def test_moments():
padb = get_proatomdb_cp2k()
record0 = padb.get_record(8, 0)
record1 = padb.get_record(8, 1)
m0 = record0.get_moment(3)
m1 = record1.get_moment(3)
assert m0 > m1
assert abs(m0-21.84) < 1e-2
assert abs(m1-12.17) < 1e-2
def test_moments():
padb = get_proatomdb_cp2k()
record0 = padb.get_record(8, 0)
record1 = padb.get_record(8, 1)
m0 = record0.get_moment(3)
m1 = record1.get_moment(3)
assert m0 > m1
assert abs(m0 - 21.84) < 1e-2
assert abs(m1 - 12.17) < 1e-2
def test_normalize():
padb = get_proatomdb_cp2k()
padb.compact(0.1)
padb.normalize()
for number in padb.get_numbers():
rgrid = padb.get_rgrid(number)
for charge in padb.get_charges(number):
r = padb.get_record(number, charge)
nel = rgrid.integrate(r.rho)
nel_integer = r.pseudo_number - charge
assert abs(nel - nel_integer) < 1e-10
def test_normalize():
padb = get_proatomdb_cp2k()
padb.compact(0.1)
padb.normalize()
for number in padb.get_numbers():
rgrid = padb.get_rgrid(number)
for charge in padb.get_charges(number):
r = padb.get_record(number, charge)
nel = rgrid.integrate(r.rho)
nel_integer = r.pseudo_number - charge
assert abs(nel - nel_integer) < 1e-10
def test_get_spline_pseudo():
padb = get_proatomdb_cp2k()
spline = padb.get_spline(8)
check_spline_pop(spline, 6.0)
check_spline_record(spline, padb.get_record(8, 0))
spline = padb.get_spline(8, -1)
check_spline_pop(spline, 7.0)
check_spline_record(spline, padb.get_record(8, -1))
spline = padb.get_spline(8, {0:0.5, -1:0.5})
check_spline_pop(spline, 6.5)
spline = padb.get_spline(14)
check_spline_pop(spline, 4.0)
check_spline_record(spline, padb.get_record(14, 0))
def test_get_spline_pseudo():
padb = get_proatomdb_cp2k()
spline = padb.get_spline(8)
check_spline_pop(spline, 6.0)
check_spline_record(spline, padb.get_record(8, 0))
spline = padb.get_spline(8, -1)
check_spline_pop(spline, 7.0)
check_spline_record(spline, padb.get_record(8, -1))
spline = padb.get_spline(8, {0: 0.5, -1: 0.5})
check_spline_pop(spline, 6.5)
spline = padb.get_spline(14)
check_spline_pop(spline, 4.0)
check_spline_record(spline, padb.get_record(14, 0))
def test_hebasis():
padb = get_proatomdb_cp2k()
numbers = np.array([8, 14, 14, 8, 8])
hebasis = HEBasis(numbers, padb)
assert hebasis.get_nbasis() == 9 # 3 for every oxygen atom
assert hebasis.get_atom_nbasis(0) == 3
assert hebasis.get_atom_nbasis(1) == 0
assert hebasis.get_atom_nbasis(2) == 0
assert hebasis.get_atom_nbasis(3) == 3
assert hebasis.get_atom_nbasis(4) == 3
for i in 0, 3, 4:
assert hebasis.get_lower_bound(i, 0) == -1
assert hebasis.get_lower_bound(i, 1) == -1
assert hebasis.get_lower_bound(i, 2) == 0
assert hebasis.get_constant_lico(i) == {0: 1}
assert (hebasis.get_initial_propars() == 0).all()
propars = np.array([0.1, 0.5, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9])
assert hebasis.get_total_lico(0, propars) == {+2: -0.1, +1: -0.4, 0: 1.2, -1: 0.3}
def test_hebasis():
padb = get_proatomdb_cp2k()
numbers = np.array([8, 14, 14, 8, 8])
hebasis = HEBasis(numbers, padb)
assert hebasis.get_nbasis() == 9 # 3 for every oxygen atom
assert hebasis.get_atom_nbasis(0) == 3
assert hebasis.get_atom_nbasis(1) == 0
assert hebasis.get_atom_nbasis(2) == 0
assert hebasis.get_atom_nbasis(3) == 3
assert hebasis.get_atom_nbasis(4) == 3
for i in 0, 3, 4:
assert hebasis.get_lower_bound(i, 0) == -1
assert hebasis.get_lower_bound(i, 1) == -1
assert hebasis.get_lower_bound(i, 2) == 0
assert hebasis.get_constant_lico(i) == {0: 1}
assert (hebasis.get_initial_propars() == 0).all()
propars = np.array([0.1, 0.5, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9])
assert hebasis.get_total_lico(0, propars) == {+2: -0.1, +1: -0.4, 0: 1.2, -1: 0.3}
def test_db_basics_pseudo():
padb = get_proatomdb_cp2k()
assert padb.get_numbers() == [8, 14]
assert padb.get_charges(8) == [2, 1, 0, -1, -2]
assert padb.get_charges(8, safe=True) == [2, 1, 0, -1]
assert padb.get_charges(14) == [0]
assert not padb.get_record(8, -2).safe
assert padb.get_rgrid(8) is padb.get_record(8, 1).rgrid
r1 = padb.get_record(8, -1)
assert r1.safe
assert abs(r1.energy - -15.866511882272) < 1e-8
assert abs(r1.homo_energy - 0.192773) < 1e-5
assert abs(r1.ipot_energy - (padb.get_record(8, 0).energy - r1.energy)) < 1e-5
r2 = padb.get_record(8, -2)
assert not r2.safe
assert abs(r2.energy - -15.464982778766) < 1e-8
assert abs(r2.homo_energy - 0.606458) < 1e-5
assert abs(r2.ipot_energy - (r1.energy - r2.energy)) < 1e-5
assert padb.get_record(8, +2).ipot_energy is None
def test_db_basics_pseudo():
padb = get_proatomdb_cp2k()
assert padb.get_numbers() == [8, 14]
assert padb.get_charges(8) == [2, 1, 0, -1, -2]
assert padb.get_charges(8, safe=True) == [2, 1, 0, -1]
assert padb.get_charges(14) == [0]
assert not padb.get_record(8, -2).safe
assert padb.get_rgrid(8) is padb.get_record(8, 1).rgrid
r1 = padb.get_record(8, -1)
assert r1.safe
assert abs(r1.energy - -15.866511882272) < 1e-8
assert abs(r1.homo_energy - 0.192773) < 1e-5
assert abs(r1.ipot_energy -
(padb.get_record(8, 0).energy - r1.energy)) < 1e-5
r2 = padb.get_record(8, -2)
assert not r2.safe
assert abs(r2.energy - -15.464982778766) < 1e-8
assert abs(r2.homo_energy - 0.606458) < 1e-5
assert abs(r2.ipot_energy - (r1.energy - r2.energy)) < 1e-5
assert padb.get_record(8, +2).ipot_energy is None
def test_empty_proatom():
padb = get_proatomdb_cp2k()
assert (padb.get_rho(8, {}) == 0.0).all()
def test_compact():
padb = get_proatomdb_cp2k()
padb.compact(0.1)
assert padb.get_rgrid(8).size < 100
assert padb.get_rgrid(14).size < 100
def test_empty_proatom():
padb = get_proatomdb_cp2k()
assert (padb.get_rho(8, {}) == 0.0).all()
def test_compact():
padb = get_proatomdb_cp2k()
padb.compact(0.1)
assert padb.get_rgrid(8).size < 100
assert padb.get_rgrid(14).size < 100