def test_gfn1_xtb_3d():
"""Test ASE interface to GFN1-xTB"""
thr = 5.0e-6
atoms = Atoms(
symbols='C4O8',
positions=np.array([
[0.9441259872, 0.9437851680, 0.9543505632],
[3.7179966528, 0.9556570368, 3.7316862240],
[3.7159517376, 3.7149292800, 0.9692330016],
[0.9529872864, 3.7220864832, 3.7296981120],
[1.6213905408, 1.6190616096, 1.6313879040],
[0.2656685664, 0.2694175776, 0.2776540416],
[4.3914553920, 1.6346256864, 3.0545920000],
[3.0440834880, 0.2764611744, 4.4080419264],
[4.3910577696, 3.0416409504, 0.2881058304],
[3.0399936576, 4.3879335936, 1.6497353376],
[0.2741322432, 4.4003734944, 3.0573754368],
[1.6312174944, 3.0434586528, 4.4023048032],
]),
cell=np.array([5.68032, 5.68032, 5.68032]),
pbc=np.array([True, True, True]),
)
forces = np.array([
[0.05008078, 0.06731033, 0.06324782],
[-0.03885473, 0.07550136, -0.06667888],
[-0.06455676, -0.04199831, 0.06908718],
[0.04672903, -0.06303119, -0.06002863],
[-1.9460667, -1.94514641, -1.94923488],
[1.92953942, 1.91109506, 1.92038457],
[-1.91269913, -1.95500822, 1.94675148],
[1.94009239, 1.91238163, -1.93489981],
[-1.90757165, 1.94211445, 1.94655816],
[1.94283273, -1.90965163, -1.95863335],
[1.91207771, -1.94256232, 1.9337591],
[-1.95160309, 1.94899525, -1.91031277],
])
charges = np.array([
0.74256902,
0.74308482,
0.74305612,
0.74300613,
-0.37010244,
-0.37234708,
-0.37134504,
-0.37177066,
-0.37176288,
-0.37133667,
-0.37178059,
-0.37127074,
])
calc = XTB(method="GFN1-xTB")
atoms.set_calculator(calc)
assert atoms.pbc.all()
assert approx(atoms.get_potential_energy(), abs=thr) == -1256.768167202048
assert approx(atoms.get_forces(), abs=thr) == forces
assert approx(atoms.get_charges(), abs=thr) == charges
def test_gfn2_xtb_0d():
"""Test ASE interface to GFN2-xTB"""
thr = 1.0e-5
atoms = Atoms(
symbols='CHOCH2CH4CH2OH',
positions=np.array([
[1.578385, 0.147690, 0.343809],
[1.394750, 0.012968, 1.413545],
[1.359929, -1.086203, -0.359782],
[0.653845, 1.215099, -0.221322],
[1.057827, 2.180283, 0.093924],
[0.729693, 1.184864, -1.311438],
[-0.817334, 1.152127, 0.208156],
[-1.303525, 2.065738, -0.145828],
[-0.883765, 1.159762, 1.299260],
[1.984120, -1.734446, -0.021385],
[2.616286, 0.458948, 0.206544],
[-1.627725, -0.034052, -0.311301],
[-2.684229, 0.151015, -0.118566],
[-1.501868, -0.118146, -1.397506],
[-1.324262, -1.260154, 0.333377],
[-0.417651, -1.475314, 0.076637],
]),
)
forces = np.array([
[-0.28561158, -0.48592026, -0.28392327],
[-0.05526158, -0.07403455, 0.09665539],
[0.18824950, 0.39170140, 0.33881928],
[-0.01166074, 0.24653252, -0.16779606],
[-0.05367503, 0.03368063, 0.05115422],
[-0.09605262, -0.10000389, 0.01097286],
[0.09423300, 0.18573616, 0.17797438],
[0.02651896, -0.04073849, -0.03655980],
[0.07886359, -0.05806479, 0.00649360],
[-0.00780520, -0.07979390, -0.03175697],
[0.13328595, 0.03209283, -0.04638514],
[0.08197778, -0.39157299, 0.12107401],
[-0.11453823, -0.01485088, 0.09974068],
[0.09786017, -0.09130861, -0.05738675],
[-0.26643400, 0.47603727, -0.27856705],
[0.19005003, -0.02949244, -0.00050938],
])
charges = np.array([
0.08239823,
0.03066406,
-0.44606929,
-0.06139043,
0.03610596,
0.05389499,
-0.06991855,
0.03384415,
0.04665524,
0.28688538,
0.02246569,
0.08251610,
0.03810481,
0.01883776,
-0.46691965,
0.31192554,
])
dipole_moment = np.array([0.62120710, 0.28006659, 0.04465985])
calc = XTB(method="GFN2-xTB", atoms=atoms)
assert approx(atoms.get_potential_energy(), abs=thr) == -592.6794366990786
assert approx(atoms.get_forces(), abs=thr) == forces
assert approx(atoms.get_charges(), abs=thr) == charges
assert approx(atoms.get_dipole_moment(), abs=thr) == dipole_moment
atoms.calc.set(
accuracy=0.1,
electronic_temperature=500.0,
max_iterations=20,
solvent="ch2cl2",
)
assert approx(atoms.get_potential_energy(), abs=thr) == -592.9940608761889
def test_gfn1_xtb_0d():
"""Test ASE interface to GFN1-xTB"""
thr = 1.0e-5
atoms = Atoms(
symbols='CHOCH2CH4CH2OH',
positions=np.array([
[1.578385, 0.147690, 0.343809],
[1.394750, 0.012968, 1.413545],
[1.359929, -1.086203, -0.359782],
[0.653845, 1.215099, -0.221322],
[1.057827, 2.180283, 0.093924],
[0.729693, 1.184864, -1.311438],
[-0.817334, 1.152127, 0.208156],
[-1.303525, 2.065738, -0.145828],
[-0.883765, 1.159762, 1.299260],
[1.984120, -1.734446, -0.021385],
[2.616286, 0.458948, 0.206544],
[-1.627725, -0.034052, -0.311301],
[-2.684229, 0.151015, -0.118566],
[-1.501868, -0.118146, -1.397506],
[-1.324262, -1.260154, 0.333377],
[-0.417651, -1.475314, 0.076637],
]),
)
forces = np.array([[-0.37070590, -0.51067739, -0.27981764],
[-0.04339461, -0.09290876, 0.22940156],
[0.11141234, 0.46678720, 0.24552625],
[0.04255709, 0.19019316, -0.23531997],
[-0.01897377, 0.10810803, 0.05314982],
[-0.07150720, -0.05182148, -0.08413638],
[0.06631826, 0.10587709, 0.29833479],
[-0.01062355, 0.02301460, -0.04964730],
[0.06610108, -0.02724994, 0.09234280],
[0.06519070, -0.19311773, -0.01152205],
[0.23879786, 0.09871398, -0.04009526],
[-0.04381577, -0.49997745, 0.08672818],
[-0.23259608, 0.13735636, 0.06783414],
[0.08297636, -0.09566973, -0.20602954],
[-0.23686052, 0.57454371, -0.17194215],
[0.35512370, -0.23317164, 0.00519275]])
charges = np.array([
0.19494678,
0.01759972,
-0.57108503,
-0.05371086,
0.02458495,
0.03915074,
-0.06889977,
0.02521441,
0.03350058,
0.34380081,
0.01442221,
0.20053193,
0.02454679,
0.01011690,
-0.58349877,
0.34877861,
])
dipole_moment = np.array([0.76943477, 0.33021928, 0.05670150])
atoms.calc = XTB(method="GFN1-xTB")
assert approx(atoms.get_potential_energy(), abs=thr) == -632.7363734598027
assert approx(atoms.get_forces(), abs=thr) == forces
assert approx(atoms.get_charges(), abs=thr) == charges
assert approx(atoms.get_dipole_moment(), abs=thr) == dipole_moment
