts.test.test_atomdb.test_script_convert_g03') as dn:
copy_atom_output('atom_001_001_hf_sto3g.fchk', 1, 0, 2, dn,
'atom.fchk')
copy_atom_output('atom_001_002_hf_sto3g.fchk', 1, -1, 1, dn,
'atom.fchk')
copy_atom_output('atom_008_007_hf_sto3g.fchk', 8, +1, 4, dn,
'atom.fchk')
copy_atom_output('atom_008_008_hf_sto3g.fchk', 8, 0, 3, dn,
'atom.fchk')
copy_atom_output('atom_008_009_hf_sto3g.fchk', 8, -1, 2, dn,
'atom.fchk')
make_fake_run_script('g03', dn)
check_script('horton-atomdb.py convert', dn)
# check presence of files
fns = [
'atoms.h5',
'dens_001__h.png',
'rdens_001__h.png',
'fukui_001__h.png',
'rfukui_001__h.png',
'dens_008__o.png',
'rdens_008__o.png',
'fukui_008__o.png',
'rfukui_008__o.png',
]
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [1, 8]
assert padb.get_charges(1) == [0, -1]
assert padb.get_charges(8) == [+1, 0, -1]
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)
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)
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']
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']
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"]
def test_script_convert_g09():
with tmpdir('horton.scripts.test.test_atomdb.test_script_convert_g09') as dn:
copy_atom_output('atom_014_013_hf_lan.fchk', 14, +1, 2, dn, 'atom.fchk')
make_fake_run_script('g09', dn)
check_script('horton-atomdb.py convert --grid medium', dn)
# check presence of files
fns = ['atoms.h5', 'dens_014_si.png', 'rdens_014_si.png', 'fukui_014_si.png', 'rfukui_014_si.png']
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [14]
assert padb.get_charges(14) == [+1]
assert padb.get_rgrid(14).size == 49
def test_script_convert_g09():
with tmpdir('horton.scripts.test.test_atomdb.test_script_convert_g09') as dn:
copy_atom_output('atom_014_013_hf_lan.fchk', 14, +1, 2, dn, 'atom.fchk')
make_fake_run_script('g09', dn)
check_script('horton-atomdb.py convert --grid medium', dn)
# check presence of files
fns = ['atoms.h5', 'dens_014_si.png', 'rdens_014_si.png', 'fukui_014_si.png', 'rfukui_014_si.png']
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [14]
assert padb.get_charges(14) == [+1]
assert padb.get_rgrid(14).size == 49
def test_script_convert_g09():
with tmpdir("horton.scripts.test.test_atomdb.test_script_convert_g09") as dn:
copy_atom_output("atom_014_013_hf_lan.fchk", 14, +1, 2, dn, "atom.fchk")
make_fake_run_script("g09", dn)
check_script("horton-atomdb.py convert --grid medium", dn)
# check presence of files
fns = ["atoms.h5", "dens_014_si.png", "rdens_014_si.png", "fukui_014_si.png", "rfukui_014_si.png"]
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, "atoms.h5"))
assert padb.get_numbers() == [14]
assert padb.get_charges(14) == [+1]
assert padb.get_rgrid(14).size == 49
def test_script():
with tmpdir('horton.scripts.test.test_hdf2csv.test_script') as dn:
with h5.File('%s/test.h5' % dn) as f:
fill_hdf5(f)
check_script('horton-hdf2csv.py test.h5:/ test.csv', dn)
check_files(dn, ['test.h5', 'test.csv'])
with open('%s/test.csv' % dn) as f:
r = csv.reader(f)
rows = [row for row in r]
with h5.File('%s/test.h5' % dn) as f:
assert rows[0][0] == 'Converted data from test.h5:/'
assert len(rows[1]) == 0
assert len(rows[2]) == 2
assert rows[2][0] == 'Dataset'
assert rows[2][1] == 'bar/foo'
assert len(rows[3]) == 3
assert rows[3][0] == 'Shape'
assert rows[3][1] == '5'
assert rows[3][2] == '2'
assert float(rows[4][0]) == f['bar/foo'][0,0]
assert float(rows[8][1]) == f['bar/foo'][4,1]
assert len(rows[9]) == 0
assert len(rows[22]) == 2
assert rows[22][0] == 'Dataset'
assert rows[22][1] == 'test2'
assert len(rows[23]) == 3
assert rows[23][0] == 'Shape'
assert rows[23][1] == '5'
assert rows[23][2] == '2'
assert float(rows[24][0]) == f['test2'][0,0]
assert float(rows[28][1]) == f['test2'][4,1]
assert rows[29] == []
assert len(rows[30]) == 2
assert rows[30][0] == 'Dataset'
assert rows[30][1] == 'zzz'
assert len(rows[31]) == 4
assert rows[31][0] == 'Shape'
assert rows[31][1] == '5'
assert rows[31][2] == '2'
assert rows[31][3] == '5'
assert float(rows[32][0]) == f['zzz'][0,0,0]
assert float(rows[32][1]) == f['zzz'][0,1,0]
assert rows[32][2] == ''
assert float(rows[32][3]) == f['zzz'][0,0,1]
assert float(rows[32][4]) == f['zzz'][0,1,1]
assert rows[32][5] == ''
assert len(rows[32]) == 3*5-1
assert float(rows[36][1]) == f['zzz'][4,1,0]
assert float(rows[36][3*5-2]) == f['zzz'][4,1,4]
assert rows[-1] == []
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)
def test_script():
with tmpdir("horton.scripts.test.test_hdf2csv.test_script") as dn:
with h5.File("%s/test.h5" % dn) as f:
fill_hdf5(f)
check_script("horton-hdf2csv.py test.h5:/ test.csv", dn)
check_files(dn, ["test.h5", "test.csv"])
with open("%s/test.csv" % dn) as f:
r = csv.reader(f)
rows = [row for row in r]
with h5.File("%s/test.h5" % dn) as f:
assert rows[0][0] == "Converted data from test.h5:/"
assert len(rows[1]) == 0
assert len(rows[2]) == 2
assert rows[2][0] == "Dataset"
assert rows[2][1] == "bar/foo"
assert len(rows[3]) == 3
assert rows[3][0] == "Shape"
assert rows[3][1] == "5"
assert rows[3][2] == "2"
assert float(rows[4][0]) == f["bar/foo"][0, 0]
assert float(rows[8][1]) == f["bar/foo"][4, 1]
assert len(rows[9]) == 0
assert len(rows[22]) == 2
assert rows[22][0] == "Dataset"
assert rows[22][1] == "test2"
assert len(rows[23]) == 3
assert rows[23][0] == "Shape"
assert rows[23][1] == "5"
assert rows[23][2] == "2"
assert float(rows[24][0]) == f["test2"][0, 0]
assert float(rows[28][1]) == f["test2"][4, 1]
assert rows[29] == []
assert len(rows[30]) == 2
assert rows[30][0] == "Dataset"
assert rows[30][1] == "zzz"
assert len(rows[31]) == 4
assert rows[31][0] == "Shape"
assert rows[31][1] == "5"
assert rows[31][2] == "2"
assert rows[31][3] == "5"
assert float(rows[32][0]) == f["zzz"][0, 0, 0]
assert float(rows[32][1]) == f["zzz"][0, 1, 0]
assert rows[32][2] == ""
assert float(rows[32][3]) == f["zzz"][0, 0, 1]
assert float(rows[32][4]) == f["zzz"][0, 1, 1]
assert rows[32][5] == ""
assert len(rows[32]) == 3 * 5 - 1
assert float(rows[36][1]) == f["zzz"][4, 1, 0]
assert float(rows[36][3 * 5 - 2]) == f["zzz"][4, 1, 4]
assert rows[-1] == []
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)
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']
def test_script():
with tmpdir('horton.scripts.test.test_hdf2csv.test_script') as dn:
with h5.File('%s/test.h5' % dn) as f:
fill_hdf5(f)
check_script('horton-hdf2csv.py test.h5:/ test.csv', dn)
check_files(dn, ['test.h5', 'test.csv'])
with open('%s/test.csv' % dn) as f:
r = csv.reader(f)
rows = [row for row in r]
with h5.File('%s/test.h5' % dn) as f:
assert rows[0][0] == 'Converted data from test.h5:/'
assert len(rows[1]) == 0
assert len(rows[2]) == 2
assert rows[2][0] == 'Dataset'
assert rows[2][1] == 'bar/foo'
assert len(rows[3]) == 3
assert rows[3][0] == 'Shape'
assert rows[3][1] == '5'
assert rows[3][2] == '2'
assert float(rows[4][0]) == f['bar/foo'][0,0]
assert float(rows[8][1]) == f['bar/foo'][4,1]
assert len(rows[9]) == 0
assert len(rows[22]) == 2
assert rows[22][0] == 'Dataset'
assert rows[22][1] == 'test2'
assert len(rows[23]) == 3
assert rows[23][0] == 'Shape'
assert rows[23][1] == '5'
assert rows[23][2] == '2'
assert float(rows[24][0]) == f['test2'][0,0]
assert float(rows[28][1]) == f['test2'][4,1]
assert rows[29] == []
assert len(rows[30]) == 2
assert rows[30][0] == 'Dataset'
assert rows[30][1] == 'zzz'
assert len(rows[31]) == 4
assert rows[31][0] == 'Shape'
assert rows[31][1] == '5'
assert rows[31][2] == '2'
assert rows[31][3] == '5'
assert float(rows[32][0]) == f['zzz'][0,0,0]
assert float(rows[32][1]) == f['zzz'][0,1,0]
assert rows[32][2] == ''
assert float(rows[32][3]) == f['zzz'][0,0,1]
assert float(rows[32][4]) == f['zzz'][0,1,1]
assert rows[32][5] == ''
assert len(rows[32]) == 3*5-1
assert float(rows[36][1]) == f['zzz'][4,1,0]
assert float(rows[36][3*5-2]) == f['zzz'][4,1,4]
assert rows[-1] == []
def test_plot_atoms():
padb = ProAtomDB.from_refatoms(numbers=[8, 1], max_cation=1, max_anion=1)
with tmpdir("horton.scripts.test.test_atomdb.test_plot_atoms") as dn:
plot_atoms(padb, dn)
fns = [
"dens_001__h.png",
"rdens_001__h.png",
"fukui_001__h.png",
"rfukui_001__h.png",
"dens_008__o.png",
"rdens_008__o.png",
"fukui_008__o.png",
"rfukui_008__o.png",
]
check_files(dn, fns)
def test_plot_atoms():
padb = ProAtomDB.from_refatoms(numbers=[8, 1], max_cation=1, max_anion=1)
with tmpdir('horton.scripts.test.test_atomdb.test_plot_atoms') as dn:
plot_atoms(padb, dn)
fns = [
'dens_001__h.png',
'rdens_001__h.png',
'fukui_001__h.png',
'rfukui_001__h.png',
'dens_008__o.png',
'rdens_008__o.png',
'fukui_008__o.png',
'rfukui_008__o.png',
]
check_files(dn, fns)
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
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)
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)
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)
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)
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)
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
def test_script_convert_cp2k():
with tmpdir('horton.scripts.test.test_atomdb.test_script_convert_cp2k') as dn:
copy_atom_output('atom_op2.cp2k.out', 8, +2, 3, dn, 'atom.cp2k.out')
copy_atom_output('atom_op1.cp2k.out', 8, +1, 4, dn, 'atom.cp2k.out')
copy_atom_output('atom_o.cp2k.out', 8, 0, 2, dn, 'atom.cp2k.out')
copy_atom_output('atom_om1.cp2k.out', 8, -1, 1, dn, 'atom.cp2k.out')
copy_atom_output('atom_om2.cp2k.out', 8, -2, 0, dn, 'atom.cp2k.out')
make_fake_run_script('cp2k', dn)
check_script('horton-atomdb.py convert', dn)
# check presence of files
fns = ['atoms.h5', 'dens_008__o.png', 'rdens_008__o.png', 'fukui_008__o.png', 'rfukui_008__o.png']
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [8]
assert padb.get_charges(8) == [+2, +1, 0, -1, -2]
assert not padb.get_record(8, -2).safe
assert padb.get_rgrid(8).size == 71
def test_script_convert_cp2k():
with tmpdir('horton.scripts.test.test_atomdb.test_script_convert_cp2k') as dn:
copy_atom_output('atom_op2.cp2k.out', 8, +2, 3, dn, 'atom.cp2k.out')
copy_atom_output('atom_op1.cp2k.out', 8, +1, 4, dn, 'atom.cp2k.out')
copy_atom_output('atom_o.cp2k.out', 8, 0, 2, dn, 'atom.cp2k.out')
copy_atom_output('atom_om1.cp2k.out', 8, -1, 1, dn, 'atom.cp2k.out')
copy_atom_output('atom_om2.cp2k.out', 8, -2, 0, dn, 'atom.cp2k.out')
make_fake_run_script('cp2k', dn)
check_script('horton-atomdb.py convert', dn)
# check presence of files
fns = ['atoms.h5', 'dens_008__o.png', 'rdens_008__o.png', 'fukui_008__o.png', 'rfukui_008__o.png']
check_files(dn, fns)
# load proatomdb file and check some contents
padb = ProAtomDB.from_file(os.path.join(dn, 'atoms.h5'))
assert padb.get_numbers() == [8]
assert padb.get_charges(8) == [+2, +1, 0, -1, -2]
assert not padb.get_record(8, -2).safe
assert padb.get_rgrid(8).size == 71
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']
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
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)
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
def test_scripts():
# Generate some random system with random esp data
natom = 5
numbers = np.random.randint(1, 20, natom)
coordinates = np.random.uniform(0, 10, (natom, 3))
origin = np.zeros(3, float)
grid_rvecs = np.identity(3, float)*1.0
shape = np.array([10, 10, 10])
pbc = np.ones(3, int)
ugrid = UniformGrid(origin, grid_rvecs, shape, pbc)
esp_cube_data = np.random.uniform(-1, 1, shape)
rho_cube_data = np.random.uniform(-1, 1, shape)
sys_esp = System(coordinates, numbers, grid=ugrid, extra={'cube_data': esp_cube_data})
sys_rho = System(coordinates, numbers, grid=ugrid, extra={'cube_data': rho_cube_data})
# Write the cube file to the tmpdir and run scripts (run 1)
with tmpdir('horton.scripts.test.test_espfit.test_scripts') as dn:
sys_esp.to_file(os.path.join(dn, 'esp.cube'))
check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5', dn)
check_script('horton-esp-fit.py esp.h5 other.h5', dn)
check_script('horton-esp-test.py esp.h5 other.h5:charges foo.h5', dn)
check_script('horton-esp-gen.py other.h5:charges esp.cube gen.h5', dn)
check_files(dn, ['esp.h5', 'other.h5', 'foo.h5', 'gen.h5'])
# Write the cube file to the tmpdir and run scripts (run 2)
with tmpdir('horton.scripts.test.test_espfit.test_scripts2') as dn:
sys_esp.to_file(os.path.join(dn, 'esp.cube'))
sys_rho.to_file(os.path.join(dn, 'rho.cube'))
check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5 --wdens=rho.cube --wsave=weight.cube', dn)
check_files(dn, ['esp.h5', 'weight.cube'])
check_script('horton-esp-fit.py esp.h5 other.h5', dn)
check_script('horton-esp-test.py esp.h5 other.h5:charges foo.h5', dn)
check_script('horton-esp-gen.py other.h5:charges esp.cube gen.h5', dn)
check_files(dn, ['esp.h5', 'other.h5', 'foo.h5', 'gen.h5'])
def test_scripts():
# Generate some random system with random esp data
natom = 5
numbers = np.random.randint(1, 20, natom)
coordinates = np.random.uniform(0, 10, (natom, 3))
origin = np.zeros(3, float)
grid_rvecs = np.identity(3, float)*1.0
shape = np.array([10, 10, 10])
pbc = np.ones(3, int)
ugrid = UniformGrid(origin, grid_rvecs, shape, pbc)
esp_cube_data = np.random.uniform(-1, 1, shape)
rho_cube_data = np.random.uniform(-1, 1, shape)
mol_esp = IOData(coordinates=coordinates, numbers=numbers, grid=ugrid, cube_data=esp_cube_data)
mol_rho = mol_esp.copy()
mol_rho.cube_data = rho_cube_data
# Write the cube file to the tmpdir and run scripts (run 1)
with tmpdir('horton.scripts.test.test_espfit.test_scripts') as dn:
mol_esp.to_file(os.path.join(dn, 'esp.cube'))
check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5', dn)
check_script('horton-esp-fit.py esp.h5 other.h5', dn)
check_script('horton-esp-test.py esp.h5 other.h5:charges foo.h5', dn)
check_script('horton-esp-gen.py other.h5:charges esp.cube gen.h5', dn)
check_files(dn, ['esp.h5', 'other.h5', 'foo.h5', 'gen.h5'])
# Write the cube file to the tmpdir and run scripts (run 2)
with tmpdir('horton.scripts.test.test_espfit.test_scripts2') as dn:
mol_esp.to_file(os.path.join(dn, 'esp.cube'))
mol_rho.to_file(os.path.join(dn, 'rho.cube'))
check_script('horton-esp-cost.py esp.cube esp.h5 --wnear=0:1.0:0.5 --wdens=rho.cube --wsave=weight.cube', dn)
check_files(dn, ['esp.h5', 'weight.cube'])
check_script('horton-esp-fit.py esp.h5 other.h5', dn)
check_script('horton-esp-test.py esp.h5 other.h5:charges foo.h5', dn)
check_script('horton-esp-gen.py other.h5:charges esp.cube gen.h5', dn)
check_files(dn, ['esp.h5', 'other.h5', 'foo.h5', 'gen.h5'])
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'])
