def test_concatMap():
"""
concatMap f == concat (map f)
"""
f = lambda x: [x * 2]
xs = [1, 2]
assert concatMap(f, xs) == list(concat(map(f, xs)))
def test_opt_gamess():
"""
Test Optimization in Gamess using methanol in water.
"""
methanol = Molecule('test/test_files/ion_methanol.xyz')
methanol.properties['symmetry'] = 'Cs'
s = Settings()
s.specific.gamess.contrl.nzvar = 12
s.specific.gamess.system.timlim = 2
s.specific.gamess.system.mwords = 2
s.specific.gamess.pcm.solvnt = 'water'
s.specific.gamess.basis.gbasis = 'sto'
s.specific.gamess.basis.ngauss = 3
s.specific.gamess.guess.guess = 'huckel'
s.specific.gamess.stapt.optol = '1d-5'
s.specific.gamess.zmat["izmat(1)"] = "1,1,2, 1,2,3, 1,3,4, 1,3,5, 1,3,6, \n"\
"2,1,2,3, 2,2,3,4, 2,2,3,5, 2,2,3,6, \n"\
"3,1,2,3,4, 3,1,2,3,5, 3,1,2,3,6"
inp = templates.geometry.overlay(s)
methanol_geometry = gamess(inp, methanol, work_dir='/tmp')
mol_opt = run(methanol_geometry.molecule)
coords = concat([a.coords for a in mol_opt.atoms])
expected_coords = [
-0.9956983464, 0.9204754677, -0.0002616586, -0.72585581, -0.0802380791,
2.18166e-05, 0.741292161, 0.0371204735, -1.69738e-05, 1.1448441964,
0.5632291664, -0.9026112278, 1.1448447102, 0.562978981, 0.9027182521,
1.1454516521, -0.9993402516, 1.04943e-05
]
assert abs(sum(zipWith(operator.sub)(coords)(expected_coords))) < 1e-7
def test_concatMap():
"""
concatMap f == concat (map f)
"""
f = lambda x: [x * 2]
xs = [1, 2]
assert concatMap(f, xs) == list(concat(map(f, xs)))
def calc_orbital_Slabels(name, fss):
"""
Most quantum packages use standard basis set which contraction is
presented usually by a format like:
c def2-SV(P)
# c (7s4p1d) / [3s2p1d] {511/31/1}
this mean that this basis set for the Carbon atom uses 7 ``s`` CGF,
4 ``p`` CGF and 1 ``d`` CGFs that are contracted in 3 groups of 5-1-1
``s`` functions, 3-1 ``p`` functions and 1 ``d`` function. Therefore
the basis set format can be represented by [[5,1,1], [3,1], [1]].
On the other hand Cp2k uses a special basis set ``MOLOPT`` which
format explanation can be found at: `C2pk
<https://github.com/cp2k/cp2k/blob/e392d1509d7623f3ebb6b451dab00d1dceb9a248/cp2k/data/BASIS_MOLOPT>`_.
:parameter name: Quantum package name
:type name: string
:parameter fss: Format basis set
:type fss: [Int] | [[Int]]
"""
def funSlabels(d, l, fs):
if isinstance(fs, list):
fs = sum(fs)
labels = [d[l]] * fs
return labels
angularM = ['s', 'p', 'd', 'f', 'g']
if name == 'cp2k':
dict_Ord_Labels = dict_cp2kOrder_spherical
else:
raise NotImplementedError
return concat(
[funSlabels(dict_Ord_Labels, l, fs) for l, fs in zip(angularM, fss)])
def create_alpha_paths(lattice_cte):
"""
Create all the initial and final paths between gamma alpha and Chi_bb
"""
def zip_path_coord(initials, finals):
return concat([
list(zip(itertools.repeat(init), fs))
for init, fs in zip(initials, finals)
])
initial_alpha_pos = [(2, 0, 0), (0, 2, 0), (0, 0, 2)]
final_alpha_x = [(1, 1, 0), (1, -1, 0), (1, 0, 1), (1, 0, -1)]
final_alpha_y = [swap(t, 0, 1) for t in final_alpha_x]
final_alpha_z = [swap(t, 1, 2) for t in final_alpha_y]
final_positives = [final_alpha_x, final_alpha_y, final_alpha_z]
positives = zip_path_coord(initial_alpha_pos, final_positives)
initial_alpha_neg = [
mirror_axis(t, i) for i, t in enumerate(initial_alpha_pos)
]
final_negatives = [
list(map(lambda xs: mirror_axis(xs, i), fs))
for i, fs in enumerate(final_positives)
]
negatives = zip_path_coord(initial_alpha_neg, final_negatives)
paths = concat([positives, negatives])
return map_fun(lambda x: x * 2 * pi / lattice_cte, paths)
def test_opt_gamess():
"""
Test Optimization in Gamess using methanol in water.
"""
methanol = Molecule('test/test_files/ion_methanol.xyz')
methanol.properties['symmetry'] = 'Cs'
s = Settings()
s.specific.gamess.contrl.nzvar = 12
s.specific.gamess.system.timlim = 2
s.specific.gamess.system.mwords = 2
s.specific.gamess.pcm.solvnt = 'water'
s.specific.gamess.basis.gbasis = 'sto'
s.specific.gamess.basis.ngauss = 3
s.specific.gamess.guess.guess = 'huckel'
s.specific.gamess.stapt.optol = '1d-5'
s.specific.gamess.zmat["izmat(1)"] = "1,1,2, 1,2,3, 1,3,4, 1,3,5, 1,3,6, \n"\
"2,1,2,3, 2,2,3,4, 2,2,3,5, 2,2,3,6, \n"\
"3,1,2,3,4, 3,1,2,3,5, 3,1,2,3,6"
inp = templates.geometry.overlay(s)
methanol_geometry = gamess(inp, methanol, work_dir='/tmp')
mol_opt = run(methanol_geometry.molecule)
coords = concat([a.coords for a in mol_opt.atoms])
expected_coords = [-0.9956983464, 0.9204754677, -0.0002616586, -0.72585581,
-0.0802380791, 2.18166e-05, 0.741292161, 0.0371204735,
-1.69738e-05, 1.1448441964, 0.5632291664, -0.9026112278,
1.1448447102, 0.562978981, 0.9027182521,
1.1454516521, -0.9993402516, 1.04943e-05]
assert abs(sum(zipWith(operator.sub)(coords)(expected_coords))) < 1e-7
def create_beta_paths(lattice_cte):
"""
Create all the initial and final paths between gamma alpha and Chi_bb
"""
gammas_beta = [(1, 1, 1), (-1, 1, 1), (1, -1, 1), (1, 1, -1), (-1, -1, 1),
(1, -1, -1), (-1, 1, -1), (-1, -1, -1)]
paths = concat([mirror_cube(gamma) for gamma in gammas_beta])
return map_fun(lambda x: x * 2 * pi / lattice_cte, paths)
def calc_orbital_Clabels(name, fss):
"""
Labels of the Cartesian CGFs
"""
def funClabels(d, l, fs):
if isinstance(fs, list):
fs = sum(fs)
labels = [d[l]] * fs
return labels
angularM = ['s', 'p', 'd', 'f', 'g']
if name == 'cp2k':
dict_Ord_Labels = dict_cp2kOrd_cartesian
if name == 'turbomole':
dict_Ord_Labels = dict_turbomoleOrd_cartesian
raise NotImplementedError
return concat(
[funClabels(dict_Ord_Labels, l, fs) for l, fs in zip(angularM, fss)])
def readTurbomoleBasis(path):
"""Read Turbomole basis set"""
bss = topParseB.parseFile(path)
atoms = [xs.atomLabel.lower() for xs in bss]
names = concat([xs.basisName.upper().split() for xs in bss])
formats = [xs.format[:] for xs in bss]
formats_int = map(lambda fss: [[int(x) for x in xs]
for xs in fss], formats)
rss = [rs.coeffs[:] for rs in bss]
rawData = [[x.contractions[:] for x in rss[i]] for i in range(len(rss))]
fst = lambda xs: xs[0]
snd = lambda xs: xs[1]
expos = list(map(mapFloat, [concatMap(fst, swapCoeff(2, rawData[i]))
for i in range(len(rawData))]))
coeffs = list(map(mapFloat, [concatMap(snd, swapCoeff(2, rawData[i]))
for i in range(len(rawData))]))
basisData = zipWith(AtomBasisData)(expos)(coeffs)
basiskey = zipWith3(AtomBasisKey)(atoms)(names)(formats_int)
return basiskey, basisData
def test_methanol_opt_orca():
"""
Run a methanol optimization and retrieve the optimized geom.
"""
methanol = Molecule('test/test_files/methanol.xyz')
s = Settings()
s.specific.orca.main = "RKS B3LYP SVP Opt TightSCF SmallPrint"
opt = orca(s, methanol)
mol_opt = run(opt.molecule)
expected_coords = [-1.311116, -0.051535, -0.000062, 0.097548, 0.033890,
-0.000077, -1.683393, -1.092152, -0.000066,
-1.734877, 0.448868, 0.891460, -1.734894, 0.448881,
-0.891567, 0.460481, -0.857621, -0.000038]
coords = concat([a.coords for a in mol_opt.atoms])
assert abs(sum(zipWith(operator.sub)(coords)(expected_coords))) < 1e-7
def fun2(ess, css, fs):
def funAcc(acc, x):
n, xs = acc
return (n + x, xs + [n + x])
def accum(l, n, xs):
def go(t, k):
index, acc = t
xss = css[index:k + index]
yss = ess[index:k + index]
rss = expandBasis_turbomole(l, yss, xss)
return (index + k, acc + rss)
return reduce(go, xs, (n, []))
# print(fs)
fss = str2ListofList(fs)
# snd . foldl' funAcc (0,[0]) (map sum fss)
lens = snd(reduce(funAcc, list(map(sum, fss)), (0, [0])))
return concat(
[snd(accum(l, n, xs)) for (l, n, xs) in zip(orbLabels, lens, fss)])
def test_concat():
"""
Test list concatenation
"""
xss = [[1], [2]]
assert concat(xss) == [1, 2]
def concatSwapCoeff(xss, m, n):
if n == 0:
return concat(swapCoeff(m)(cs.coeffs[:] for cs in xss))
else:
xs = concat(swapCoeff(m)(cs.coeffs[:] for cs in xss[:-1]))
return xs + concat(swapCoeff(n)([list(xss[-1].lastCoeffs)]))
def test_concat():
"""
Test list concatenation
"""
xss = [[1], [2]]
assert concat(xss) == [1, 2]
def zip_path_coord(initials, finals):
return concat([
list(zip(itertools.repeat(init), fs))
for init, fs in zip(initials, finals)
])