def test_from_string(self):
k1 = AdfKey.from_string("CHARGE -1 0")
self.assertEqual(k1.key, "CHARGE")
self.assertListEqual(k1.options, [-1, 0])
k2 = AdfKey.from_string("step rad=0.15 angle=10.0")
self.assertEqual(k2.key, "step")
self.assertListEqual(k2.options[0], ['rad', 0.15])
self.assertListEqual(k2.options[1], ['angle', 10.0])
k3 = AdfKey.from_string("GEOMETRY\noptim all\niterations 100\nEND\n")
self.assertEqual(k3.key, "GEOMETRY")
self.assertEqual(k3.subkeys[0].options[0], "all")
self.assertEqual(k3.subkeys[1].options[0], 100)
k4 = AdfKey.from_string(
"""SCF
iterations 300
converge 1.0e-7 1.0e-7
mixing 0.2
diis n=100 ok=0.0001 cyc=100 cx=5.0 cxx=10.0
END"""
)
self.assertEqual(k4.key, "SCF")
self.assertEqual(k4.subkeys[0].key, "iterations")
self.assertEqual(k4.subkeys[1].key, "converge")
self.assertEqual(k4.subkeys[1].options[0], 1E-7)
self.assertEqual(k4.subkeys[2].options[0], 0.2)
def test_from_string(self):
k1 = AdfKey.from_string("CHARGE -1 0")
self.assertEqual(k1.key, "CHARGE")
self.assertListEqual(k1.options, [-1, 0])
k2 = AdfKey.from_string("step rad=0.15 angle=10.0")
self.assertEqual(k2.key, "step")
self.assertListEqual(k2.options[0], ['rad', 0.15])
self.assertListEqual(k2.options[1], ['angle', 10.0])
k3 = AdfKey.from_string("GEOMETRY\noptim all\niterations 100\nEND\n")
self.assertEqual(k3.key, "GEOMETRY")
self.assertEqual(k3.subkeys[0].options[0], "all")
self.assertEqual(k3.subkeys[1].options[0], 100)
k4 = AdfKey.from_string("""SCF
iterations 300
converge 1.0e-7 1.0e-7
mixing 0.2
diis n=100 ok=0.0001 cyc=100 cx=5.0 cxx=10.0
END""")
self.assertEqual(k4.key, "SCF")
self.assertEqual(k4.subkeys[0].key, "iterations")
self.assertEqual(k4.subkeys[1].key, "converge")
self.assertEqual(k4.subkeys[1].options[0], 1E-7)
self.assertEqual(k4.subkeys[2].options[0], 0.2)
def test_subkeys_subkeys(self):
atom_dep_quality = AdfKey("AtomDepQuality",
subkeys=[AdfKey("10", ["good"]),
AdfKey("12", ["normal"])])
zlmfit = AdfKey("zlmfit", subkeys=[atom_dep_quality])
self.assertEqual(str(zlmfit), zlmfit_string)
self.assertEqual(str(AdfKey.from_dict(zlmfit.as_dict())), zlmfit_string)
def test_subkeys(self):
smooth = AdfKey("smooth", ["conservepoints"])
optim = AdfKey("optim", ["all", "cartesian"])
iterations = AdfKey("iterations", [250])
step = AdfKey("step", [("rad", 0.15), ("angle", 10.0)])
hessupd = AdfKey("hessupd", ["BFGS"])
converge = AdfKey("converge", [("e", 1.0e-3), ("grad", 3.0e-4),
("rad", 1.0e-2), ("angle", 0.5)])
geo = AdfKey("geometry", subkeys=[smooth, optim, iterations, step,
hessupd, converge])
self.assertEqual(str(geo), geometry_string)
self.assertEqual(str(AdfKey.from_dict(geo.as_dict())), geometry_string)
self.assertTrue(geo.has_subkey("optim"))
def test_subkeys_subkeys(self):
atom_dep_quality = AdfKey(
"AtomDepQuality",
subkeys=[AdfKey("10", ["good"]),
AdfKey("12", ["normal"])])
zlmfit = AdfKey("zlmfit", subkeys=[atom_dep_quality])
self.assertEqual(str(zlmfit), zlmfit_string)
self.assertEqual(str(AdfKey.from_dict(zlmfit.as_dict())),
zlmfit_string)
def test_option_operations(self):
k1 = AdfKey("Charge", [-1, 0])
k1.add_option(2)
self.assertListEqual(k1.options, [-1, 0, 2])
k1.remove_option(0)
self.assertListEqual(k1.options, [0, 2])
k2 = AdfKey.from_string("step rad=0.15 angle=10.0")
k2.add_option(["length", 0.1])
self.assertListEqual(k2.options[2], ["length", 0.1])
k2.remove_option("rad")
self.assertListEqual(k2.options[0], ["angle", 10.0])
def test_option_operations(self):
k1 = AdfKey("Charge", [-1, 0])
k1.add_option(2)
self.assertListEqual(k1.options, [-1, 0, 2])
k1.remove_option(0)
self.assertListEqual(k1.options, [0, 2])
k2 = AdfKey.from_string("step rad=0.15 angle=10.0")
k2.add_option(["length", 0.1])
self.assertListEqual(k2.options[2], ["length", 0.1])
k2.remove_option("rad")
self.assertListEqual(k2.options[0], ["angle", 10.0])
def test_simple(self):
unrestricted = AdfKey("unrestricted")
self.assertEqual(str(unrestricted).strip(), 'UNRESTRICTED')
def test_atom_block_key(self):
block = AdfKey("atoms")
o = Molecule.from_str(h2oxyz, "xyz")
for site in o:
block.add_subkey(AdfKey(str(site.specie), list(site.coords)))
self.assertEqual(str(block), atoms_string)
def test_end(self):
geo = AdfKey("Geometry")
self.assertEqual(str(geo), "GEOMETRY\nEND\n")
def test_subkeys(self):
smooth = AdfKey("smooth", ["conservepoints"])
optim = AdfKey("optim", ["all", "cartesian"])
iterations = AdfKey("iterations", [250])
step = AdfKey("step", [("rad", 0.15), ("angle", 10.0)])
hessupd = AdfKey("hessupd", ["BFGS"])
converge = AdfKey("converge", [("e", 1.0e-3), ("grad", 3.0e-4),
("rad", 1.0e-2), ("angle", 0.5)])
geo = AdfKey(
"geometry",
subkeys=[smooth, optim, iterations, step, hessupd, converge])
self.assertEqual(str(geo), geometry_string)
self.assertEqual(str(AdfKey.from_dict(geo.as_dict())), geometry_string)
self.assertTrue(geo.has_subkey("optim"))
def test_options(self):
charge = AdfKey("charge", [-1, 0])
charge_string = "CHARGE -1 0\n"
self.assertEqual(str(charge), "CHARGE -1 0\n")
self.assertEqual(str(AdfKey.from_dict(charge.as_dict())),
charge_string)
task = AdfTask()
o = AdfTask.from_dict(task.as_dict())
self.assertEqual(task.title, o.title)
self.assertEqual(task.basis_set, o.basis_set)
self.assertEqual(task.scf, o.scf)
self.assertEqual(task.geo, o.geo)
self.assertEqual(task.operation, o.operation)
self.assertEqual(task.units, o.units)
self.assertEqual(str(task), str(o))
rhb18 = {
"title":
"RhB18",
"basis_set":
AdfKey.from_string("BASIS\ntype TZP\ncore small\nEND"),
"xc":
AdfKey.from_string("XC\nHybrid PBE0\nEND"),
"units":
AdfKey.from_string("UNITS\nlength angstrom\nEND"),
"other_directives": [
AdfKey.from_string("SYMMETRY"),
AdfKey.from_string("RELATIVISTIC scalar zora"),
AdfKey.from_string("INTEGRATION 6.0 6.0 6.0"),
AdfKey.from_string("SAVE TAPE21"),
AdfKey.from_string("A1FIT 10.0")
],
"geo_subkeys": [
AdfKey.from_string("optim all"),
AdfKey.from_string("iterations 300"),
AdfKey.from_string("step rad=0.15 angle=10.0"),
def test_atom_block_key(self):
block = AdfKey("atoms")
o = Molecule.from_str(h2oxyz, "xyz")
for site in o:
block.add_subkey(AdfKey(str(site.specie), list(site.coords)))
self.assertEqual(str(block), atoms_string)
def test_options(self):
charge = AdfKey("charge", [-1, 0])
charge_string = "CHARGE -1 0\n"
self.assertEqual(str(charge), "CHARGE -1 0\n")
self.assertEqual(str(AdfKey.from_dict(charge.as_dict())), charge_string)
self.assertEqual(str(task), energy_task)
def test_serialization(self):
task = AdfTask()
o = AdfTask.from_dict(task.as_dict())
self.assertEqual(task.title, o.title)
self.assertEqual(task.basis_set, o.basis_set)
self.assertEqual(task.scf, o.scf)
self.assertEqual(task.geo, o.geo)
self.assertEqual(task.operation, o.operation)
self.assertEqual(task.units, o.units)
self.assertEqual(str(task), str(o))
rhb18 = {"title": "RhB18",
"basis_set": AdfKey.from_string("BASIS\ntype TZP\ncore small\nEND"),
"xc": AdfKey.from_string("XC\nHybrid PBE0\nEND"),
"units": AdfKey.from_string("UNITS\nlength angstrom\nEND"),
"other_directives": [AdfKey.from_string("SYMMETRY"),
AdfKey.from_string("RELATIVISTIC scalar zora"),
AdfKey.from_string("INTEGRATION 6.0 6.0 6.0"),
AdfKey.from_string("SAVE TAPE21"),
AdfKey.from_string("A1FIT 10.0")],
"geo_subkeys": [AdfKey.from_string("optim all"),
AdfKey.from_string("iterations 300"),
AdfKey.from_string("step rad=0.15 angle=10.0"),
AdfKey.from_string("hessupd BFGS")],
"scf": AdfKey.from_string(
"""SCF
iterations 300
converge 1.0e-7 1.0e-7