def test_qr_R(self):
A = init([[12, 6, -4], [-51, 167, 24], [4, -68, -41]])
Q, R = A.qr()
np.testing.assert_almost_equal(
R, -init([[14, 0, 0], [21, 175, 0], [-14, -70, 35]])
)
np.testing.assert_almost_equal(A, Q * R)
def test_qr_R(self):
A = BlockDiagonalMatrix([3], [3])
A.subblock[0] = init([[12, 6, -4], [-51, 167, 24], [4, -68, -41]])
Q, R = A[0].qr()
numpy.testing.assert_almost_equal(
R, -init([[14, 0, 0], [21, 175, 0], [-14, -70, 35]]))
numpy.testing.assert_almost_equal(A[0], Q * R)
def setUp(self):
n, _ = os.path.splitext(__file__)
suppdir = n + ".d"
self.ao2soint = os.path.join(suppdir, "AO2SOINT")
self.dc = init([
[ 2.10662148, -0.44832042, 0.00000000, 0.10863721, 0.00000000, -0.02702924, -0.02702924],
[-0.44832042, 1.97509195, -0.00000000, -0.61381008, 0.00000000, -0.03765992, -0.03765992],
[ 0.00000000, -0.00000000, 0.73437339, 0.00000000, 0.00000000, 0.54049192, -0.54049192],
[ 0.10863721, -0.61381008, 0.00000000, 1.22749198, 0.00000000, 0.47809924, 0.47809924],
[ 0.00000000, 0.00000000, 0.00000000, 0.00000000, 2.00000000, 0.00000000, 0.00000000],
[-0.02702924, -0.03765992, 0.54049192, 0.47809924, 0.00000000, 0.60856871, -0.18702525],
[-0.02702924, -0.03765992, -0.54049192, 0.47809924, 0.00000000, -0.18702525, 0.60856871]
])
self.fcref = -init([
[ 0.00000000, 0.00000000, 0.37936213, -0.00000000, 0.00000000, 0.00253951, -0.00253951],
[-0.00000000, 0.00000000, 0.10878631, -0.00000000, 0.00000000, -0.01699688, 0.01699688],
[-0.37936213, -0.10878631, 0.00000000, -11.60434639, 0.00000000, -0.98565692, -0.98565692],
[ 0.00000000, 0.00000000, 11.60434639, 0.00000000, 0.00000000, 1.20385366, -1.20385366],
[ 0.00000000, 0.00000000, 0.00000000, 0.00000000, 0.00000000, 0.00000000, 0.00000000],
[-0.00253951, 0.01699688, 0.98565692, -1.20385366, 0.00000000, 0.00000000, -0.36840521],
[ 0.00253951, -0.01699688, 0.98565692, 1.20385366, 0.00000000, 0.36840521, 0.00000000]
])
def lr_solve(self, ops="xyz", freqs=(0.), **kwargs):
V1 = {op: v for op, v in zip(ops, self.get_rhs(*ops))}
row_dim = V1[ops[0]].shape[0]
E2 = full.init([self.e2n(i) for i in numpy.eye(row_dim)])
S2 = full.init([self.s2n(i) for i in numpy.eye(row_dim)])
solutions = {(op, freq): (V1[op] / (E2 - freq * S2))
for freq in freqs for op in ops}
return solutions
def setUp(self):
Nod.S = init([[1.0, 0.1], [0.1, 1.0]])
Nod.C = init([[0.7, 0.7], [0.7, -0.7]])
self.alpha0 = Nod([0], [])
self.alpha1 = Nod([1], [])
self.beta0 = Nod([], [0])
self.beta1 = Nod([], [1])
self.ab00 = Nod([0], [0])
def test_rephase_inplase(self):
mat = init([[-1, 0], [0, 1]])
none = mat.rephase_columns(inplace=True)
assert none is None
np.testing.assert_allclose(
init([[-1, 0], [0, 1]]).rephase_columns(),
init([[1, 0], [0, 1]])
)
def test_Dab(self):
na = 2
nb = 1
C = full.unit(3)
da, db = dens.C2Dab(C, na, nb)
daref = full.init([[1.0, 0.0, 0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]])
dbref = full.init([[1.0, 0.0, 0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])
np.testing.assert_almost_equal(da, daref)
np.testing.assert_almost_equal(db, dbref)
def test_new_trials1(mod, qcp):
td = {0.5: np.array([2.5, 1.5, 1.5, 0.5])}
residuals = {('op', 0.5): full.init([1, 1, 0, 0])}
b = full.init([[1, 0, 0, 0], [0, 0, 1, 0]])
new_trials = qcp.generate_new_trials(residuals, td, b)
npt.assert_allclose(new_trials.T, [
[0., 1, 0., 0.],
[0., 0., 0., 1],
])
def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-H", "--head", dest="head", action="store_true")
parser.add_argument("-i", "--isordk", dest="isordk", action="store_true")
parser.add_argument("-s", "--scfinp", dest="scfinp", action="store_true")
parser.add_argument("-v", "--verbose", dest="verbose", action="store_true")
parser.add_argument("-u", "--unpack", dest="unpack", action="store_true")
parser.add_argument("-o", "--savetxt", dest="savetxt")
parser.add_argument("-l", "--label")
# breakpoint()
parser.add_argument("aooneint")
args = parser.parse_args()
if args.head:
head = readhead(args.aooneint)
print("Header on AOONEINT")
for k in head:
if type(head[k]) is float:
print("%s %10.5f" % (k, head[k]))
else:
print("%s %s" % (k, head[k]))
if args.isordk:
isordk = readisordk(args.aooneint)
n = isordk["nucdep"]
chrn = isordk["chrn"]
cooo = isordk["cooo"]
mxcent = len(chrn)
print("nucdep=%i" % n + " mxcent=%i" % mxcent)
print(full.init(chrn)[:n])
print(full.init(cooo).reshape((3, mxcent))[:, :n])
if args.scfinp:
scfinp = readscfinp(args.aooneint)
for k in scfinp:
if type(scfinp[k]) is float and k != "dummy":
print("%s%10.6f" % (k, scfinp[k]))
else:
print(k + " " + str(scfinp[k]))
if args.label is not None:
s1 = read(label=args.label, filename=args.aooneint)
if args.unpack:
s2 = s1.unpack()
S = s2.unblock()
else:
S = s1
if args.verbose:
print("%s %s" % (args.label, str(S)))
if args.savetxt:
np.savetxt(args.savetxt, S)
def test_gram_schmidt(self):
S = BlockDiagonalMatrix([2], [2])
v = BlockDiagonalMatrix([2], [2])
Delta = 0.1
S.subblock[0] = init([[1.0, Delta], [Delta, 1.0]])
v.subblock[0] = init([[1.0, 0.0], [0.0, 1.0]])
u = v.GS(S)
u_ref = init([
[1.0, 0.0],
[-Delta / math.sqrt(1 - Delta**2), 1.0 / math.sqrt(1 - Delta**2)],
])
numpy.testing.assert_almost_equal(u[0], u_ref)
def test_qr_Q(self):
A = BlockDiagonalMatrix([3], [3])
A.subblock[0] = init([[12, 6, -4], [-51, 167, 24], [4, -68, -41]])
Q, R = A.qr()
numpy.testing.assert_almost_equal(
Q[0],
-init([
[6.0 / 7, 3.0 / 7, -2.0 / 7],
[-69.0 / 175, 158.0 / 175, 6.0 / 35],
[-58.0 / 175, 6.0 / 175, -33.0 / 35],
]),
)
def test_gram_schmidt(self):
Delta = 0.1
S = init([[1.0, Delta], [Delta, 1.0]])
v = init([[1.0, 0.0], [0.0, 1.0]])
u = v.GS(S)
u_ref = init(
[
[1.0, 0.0],
[-Delta/sqrt(1 - Delta**2), 1.0/sqrt(1 - Delta**2)]
]
)
np.testing.assert_almost_equal(u, u_ref)
def test_qr_Q(self):
A = init([[12, 6, -4], [-51, 167, 24], [4, -68, -41]])
Q, R = A.qr()
np.testing.assert_almost_equal(
Q,
-init(
[
[6.0 / 7, 3.0 / 7, -2.0 / 7],
[-69.0 / 175, 158.0 / 175, 6.0 / 35],
[-58.0 / 175, 6.0 / 175, -33.0 / 35],
]
),
)
def test_gram_schmidt_as_transformation(self):
Delta = 0.1
S = init([[1.0, Delta], [Delta, 1.0]])
v = init([[1.0, 0.0], [0.0, 1.0]])
T = v.GST(S)
u = v * T
u_ref = init(
[
[1.0, 0.0],
[-Delta/sqrt(1 - Delta**2), 1.0/sqrt(1 - Delta**2)]
]
)
np.testing.assert_almost_equal(u, u_ref)
def test_new_trials1(mod, qcp):
td = {0.5: np.array([2.5, 1.5, 1.5, 0.5])}
residuals = {('op', 0.5): full.init([1, 1, 0, 0])}
b = full.init([[1, 0, 0, 0], [0, 0, 1, 0]])
new_trials = qcp.generate_new_trials(residuals, td, b)
npt.assert_allclose(new_trials.T,
[
[0., 1, 0., 0.],
[0., 0., 0., 1],
]
)
def setUp(self):
"""
"""
VBTest.setUp(self, 'test_h2_c')
#
# Setup VB wave function
#
Nod.C=full.init(
[
[0.7633862173, 0.3075441467,
0.0000000000, 0.0000000000, 0.0328937818,
0, 0, 0, 0, 0],
[0, 0, 0, 0, 0,
0.7633862173, 0.3075441467,
0.0000000000, 0.0000000000, -0.0328937818]
]
)
ion_a = Structure([Nod([0],[0])], [1.0])
ion_b = Structure([Nod([1],[1])], [1.0])
cov = Structure([Nod([0],[1]),Nod([1],[0])], [1.0, 1.0])
self.WF=WaveFunctionND(
[cov, ion_a, ion_b],[0.83675, 0.09850, 0.09850],
tmpdir=self.tmpdir
)
self.WF.normalize()
def test_rephase_copy(self):
mat = init([[-1, 0], [0, 1]])
mat2 = mat.rephase_columns()
np.testing.assert_allclose(
mat2,
[[1, 0], [0, 1]],
)
def read(*args, **kwargs):
"""Read property integral"""
propfile = kwargs.get("filename")
if not propfile:
tmpdir = pathlib.Path(kwargs.get("tmpdir", "/tmp"))
propfile = tmpdir / "AOPROPER"
unpack = kwargs.get("unpack", True)
AOPROPER = FortranBinary(propfile)
mat = {}
for rec in AOPROPER:
buf = rec.read(32, "c")
# stars, data, symtype, label = (
# buf[:8], buf[8:16], buf[16:24], buf[24:32]
# )
b"".join(buf[:8])
symtype = b"".join(buf[16:24])
blabel = b"".join(buf[24:32]).strip()
bargs = (s.encode() for s in args)
if blabel.strip() in bargs:
label = blabel.decode()
rec = next(AOPROPER)
buffer_ = rec.read(len(rec) // 8, "d")
if symtype == b"SQUARE ":
n = int(round(math.sqrt(len(buffer_))))
mat[label] = full.init(buffer_).reshape((n, n))
else:
mat[label] = np.array(buffer_).view(full.triangular)
mat[label].anti = symtype == b"ANTISYMM"
if unpack:
return tuple([mat[lab].unpack() for lab in args])
else:
return tuple([mat[lab] for lab in args])
def test_newton_step_with_update(self):
x0 = [0.75133256,0.74762074, -0.69209032]
self.pfg.x = x0
dL = self.pfg.lagrangian_derivative()
d2L = self.pfg.lagrangian_hessian()
self.pfg.x = self.pfg.x - dL(x0, self.pfg)/d2L(x0, self.pfg)
ref_x1 = full.init([0.70827179, 0.70834183, -0.70514972])
numpy.testing.assert_allclose(self.pfg.x, ref_x1)
def test_imag_polarizability_total(self):
self.m.set_imag_pol()
ref_Am = full.init([
[1.228334, 0.000000, 0.000000],
[0.000000, 1.228335, 0.000000],
[0.000000, 0.000000, 1.228333]])
Am = self.m.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-6, atol=1e-6)
def test_h1diag(self):
diref = full.init([
[0.5370962, 0.33768834, 0.0],
[0.33768834, 0.21231469, 0.0],
[0.0, 0.0, 0.0],
])
di, da = dens.h1diag(1, 1, filename=self.tmpdir / "AOONEINT")
np.testing.assert_almost_equal(di, diref)
def structure_weights(self):
"""
Returns structure weights
w_S = C(S) sum(T) <S|T>C(T)
"""
SO = self.structure_overlap()
C = full.init(self.coef)
SOC = SO*C
W = [c*sc for c, sc in zip(C, SOC)]
return W
def test_real_polarizability_total(self):
self.m.set_real_pol()
ref_Am = full.init([
[30.854533, -0.000004, 0.000000],
[-0.000004, 30.854527, 0.000000],
[ 0.000000, 0.000000, 30.854522]
])
Am = self.m.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-6, atol=1e-6)
def test_imag_polarizability_total(self):
self.m.set_imag_pol()
ref_Am = full.init([
[0.063679, -0.000000, 0.000000],
[-0.000004, 0.063679, 0.000000],
[ 0.000000, 0.000000, 2.767574]
])
Am = self.m.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-5, atol=1e-5)
def test_real_polarizability_total(self, mf):
mf.set_real_pol()
ref_Am = full.init([
[30.854533, -0.000004, 0.000000],
[-0.000004, 30.854527, 0.000000],
[0.000000, 0.000000, 30.854522],
])
Am = mf.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-6, atol=1e-6)
def test_real_polarizability_total(self):
self.m.set_real_pol()
ref_Am = full.init([
[7.626564, 0.000000, 0.000000],
[0.000000, 7.626564, 0.000000],
[0.000000, 0.000000,42.786381]
])
Am = self.m.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-5, atol=1e-5)
def test_imag_polarizability_total(self, mf):
mf.set_imag_pol()
ref_Am = full.init([
[1.228334, 0.000000, 0.000000],
[0.000000, 1.228335, 0.000000],
[0.000000, 0.000000, 1.228333],
])
Am = mf.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-6, atol=1e-6)
def test_c1d(self):
C = full.init(np.random.random((3, 2)).T)
np.testing.assert_allclose(
dens.C1D(C, 1),
[
[0.301196, 0.330805, 0.232507],
[0.330805, 0.363324, 0.255364],
[0.232507, 0.255364, 0.179483],
],
atol=1e-6,
)
def __init__(self, p, f, g, *args, **kwargs):
self.p = full.init(p)
self.l = numpy.ones(len(kwargs['constraints']))
Minimizer.__init__(
self,
self.x, self.lagrangian(), g=self.lagrangian_derivative(),
method=kwargs.get('method', 'BFGS'), constraints=())
self.fp = f
self.gp = g
self.hp = kwargs.get('hessian', None)
self.cp = kwargs['constraints']
def test_imag_polarizability_total(self, molfrag):
molfrag.set_imag_pol()
ref_Am = full.init(
[
[0.063679, -0.000000, 0.000000],
[-0.000004, 0.063679, 0.000000],
[0.000000, 0.000000, 2.767574],
]
)
Am = molfrag.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-5, atol=1e-5)
def test_solver_start_covalent(self):
start_covalent = full.init(
[1.0, 0.1, 0.1] + [
1., .1, 0., 0., 0.1, 0., 0., 0., 0., 0,
0., 0., 0., 0., 0., 1., .1, 0., 0., -0.1
]
)
result = scipy.optimize.minimize(
self.wf_energy, start_covalent, jac=self.wf_gradient, args=(self.wf),
constraints=self.constraints, method='SLSQP'
)
self.assertAlmostEqual(result.fun, -1.14660543)
def test_real_polarizability_total(self, molfrag):
molfrag.set_real_pol()
ref_Am = full.init(
[
[7.626564, 0.000000, 0.000000],
[0.000000, 7.626564, 0.000000],
[0.000000, 0.000000, 42.786381],
]
)
Am = molfrag.Am[0]
np.testing.assert_allclose(Am, ref_Am, rtol=1e-5, atol=1e-5)
def test_orbital_overlap(self):
ref_overlap = full.init([
[ 1.000000, 0.000000, 0.000000, 0.000000, 0.074261, 0.064405],
[-0.000000, 1.000000, 0.000000, 0.000000, 0.214777, 0.361800],
[ 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000],
[ 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000],
[ 0.074261, 0.214777, 0.000000, 0.000000, 1.000000, -0.419052],
[ 0.064405, 0.361800, 0.000000, 0.000000, -0.419052, 1.000000]
])
self.wf.normalize_mo()
overlap = self.wf.C.T*Nod.S*self.wf.C
print(overlap); print(ref_overlap)
np.testing.assert_allclose(overlap, ref_overlap, atol=1e-6)
def setUp(self):
"""Setup supporting directory"""
name, _ = os.path.splitext(__file__)
self.suppdir = name + ".d"
self.faref = init([
[2.02818057, 0.26542036, 0.00000000, 0.06037429, 0.00000000, 0.00000000],
[0.26542036, 0.74551226, 0.00000000, 0.28646605, 0.00000000, 0.00000000],
[0.00000000, 0.00000000, 1.01061061, -0.47343699, 0.00000000, 0.00000000],
[0.06037429, 0.28646605, -0.47343699, 0.86039561, 0.00000000, 0.00000000],
[0.00000000, 0.00000000, 0.00000000, 0.00000000, 1.01061061, 0.00000000],
[0.00000000, 0.00000000, 0.00000000, 0.00000000, 0.00000000, 1.01061061],
])
self.fbref = init([
[2.07812203, 0.35828051, 0.00000000, 0.09571548, 0.00000000, 0.00000000],
[0.35828051, 1.03607456, 0.00000000, 0.40151695, 0.00000000, 0.00000000],
[0.00000000, 0.00000000, 1.07479494, -0.50700370, 0.00000000, 0.00000000],
[0.09571548, 0.40151695, -0.50700370, 0.93374109, 0.00000000, 0.00000000],
[0.00000000, 0.00000000, 0.00000000, 0.00000000, 1.07479494, 0.00000000],
[0.00000000, 0.00000000, 0.00000000, 0.00000000, 0.00000000, 1.07479494],
])
def setUp(self):
"""Opimize x+y constrained to a circle"""
# Initial values
self.p0 = (1.0, 0.0)
self.p1 = (SQRTH, SQRTH)
self.l0 = (1.0,)
self.l1 = (-SQRTH,)
self.x0 = self.p0 + self.l0 # (p, l)
self.x1 = self.p1 + self.l1 # (p, l)
#
self.f = lambda p: -(p[0] + p[1])
self.g = lambda p: full.init((-1.0, -1.0))
self.h = lambda p: full.matrix((2, 2))
self.c = (
{'type': 'eq',
'fun': lambda p: p[0]**2 + p[1]**2 - 1.0,
'jac': lambda p: full.init((2*p[0], 2*p[1])),
'hes': lambda p: full.init([[2, 0], [0, 2]])
},
)
self.pfg = LagrangianMinimizer(
self.p0, self.f, self.g, hessian=self.h, constraints=self.c
)
def structure_hamiltonian(self):
"""Returns Hamiltonian matrix in basis of structures"""
SH = []
# Structures left
for S in self.structs:
for T in self.structs:
#Determinants in left structure
H = 0
for K, CKS in zip(S.nods, S.coef):
for L, CLT in zip(T.nods, T.coef):
KL = BraKet(K, L)
H += CKS*CLT*(KL.energy((self.h, self.h)) + self.Z)*KL.overlap()
SH.append(H)
LS = len(self.structs)
return full.init(SH).reshape((LS, LS))
def __init__(self, nods, coef, normalize=True):
if len(nods) != len(coef):
raise StructError
self.nods = nods
self.assert_consistent_electron_number()
self.coef = full.init(coef)
#
# Also have MOs as a structure member
# In BOVB these are unique to a structure
# reference the first determinant MO
#
self._C = nods[0].C
if normalize:
self.normalize()
def __init__(self, structs, coef, VBSCF=True, tmpdir=None, blockdims=None):
self.structs = structs
self.coef = full.init(coef)
if tmpdir is not None:
self.tmpdir = tmpdir
self.qcifc.set_workdir(tmpdir)
self.Z = self.qcifc.get_nuclear_repulsion()
self.h = self.qcifc.get_one_el_hamiltonian()
BraKet.tmpdir = self.tmpdir
BraKet.qcifc = self.qcifc
#
# For VBSCF all structures share orbitals
#
if VBSCF:
self.C = Nod.C
else:
raise NotImplementedError
self.blockdims = blockdims
def setUp(self):
self.tmp = os.path.join(os.path.dirname(__file__), 'test_h2_c')
def tmp(fil):
return os.path.join(self.tmp, fil)
self.qcifc = QuantumChemistry.get_factory('Dalton', tmpdir=self.tmp)
vb.Nod.tmpdir = self.tmp
vb.Nod.C = full.matrix((10, 2))
vb.Nod.C[0, 0] = 1.0
vb.Nod.C[5, 1] = 1.0
vb.Nod.S = self.qcifc.get_overlap()
self.blockdims = ((5, 5), (1, 1))
self.wf = vb.WaveFunction(
[vb.Structure(
[vb.Nod([0], [1]), vb.Nod([1], [0])],
[1.0, 1.0]
),
vb.Structure([vb.Nod([0], [0])], [1.0]),
vb.Structure([vb.Nod([1], [1])], [1.0]),
],
[1.0, 0.0, 0.0],
tmpdir = self.tmp,
blockdims=self.blockdims
)
# In this setup we have local expansions of mos, leading to a block diagonal C
self.final = full.matrix(13)
self.final_coef =[0.83675, 0.09850, 0.09850]
self.final[:3] = self.final_coef
self.final_C = full.init([
[0.7633862173, 0.3075441467, 0.0, 0.0, 0.0328947818,0,0,0,0,0],
[0,0,0,0,0, 0.7633862173, 0.3075441467, 0.0, 0.0, -0.0328947818]
])
self.final[3:8] = self.final_C[:5, 0]
self.final[8:13] = self.final_C[5:, 1]
self.wf.normalize_structures()
self.xfg = VBMinimizer(self.wf)
def normgrad(self):
"""
# N = <0|0>
# dN = 2<d0|0>
"""
NGS = []
r, c = Nod.C.shape
n_orb_grad = full.matrix((r, c))
#
for S, CS in zip(self.structs, self.coef):
GS = 0
for T, CT in zip(self.structs, self.coef):
GS += (S*T)*CT
for K, CK in zip(S.nods, S.coef):
for L, CL in zip(T.nods, T.coef):
n_orb_grad += (CS*CT*CK*CL) * \
BraKet(K, L).right_overlap_gradient()
NGS.append(GS)
n_struct_grad = full.init(NGS)
n_struct_grad *= 2
n_orb_grad *= 2
return (n_struct_grad, n_orb_grad[:, :])
def setup_trials(self, vectors, td=None, b=None, renormalize=True):
"""
Set up initial trial vectors from a set of intial guesses
"""
trials = []
for (op, freq), vec in vectors.items():
if td is not None:
v = vec / td[freq]
else:
v = vec
if numpy.linalg.norm(v) > SMALL:
trials.append(v)
if freq > SMALL:
trials.append(swap(v))
new_trials = full.init(trials)
if b is not None:
new_trials = new_trials - b * b.T * new_trials
if trials and renormalize:
t = get_transform(new_trials)
truncated = new_trials * t
S12 = (truncated.T * truncated).invsqrt()
new_trials = truncated * S12
return new_trials
from util.full import init
Z = [8.0, 1.0, 1.0]
Rc = init([0.00000000, 0.00000000, 0.48860959])
Dtot = [0, 0, -0.76539388]
Daa = init([
[0.00000000, 0.00000000, -0.28357300],
[0.15342658, 0.00000000, 0.12734703],
[-0.15342658, 0.00000000, 0.12734703],
])
QUc = init([-7.31176220, 0.0, 0.0, -5.43243232, 0.0, -6.36258665])
QUN = init([4.38968295, 0.0, 0.0, 0.0, 0.0, 1.75400326])
QUaa = init([
[
-3.29253618, 0.00000000, 0.00000000, -4.54316657, 0.00000000,
-4.00465380
],
[
-0.13213704, 0.00000000, 0.24980518, -0.44463288, 0.00000000,
-0.26059139
],
[
-0.13213704, 0.00000000, -0.24980518, -0.44463288, 0.00000000,
-0.26059139
],
])
Fab = init([
[-0.11e-03, 0.55e-04, 0.55e-04],
[0.55e-04, -0.55e-04, 0.16e-30],
[0.55e-04, 0.16e-30, -0.55e-04],
])
def test_unit(self):
identity = init([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
np.testing.assert_almost_equal(unit(3), identity)
def test_struct_mo_propagated(self):
ab = Structure([self.ab00], [1.0])
ab.C = init([1,2,3,4])
self.assertEqual(id(ab.C), id(ab.nods[0].C))
def test_unit2(self):
identity = init([[2, 0, 0], [0, 2, 0], [0, 0, 2]])
np.testing.assert_almost_equal(unit(3, factor=2), identity)
def test_s2n_S():
refs2 = matrix.diag([1, -1])
s2 = init([oli.s2n(n, tmpdir=suppdir) for n in unit(2)])
assert_(s2, refs2)
import os
from util.full import init
Z = [8., 1., 1.]
Rc = init([0.00000000, 0.00000000, 0.48860959])
Dtot = [0, 0, -0.76539388]
Daa = init([
[ 0.00000000, 0.00000000, -0.28357300],
[ 0.15342658, 0.00000000, 0.12734703],
[-0.15342658, 0.00000000, 0.12734703],
])
QUc = init([-7.31176220, 0., 0., -5.43243232, 0., -6.36258665])
QUN = init([4.38968295, 0., 0., 0., 0., 1.75400326])
QUaa = init([
[-3.29253618, 0.00000000, 0.00000000, -4.54316657, 0.00000000, -4.00465380],
[-0.13213704, 0.00000000, 0.24980518, -0.44463288, 0.00000000, -0.26059139],
[-0.13213704, 0.00000000,-0.24980518, -0.44463288, 0.00000000, -0.26059139]
])
Fab = init([
[-0.11E-03, 0.55E-04, 0.55E-04],
[ 0.55E-04, -0.55E-04, 0.16E-30],
[ 0.55E-04, 0.16E-30, -0.55E-04]
])
Lab = init([
[0.11E-03, 0.28E-03, 0.28E-03],
[0.28E-03, 0.17E-03, 0.22E-03],
[0.28E-03, 0.22E-03, 0.17E-03]
])
la = init([
[0.0392366,-27.2474016 , 27.2081650],
[0.0358964, 27.2214515 ,-27.2573479],
def test_setup_initial_multiplier(self):
self.pfg.x = full.init(self.p0 + self.l0)
numpy.testing.assert_allclose(self.pfg.l, self.l0)
def test_setup_final_multiplier(self):
self.pfg.x = full.init(self.p1 + self.l1)
numpy.testing.assert_allclose(self.pfg.l, self.l1)
def test_setup_initial_function(self):
self.pfg.x = full.init(self.p0 + self.l0)
numpy.testing.assert_allclose(self.pfg.fp(self.pfg.p), -1.0)
def x(self):
_x = full.init(tuple(self.p) + tuple(self.l))
return _x
def test_e2n_S():
refe2 = init([[0.78643356, -0.50624296], [-0.50624296, 0.78643356]])
e2 = [oli.e2n(n, tmpdir=suppdir) for n in unit(2)]
assert_(e2, refe2)
def test_svd(self):
A = init([[1, 1, sqrt(3)], [-1, -1, 0]])
u, s, v = A.svd()
np.testing.assert_almost_equal(A, u * s * v.T)
def test_dihedral_eclipsed(self):
A = init([1, 1, 0])
B = init([1, 0, 0])
C = init([0, 0, 0])
D = init([0, 1, 0])
np.testing.assert_equal(A.dihedral(B, C, D), 0)
def test_setup_initial_point(self):
self.pfg.x = full.init(self.p0 + self.l0)
numpy.testing.assert_allclose(self.pfg.p, self.p0)
def test_e2n_S():
refe2 = init([[0.91587038, -0.00000000], [0.00000000, 0.91587038]])
e2 = init([oli.e2n(n, tmpdir=suppdir) for n in unit(2)])
assert_(e2, refe2)
def test_minimize_from_final_plus_noise(self):
self.pfg.x = full.init(self.p1 + self.l1) + 1e-4*numpy.random.random(3)
self.pfg.minimize()
numpy.testing.assert_allclose(self.pfg.p, self.p1, atol=1e-4)
def test_setup_final_point(self):
self.pfg.x = full.init(self.p1 + self.l1)
numpy.testing.assert_allclose(self.pfg.p, self.p1)
def structure_overlap(self):
"""Calculate structure overlap matrix"""
return full.init([[s*t for t in self.structs] for s in self.structs])