alpha_tot += alpha
beta_tot += beta
l_zeff.append(zeff)
# _
# /\ _| _| _|_ _ _ _ _|_ o _
# /--\ (_| (_| |_ (_) (/_ /_ | | (_)
#
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.nuclei_nucl_charge = l_zeff
alpha_tot = ezfio.get_electrons_elec_alpha_num() - alpha_tot
beta_tot = ezfio.get_electrons_elec_beta_num() - beta_tot
ezfio.electrons_elec_alpha_num = alpha_tot
ezfio.electrons_elec_beta_num = beta_tot
# Change all the array 'cause EZFIO
# v_kl (v, l) => v_kl(l,v)
# v_kl => zip(*_v_kl)
# [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]]
# [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)]
# ~#~#~#~#~ #
# L o c a l #
# ~#~#~#~#~ #
alpha_tot += alpha
beta_tot += beta
l_zeff.append(zeff)
# _
# /\ _| _| _|_ _ _ _ _|_ o _
# /--\ (_| (_| |_ (_) (/_ /_ | | (_)
#
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.nuclei_nucl_charge = l_zeff
alpha_tot = ezfio.get_electrons_elec_alpha_num() - alpha_tot
beta_tot = ezfio.get_electrons_elec_beta_num() - beta_tot
ezfio.electrons_elec_alpha_num = alpha_tot
ezfio.electrons_elec_beta_num = beta_tot
# Change all the array 'cause EZFIO
# v_kl (v, l) => v_kl(l,v)
# v_kl => zip(*_v_kl)
# [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]]
# [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)]
# ~#~#~#~#~ #
# L o c a l #
# ~#~#~#~#~ #
# |\/| o _ _
# | | | _> (_
#
def list_to_string(l):
return " ".join(map(str, l))
ao_num = ezfio.get_ao_basis_ao_num()
print "ao_num", ao_num
mo_num = ezfio.get_mo_basis_mo_tot_num()
print "mo_num", mo_num
alpha = ezfio.get_electrons_elec_alpha_num()
beta = ezfio.get_electrons_elec_beta_num()
print "elec_alpha_num", alpha
print "elec_beta_num", beta
print "elec_tot_num", alpha + beta
print "spin_multiplicity", (alpha - beta) + 1
l_label = ezfio.get_nuclei_nucl_label()
l_charge = ezfio.get_nuclei_nucl_charge()
l_coord = ezfio.get_nuclei_nucl_coord()
l_coord_str = [list_to_string(i) for i in zip(*l_coord)]
print "nucl_num", len(l_label)
# _
def write_ezfio(res, filename):
res.clean_uncontractions()
ezfio.set_file(filename)
# _
# |_ | _ _ _|_ ._ _ ._ _
# |_ | (/_ (_ |_ | (_) | | _>
#
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
ezfio.set_electrons_elec_beta_num(res.num_beta)
#
# |\ | _ | _ o
# | \| |_| (_ | (/_ |
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
charge = []
coord_x = []
coord_y = []
coord_z = []
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
for a in res.geometry:
charge.append(a.charge)
if res.units == 'BOHR':
coord_x.append(a.coord[0])
coord_y.append(a.coord[1])
coord_z.append(a.coord[2])
else:
coord_x.append(a.coord[0] / a0)
coord_y.append(a.coord[1] / a0)
coord_z.append(a.coord[2] / a0)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_nuclei_nucl_num(len(res.geometry))
ezfio.set_nuclei_nucl_charge(charge)
# Transformt H1 into H
import re
p = re.compile(ur'(\d*)$')
label = [p.sub("", x.name).capitalize() for x in res.geometry]
ezfio.set_nuclei_nucl_label(label)
ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
# _
# /\ _ _ |_) _. _ o _
# /--\ (_) _> |_) (_| _> | _>
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
import string
at = []
num_prim = []
power_x = []
power_y = []
power_z = []
coefficient = []
exponent = []
res.clean_contractions()
res.convert_to_cartesian()
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
for b in res.basis:
c = b.center
for i, atom in enumerate(res.geometry):
if atom.coord == c:
at.append(i + 1)
num_prim.append(len(b.prim))
s = b.sym
power_x.append(string.count(s, "x"))
power_y.append(string.count(s, "y"))
power_z.append(string.count(s, "z"))
coefficient.append(b.coef)
exponent.append([p.expo for p in b.prim])
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_ao_basis_ao_num(len(res.basis))
ezfio.set_ao_basis_ao_nucl(at)
ezfio.set_ao_basis_ao_prim_num(num_prim)
ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
for i in range(len(res.basis)):
coefficient[i] += [
0. for j in range(len(coefficient[i]), prim_num_max)
]
exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)]
coefficient = reduce(lambda x, y: x + y, coefficient, [])
exponent = reduce(lambda x, y: x + y, exponent, [])
coef = []
expo = []
for i in range(prim_num_max):
for j in range(i, len(coefficient), prim_num_max):
coef.append(coefficient[j])
expo.append(exponent[j])
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_ao_basis_ao_coef(coef)
ezfio.set_ao_basis_ao_expo(expo)
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
# _
# |\/| _ _ |_) _. _ o _
# | | (_) _> |_) (_| _> | _>
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
MoTag = res.determinants_mo_type
ezfio.set_mo_basis_mo_label('Orthonormalized')
MO_type = MoTag
allMOs = res.mo_sets[MO_type]
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
try:
closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos]
active = [(allMOs[i].eigenvalue, i) for i in res.active_mos]
virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos]
except:
closed = []
virtual = []
active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
closed = map(lambda x: x[1], closed)
active = map(lambda x: x[1], active)
virtual = map(lambda x: x[1], virtual)
MOindices = closed + active + virtual
MOs = []
for i in MOindices:
MOs.append(allMOs[i])
mo_tot_num = len(MOs)
while len(MOindices) < mo_tot_num:
MOindices.append(len(MOindices))
MOmap = list(MOindices)
for i in range(len(MOindices)):
MOmap[i] = MOindices.index(i)
energies = []
for i in xrange(mo_tot_num):
energies.append(MOs[i].eigenvalue)
if res.occ_num is not None:
OccNum = []
for i in MOindices:
OccNum.append(res.occ_num[MO_type][i])
while len(OccNum) < mo_tot_num:
OccNum.append(0.)
MoMatrix = []
sym0 = [i.sym for i in res.mo_sets[MO_type]]
sym = [i.sym for i in res.mo_sets[MO_type]]
for i in xrange(len(sym)):
sym[MOmap[i]] = sym0[i]
MoMatrix = []
for i in xrange(len(MOs)):
m = MOs[i]
for coef in m.vector:
MoMatrix.append(coef)
while len(MoMatrix) < len(MOs[0].vector)**2:
MoMatrix.append(0.)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
ezfio.set_mo_basis_mo_occ(OccNum)
ezfio.set_mo_basis_mo_coef(MoMatrix)
# ______ _
# | ___ \ | |
# | |_/ /__ ___ _ _ __| | ___
# | __/ __|/ _ \ | | |/ _` |/ _ \
# | | \__ \ __/ |_| | (_| | (_) |
# \_| |___/\___|\__,_|\__,_|\___/
#
# INPUT
# {% for lanel,zcore, l_block in l_atom $}
# #local l_block l=0}
# {label} GEN {zcore} {len(l_block)-1 #lmax_block}
# {% for l_param in l_block%}
# {len(l_param) # list of parameter aka n_max_bock_max(n)}
# {% for coef,n,zeta for l_param}
# {coef,n, zeta}
# OUTPUT
# Local are 1 array padded by max(n_max_block) when l == 0 (output:k_loc_max)
# v_k[n-2][atom] = value
#Non Local are 2 array padded with max of lmax_block when l!=0 (output:lmax+1) and max(n_max_block)whem l !=0 (kmax)
# v_kl[l][n-2][atom] = value
def pad(array, size, value=0):
new_array = array
for add in xrange(len(array), size):
new_array.append(value)
return new_array
def parse_str(pseudo_str):
'''Return 4d array atom,l,n, attribute (attribute is coef, n, zeta)'''
matrix = []
array_l_max_block = []
array_z_remove = []
for block in [b for b in pseudo_str.split('\n\n') if b]:
#First element is header, the rest are l_param
array_party = [i for i in re.split(r"\n\d+\n", block) if i]
z_remove, l_max_block = map(int, array_party[0].split()[-2:])
array_l_max_block.append(l_max_block)
array_z_remove.append(z_remove)
x = []
for l in array_party[1:]:
y = []
for coef_n_zeta in l.split('\n'):
z = coef_n_zeta.split()
if z: y.append(z)
x.append(y)
matrix.append(x)
return (matrix, array_l_max_block, array_z_remove)
def get_local_stuff(matrix):
matrix_local_unpad = [atom[0] for atom in matrix]
k_loc_max = max(len(i) for i in matrix_local_unpad)
matrix_local = [
pad(ll, k_loc_max, [0., 2, 0.]) for ll in matrix_local_unpad
]
m_coef = [[float(i[0]) for i in atom] for atom in matrix_local]
m_n = [[int(i[1]) - 2 for i in atom] for atom in matrix_local]
m_zeta = [[float(i[2]) for i in atom] for atom in matrix_local]
return (k_loc_max, m_coef, m_n, m_zeta)
def get_non_local_stuff(matrix):
matrix_unlocal_unpad = [atom[1:] for atom in matrix]
l_max_block = max(len(i) for i in matrix_unlocal_unpad)
k_max = max(
[len(item) for row in matrix_unlocal_unpad for item in row])
matrix_unlocal_semipaded = [[
pad(item, k_max, [0., 2, 0.]) for item in row
] for row in matrix_unlocal_unpad]
empty_row = [[0., 2, 0.] for k in range(l_max_block)]
matrix_unlocal = [
pad(ll, l_max_block, empty_row) for ll in matrix_unlocal_semipaded
]
m_coef_noloc = [[[float(k[0]) for k in j] for j in i]
for i in matrix_unlocal]
m_n_noloc = [[[int(k[1]) - 2 for k in j] for j in i]
for i in matrix_unlocal]
m_zeta_noloc = [[[float(k[2]) for k in j] for j in i]
for i in matrix_unlocal]
return (l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc)
try:
pseudo_str = []
label = ezfio.get_nuclei_nucl_label()
for ecp in res.pseudo:
pseudo_str += [
"%(label)s GEN %(zcore)d %(lmax)d" % {
"label": label[ecp["atom"] - 1],
"zcore": ecp["zcore"],
"lmax": ecp["lmax"]
}
]
lmax = ecp["lmax"]
for l in [lmax] + list(range(0, lmax)):
pseudo_str += ["%d" % len(ecp[str(l)])]
for t in ecp[str(l)]:
pseudo_str += ["%f %d %f" % t]
pseudo_str += [""]
pseudo_str = "\n".join(pseudo_str)
matrix, array_l_max_block, array_z_remove = parse_str(pseudo_str)
array_z_remove = map(float, array_z_remove)
except:
ezfio.set_pseudo_do_pseudo(False)
else:
ezfio.set_pseudo_do_pseudo(True)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.set_pseudo_nucl_charge_remove(array_z_remove)
charge = ezfio.get_nuclei_nucl_charge()
charge = [i - j for i, j in zip(charge, array_z_remove)]
ezfio.set_nuclei_nucl_charge(charge)
import math
num_elec_diff = sum(array_z_remove) / 2
nalpha = ezfio.get_electrons_elec_alpha_num() - num_elec_diff
nbeta = ezfio.get_electrons_elec_beta_num() - num_elec_diff
ezfio.set_electrons_elec_alpha_num(nalpha)
ezfio.set_electrons_elec_beta_num(nbeta)
# Change all the array 'cause EZFIO
# v_kl (v, l) => v_kl(l,v)
# v_kl => zip(*_v_kl)
# [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]]
# [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)]
# ~#~#~#~#~ #
# L o c a l #
# ~#~#~#~#~ #
klocmax, m_coef, m_n, m_zeta = get_local_stuff(matrix)
ezfio.pseudo_pseudo_klocmax = klocmax
ezfio.pseudo_pseudo_v_k = zip(*m_coef)
ezfio.pseudo_pseudo_n_k = zip(*m_n)
ezfio.pseudo_pseudo_dz_k = zip(*m_zeta)
# ~#~#~#~#~#~#~#~#~ #
# N o n _ L o c a l #
# ~#~#~#~#~#~#~#~#~ #
l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc = get_non_local_stuff(
matrix)
ezfio.pseudo_pseudo_lmax = l_max_block - 1
ezfio.pseudo_pseudo_kmax = k_max
ezfio.pseudo_pseudo_v_kl = zip(*m_coef_noloc)
ezfio.pseudo_pseudo_n_kl = zip(*m_n_noloc)
ezfio.pseudo_pseudo_dz_kl = zip(*m_zeta_noloc)
#
# |\/| o _ _
# | | | _> (_
#
def list_to_string(l):
return " ".join(map(str, l))
ao_num = ezfio.get_ao_basis_ao_num()
print "ao_num", ao_num
mo_num = ezfio.get_mo_basis_mo_tot_num()
print "mo_num", mo_num
alpha = ezfio.get_electrons_elec_alpha_num()
beta = ezfio.get_electrons_elec_beta_num()
print "elec_alpha_num", alpha
print "elec_beta_num", beta
print "elec_tot_num", alpha + beta
print "spin_multiplicity", 2 * (alpha - beta) + 1
l_label = ezfio.get_nuclei_nucl_label()
l_charge = ezfio.get_nuclei_nucl_charge()
l_coord = ezfio.get_nuclei_nucl_coord()
l_coord_str = [list_to_string(i) for i in zip(*l_coord)]
print "nucl_num", len(l_label)
# _
def write_ezfio(res, filename):
res.clean_uncontractions()
ezfio.set_file(filename)
# _
# |_ | _ _ _|_ ._ _ ._ _
# |_ | (/_ (_ |_ | (_) | | _>
#
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
ezfio.set_electrons_elec_beta_num(res.num_beta)
#
# |\ | _ | _ o
# | \| |_| (_ | (/_ |
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
charge = []
coord_x = []
coord_y = []
coord_z = []
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
for a in res.geometry:
charge.append(a.charge)
if res.units == 'BOHR':
coord_x.append(a.coord[0])
coord_y.append(a.coord[1])
coord_z.append(a.coord[2])
else:
coord_x.append(a.coord[0] / a0)
coord_y.append(a.coord[1] / a0)
coord_z.append(a.coord[2] / a0)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_nuclei_nucl_num(len(res.geometry))
ezfio.set_nuclei_nucl_charge(charge)
# Transformt H1 into H
import re
p = re.compile(ur'(\d*)$')
label = [p.sub("", x.name).capitalize() for x in res.geometry]
ezfio.set_nuclei_nucl_label(label)
ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
# _
# /\ _ _ |_) _. _ o _
# /--\ (_) _> |_) (_| _> | _>
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
import string
at = []
num_prim = []
power_x = []
power_y = []
power_z = []
coefficient = []
exponent = []
res.clean_contractions()
res.convert_to_cartesian()
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
for b in res.basis:
c = b.center
for i, atom in enumerate(res.geometry):
if atom.coord == c:
at.append(i + 1)
num_prim.append(len(b.prim))
s = b.sym
power_x.append(string.count(s, "x"))
power_y.append(string.count(s, "y"))
power_z.append(string.count(s, "z"))
coefficient.append(b.coef)
exponent.append([p.expo for p in b.prim])
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_ao_basis_ao_num(len(res.basis))
ezfio.set_ao_basis_ao_nucl(at)
ezfio.set_ao_basis_ao_prim_num(num_prim)
ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
for i in range(len(res.basis)):
coefficient[
i] += [0. for j in range(len(coefficient[i]), prim_num_max)]
exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)]
coefficient = reduce(lambda x, y: x + y, coefficient, [])
exponent = reduce(lambda x, y: x + y, exponent, [])
coef = []
expo = []
for i in range(prim_num_max):
for j in range(i, len(coefficient), prim_num_max):
coef.append(coefficient[j])
expo.append(exponent[j])
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_ao_basis_ao_coef(coef)
ezfio.set_ao_basis_ao_expo(expo)
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
# _
# |\/| _ _ |_) _. _ o _
# | | (_) _> |_) (_| _> | _>
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
MoTag = res.determinants_mo_type
ezfio.set_mo_basis_mo_label('Orthonormalized')
MO_type = MoTag
allMOs = res.mo_sets[MO_type]
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
try:
closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos]
active = [(allMOs[i].eigenvalue, i) for i in res.active_mos]
virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos]
except:
closed = []
virtual = []
active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
closed = map(lambda x: x[1], closed)
active = map(lambda x: x[1], active)
virtual = map(lambda x: x[1], virtual)
MOindices = closed + active + virtual
MOs = []
for i in MOindices:
MOs.append(allMOs[i])
mo_tot_num = len(MOs)
while len(MOindices) < mo_tot_num:
MOindices.append(len(MOindices))
MOmap = list(MOindices)
for i in range(len(MOindices)):
MOmap[i] = MOindices.index(i)
energies = []
for i in xrange(mo_tot_num):
energies.append(MOs[i].eigenvalue)
if res.occ_num is not None:
OccNum = []
for i in MOindices:
OccNum.append(res.occ_num[MO_type][i])
while len(OccNum) < mo_tot_num:
OccNum.append(0.)
MoMatrix = []
sym0 = [i.sym for i in res.mo_sets[MO_type]]
sym = [i.sym for i in res.mo_sets[MO_type]]
for i in xrange(len(sym)):
sym[MOmap[i]] = sym0[i]
MoMatrix = []
for i in xrange(len(MOs)):
m = MOs[i]
for coef in m.vector:
MoMatrix.append(coef)
while len(MoMatrix) < len(MOs[0].vector)**2:
MoMatrix.append(0.)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
ezfio.set_mo_basis_mo_occ(OccNum)
ezfio.set_mo_basis_mo_coef(MoMatrix)
# ______ _
# | ___ \ | |
# | |_/ /__ ___ _ _ __| | ___
# | __/ __|/ _ \ | | |/ _` |/ _ \
# | | \__ \ __/ |_| | (_| | (_) |
# \_| |___/\___|\__,_|\__,_|\___/
#
# INPUT
# {% for lanel,zcore, l_block in l_atom $}
# #local l_block l=0}
# {label} GEN {zcore} {len(l_block)-1 #lmax_block}
# {% for l_param in l_block%}
# {len(l_param) # list of parameter aka n_max_bock_max(n)}
# {% for coef,n,zeta for l_param}
# {coef,n, zeta}
# OUTPUT
# Local are 1 array padded by max(n_max_block) when l == 0 (output:k_loc_max)
# v_k[n-2][atom] = value
#Non Local are 2 array padded with max of lmax_block when l!=0 (output:lmax+1) and max(n_max_block)whem l !=0 (kmax)
# v_kl[l][n-2][atom] = value
def pad(array, size, value=0):
new_array = array
for add in xrange(len(array), size):
new_array.append(value)
return new_array
def parse_str(pseudo_str):
'''Return 4d array atom,l,n, attribute (attribute is coef, n, zeta)'''
matrix = []
array_l_max_block = []
array_z_remove = []
for block in [b for b in pseudo_str.split('\n\n') if b]:
#First element is header, the rest are l_param
array_party = [i for i in re.split(r"\n\d+\n", block) if i]
z_remove, l_max_block = map(int, array_party[0].split()[-2:])
array_l_max_block.append(l_max_block)
array_z_remove.append(z_remove)
x = []
for l in array_party[1:]:
y = []
for coef_n_zeta in l.split('\n'):
z = coef_n_zeta.split()
if z : y.append(z)
x.append(y)
matrix.append(x)
return (matrix, array_l_max_block, array_z_remove)
def get_local_stuff(matrix):
matrix_local_unpad = [atom[0] for atom in matrix]
k_loc_max = max(len(i) for i in matrix_local_unpad)
matrix_local = [ pad(ll, k_loc_max, [0., 2, 0.]) for ll in matrix_local_unpad]
m_coef = [[float(i[0]) for i in atom] for atom in matrix_local]
m_n = [[int(i[1]) - 2 for i in atom] for atom in matrix_local]
m_zeta = [[float(i[2]) for i in atom] for atom in matrix_local]
return (k_loc_max, m_coef, m_n, m_zeta)
def get_non_local_stuff(matrix):
matrix_unlocal_unpad = [atom[1:] for atom in matrix]
l_max_block = max(len(i) for i in matrix_unlocal_unpad)
k_max = max([len(item) for row in matrix_unlocal_unpad for item in row])
matrix_unlocal_semipaded = [[pad(item, k_max, [0., 2, 0.]) for item in row] for row in matrix_unlocal_unpad]
empty_row = [[0., 2, 0.] for k in range(l_max_block)]
matrix_unlocal = [ pad(ll, l_max_block, empty_row) for ll in matrix_unlocal_semipaded ]
m_coef_noloc = [[[float(k[0]) for k in j] for j in i] for i in matrix_unlocal]
m_n_noloc = [[[int(k[1]) - 2 for k in j] for j in i] for i in matrix_unlocal]
m_zeta_noloc = [[[float(k[2]) for k in j] for j in i] for i in matrix_unlocal]
return (l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc)
try:
pseudo_str = []
label = ezfio.get_nuclei_nucl_label()
for ecp in res.pseudo:
pseudo_str += [ "%(label)s GEN %(zcore)d %(lmax)d" % { "label": label[ ecp["atom"]-1 ],
"zcore": ecp["zcore"], "lmax": ecp["lmax"] } ]
lmax = ecp["lmax"]
for l in [lmax] + list(range(0,lmax)):
pseudo_str += [ "%d"%len(ecp[str(l)]) ]
for t in ecp[str(l)]:
pseudo_str += [ "%f %d %f"%t ]
pseudo_str += [""]
pseudo_str = "\n".join(pseudo_str)
matrix, array_l_max_block, array_z_remove = parse_str(pseudo_str)
array_z_remove = map(float,array_z_remove)
except:
ezfio.set_pseudo_do_pseudo(False)
else:
ezfio.set_pseudo_do_pseudo(True)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.set_pseudo_nucl_charge_remove(array_z_remove)
charge = ezfio.get_nuclei_nucl_charge()
charge = [ i - j for i, j in zip(charge, array_z_remove) ]
ezfio.set_nuclei_nucl_charge (charge)
import math
num_elec_diff = sum(array_z_remove)/2
nalpha = ezfio.get_electrons_elec_alpha_num() - num_elec_diff
nbeta = ezfio.get_electrons_elec_beta_num() - num_elec_diff
ezfio.set_electrons_elec_alpha_num(nalpha)
ezfio.set_electrons_elec_beta_num( nbeta )
# Change all the array 'cause EZFIO
# v_kl (v, l) => v_kl(l,v)
# v_kl => zip(*_v_kl)
# [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]]
# [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)]
# ~#~#~#~#~ #
# L o c a l #
# ~#~#~#~#~ #
klocmax, m_coef, m_n, m_zeta = get_local_stuff(matrix)
ezfio.pseudo_pseudo_klocmax = klocmax
ezfio.pseudo_pseudo_v_k = zip(*m_coef)
ezfio.pseudo_pseudo_n_k = zip(*m_n)
ezfio.pseudo_pseudo_dz_k = zip(*m_zeta)
# ~#~#~#~#~#~#~#~#~ #
# N o n _ L o c a l #
# ~#~#~#~#~#~#~#~#~ #
l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc = get_non_local_stuff(
matrix)
ezfio.pseudo_pseudo_lmax = l_max_block - 1
ezfio.pseudo_pseudo_kmax = k_max
ezfio.pseudo_pseudo_v_kl = zip(*m_coef_noloc)
ezfio.pseudo_pseudo_n_kl = zip(*m_n_noloc)
ezfio.pseudo_pseudo_dz_kl = zip(*m_zeta_noloc)