def write_ezfio(self,filename): ezfio.set_file(filename) ezfio.set_ao_basis_used_ao_num(self.nb_ao) ezfio.set_ao_basis_slater_ao_num(self.nb_ao) ezfio.set_ao_basis_slater_ao_prim_num(self.ao_prim_num_list) ezfio.set_ao_basis_slater_ao_nucl(self.ao_nucl_list) ezfio.set_ao_basis_slater_ao_n(self.n_list) ezfio.set_ao_basis_slater_ao_m(self.m_list) ezfio.set_ao_basis_slater_ao_l(self.l_list) ezfio.set_ao_basis_slater_ao_gamma(self.g_list) ezfio.set_ao_basis_slater_ao_coef(self.ao_coef_list) ezfio.set_mo_basis_mo_tot_num(self.nb_ao) ezfio.set_mo_basis_mo_coef(self.m_coef_list) ezfio.set_nuclei_nucl_num(1) ezfio.set_nuclei_nucl_charge([self.Z]) ezfio.set_nuclei_nucl_coord([0.,0.,0.]) ezfio.set_electrons_elec_beta_num(self.Z // 2) ezfio.set_electrons_elec_alpha_num(self.Z // 2 + self.Z % 2) ezfio.set_parameters_n_act(self.n_act) ezfio.set_parameters_n_virt(0) ezfio.set_parameters_n_core(0)
def check_convert(path_out):
'''
Path_out is the out_file
'''
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy = defaultdict(dict)
ref_energy["HBO.out"] = -100.0185822589
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
cmd = "cp {0}/tests/{1} .".format(qpackage_root, path_out)
subprocess.check_call([cmd], shell=True)
cmd = "qp_convert_output_to_ezfio.py {0}".format(path_out)
subprocess.check_call([cmd], shell=True)
# Test 2
cmd = "qp_edit -c {0}.ezfio".format(path_out)
subprocess.check_call([cmd], shell=True)
cmd = "qp_run SCF {0}.ezfio".format(path_out)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(path_out))
cur_e = ezfio.get_hartree_fock_energy()
ref_e = ref_energy[path_out]
if abs(cur_e - ref_e) <= precision:
subprocess.call(["rm {0}".format(path_out)], shell=True)
subprocess.call(["rm -R {0}.ezfio".format(path_out)], shell=True)
return True
else:
raise ValueError(get_error_message([ref_e], [cur_e]))
def check_convert(path_out):
'''
Path_out is the out_file
'''
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy = defaultdict(dict)
ref_energy["HBO.out"] = -100.0185822589
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
cmd = "qp_convert_output_to_ezfio.py {0}".format(path_out)
subprocess.check_call([cmd], shell=True)
# Test 2
cmd = "qp_edit -c {0}.ezfio".format(path_out)
subprocess.check_call([cmd], shell=True)
cmd = "qp_run SCF {0}.ezfio".format(path_out)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(path_out))
cur_e = ezfio.get_hartree_fock_energy()
ref_e = ref_energy[path_out]
if abs(cur_e - ref_e) <= precision:
subprocess.call(["rm -R {0}.ezfio".format(path_out)], shell=True)
return True
else:
raise ValueError(get_error_message([ref_e], [cur_e]))
def check_disk_acess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.integrals_bielec_disk_access_ao_integrals = "Write"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.integrals_bielec_disk_access_ao_integrals = "IculeAcess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
def check_mo_guess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.hartree_fock_mo_guess_type = "Huckel"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.hartree_fock_mo_guess_type = "IculeGuess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
def check_mo_guess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.hartree_fock_mo_guess_type = "Huckel"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.hartree_fock_mo_guess_type = "IculeGuess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
def check_disk_acess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.integrals_bielec_disk_access_ao_integrals = "Write"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.integrals_bielec_disk_access_ao_integrals = "IculeAcess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
arguments = docopt(__doc__)
# ___
# | ._ o _|_
# _|_ | | | |_
#
# ~#~#~#~#~ #
# E Z F I O #
# ~#~#~#~#~ #
ezfio_path = arguments["<ezfio_path>"]
ezfio_path = os.path.expanduser(ezfio_path)
ezfio_path = os.path.expandvars(ezfio_path)
ezfio_path = os.path.abspath(ezfio_path)
ezfio.set_file("{0}".format(ezfio_path))
# ~#~#~#~#~#~#~#~#~#~#~ #
# P s e u d o _ d a t a #
# ~#~#~#~#~#~#~#~#~#~#~ #
l_ele = ezfio.get_nuclei_nucl_label()
str_ = get_pseudo_str(l_ele)
# _
# |_) _. ._ _ _
# | (_| | _> (/_
#
l_str_ele = [
str_ele for str_ele in str_.split("Element Symbol: ") if str_ele
arguments = docopt(__doc__)
# ___
# | ._ o _|_
# _|_ | | | |_
#
# ~#~#~#~#~ #
# E Z F I O #
# ~#~#~#~#~ #
ezfio_path = arguments["<ezfio_path>"]
ezfio_path = os.path.expanduser(ezfio_path)
ezfio_path = os.path.expandvars(ezfio_path)
ezfio_path = os.path.abspath(ezfio_path)
ezfio.set_file("{0}".format(ezfio_path))
# ~#~#~#~#~#~#~#~#~#~#~ #
# P s e u d o _ d a t a #
# ~#~#~#~#~#~#~#~#~#~#~ #
l_ele = ezfio.get_nuclei_nucl_label()
str_ = get_pseudo_str(l_ele)
# _
# |_) _. ._ _ _
# | (_| | _> (/_
#
l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ")
if str_ele]
#!/usr/bin/env python2
print "#QP -> QMCPACK"
# ___
# | ._ o _|_
# _|_ | | | |_
#
from ezfio import ezfio
import os
import sys
ezfio_path = sys.argv[1]
ezfio.set_file(ezfio_path)
do_pseudo = ezfio.get_pseudo_do_pseudo()
if do_pseudo:
print "do_pseudo True"
from qp_path import QP_ROOT
l_ele_path = os.path.join(QP_ROOT, "data", "list_element.txt")
with open(l_ele_path, "r") as f:
data_raw = f.read()
l_element_raw = data_raw.split("\n")
l_element = [element_raw.split() for element_raw in l_element_raw]
d_z = dict(
(abr, z) for (z, abr, ele, _) in filter(lambda x: x != [], l_element))
else:
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)
#!/usr/bin/python
print "#QP -> QMCPACK"
# ___
# | ._ o _|_
# _|_ | | | |_
#
from ezfio import ezfio
import os
import sys
ezfio_path = sys.argv[1]
ezfio.set_file(ezfio_path)
do_pseudo = ezfio.get_pseudo_do_pseudo()
if do_pseudo:
print "do_pseudo True"
from qp_path import QP_ROOT
l_ele_path = os.path.join(QP_ROOT,"data","list_element.txt")
with open(l_ele_path, "r") as f:
data_raw = f.read()
l_element_raw = data_raw.split("\n")
l_element = [element_raw.split() for element_raw in l_element_raw]
d_z = dict((abr, z) for (z, abr, ele) in l_element)
else:
print "do_pseudo False"
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)
# ______ _
# | ___ \ | |
# | |_/ /__ ___ _ _ __| | ___
# | __/ __|/ _ \ | | |/ _` |/ _ \
# | | \__ \ __/ |_| | (_| | (_) |
# \_| |___/\___|\__,_|\__,_|\___/
#
ezfio.set_pseudo_do_pseudo(False)
def run_full_ci_10k_pt2_end(geo, basis, pseudo):
"""
Run a Full_ci with 10k with the TruePT2
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy_var = defaultdict(dict)
ref_energy_pt2 = defaultdict(dict)
ref_energy_var["sto-3g"]["methane"] = Energy(-39.8058687211, None)
ref_energy_pt2["sto-3g"]["methane"] = Energy(-39.8059180427, None)
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.determinants_n_det_max = 10000
ezfio.determinants_n_det_max_jacobi = 10000
ezfio.determinants_n_states = 1
ezfio.determinants_read_wf = 1
ezfio.determinants_s2_eig = False
ezfio.determinants_threshold_generators = 0.99
ezfio.determinants_threshold_selectors = 0.999
ezfio.perturbation_do_pt2_end = True
ezfio.perturbation_pt2_max = 1.e-4
# ~#~#~ #
# R u n #
# ~#~#~ #
# cmd = "{0}/Full_CI/full_ci {1}.ezfio/".format(QP_src,geo)
cmd = "qp_run full_ci {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_var = ezfio.get_full_ci_energy()
cur_pt2 = ezfio.get_full_ci_energy_pt2()
ref_var = ref_energy_var[basis][geo]
ref_pt2 = ref_energy_pt2[basis][geo]
if pseudo:
ref_var = ref_var.with_pseudo
ref_pt2 = ref_pt2.with_pseudo
else:
ref_var = ref_var.without_pseudo
ref_pt2 = ref_pt2.without_pseudo
t = [
abs(cur_var - ref_var) <= precision,
abs(cur_pt2 - ref_pt2) <= precision
]
if all(t):
return True
else:
raise ValueError(
get_error_message([ref_var, ref_pt2], [cur_var, cur_pt2]))
def run_hf(geo, basis, mult=1, pseudo=False, remove_after_sucess=True):
"""
Run a simle by default hf
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy = defaultdict(defaultdict)
ref_energy["sto-3g"]["methane"] = Energy(-39.7267433402, None)
ref_energy["vdz"]["SO2"] = Energy(None, -41.48912297776174)
ref_energy["vdz"]["HBO"] = Energy(None, -19.11982530413317)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# G l o b a l _ v a r i a b l e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
global has_hf_alredy
has_hf_alredy = True
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, pseudo)
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.bielec_integrals_direct = False
ezfio.bielec_integrals_threshold_ao = 1.e-15
ezfio.bielec_integrals_disk_access_ao_integrals = "None"
ezfio.bielec_integrals_threshold_mo = 1.e-15
ezfio.bielec_integrals_disk_access_mo_integrals = "None"
ezfio.hartree_fock_mo_guess_type = "Huckel"
ezfio.hartree_fock_thresh_scf = 1.e-10
ezfio.hartree_fock_n_it_scf_max = 100
ezfio.pseudo_do_pseudo = pseudo
# ~#~#~ #
# R u n #
# ~#~#~ #
cmd = "qp_run SCF {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_e = ezfio.get_hartree_fock_energy()
ref_e = ref_energy[basis][geo]
if pseudo:
ref_e = ref_e.with_pseudo
else:
ref_e = ref_e.without_pseudo
if abs(cur_e - ref_e) <= precision:
if remove_after_sucess:
subprocess.call(["rm -R {0}.ezfio".format(geo)], shell=True)
return True
else:
raise ValueError(get_error_message([ref_e], [cur_e]))
def run_full_ci_10k_pt2_end(geo, basis, pseudo):
"""
Run a Full_ci with 10k with the TruePT2
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy_var = defaultdict(dict)
ref_energy_pt2 = defaultdict(dict)
ref_energy_var["sto-3g"]["methane"] = Energy(-39.8058687211, None)
ref_energy_pt2["sto-3g"]["methane"] = Energy(-39.8059180427, None)
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.full_ci_do_pt2_end = True
ezfio.full_ci_n_det_max_fci = 10000
ezfio.full_ci_pt2_max = 1.e-8
# ~#~#~ #
# R u n #
# ~#~#~ #
cmd = "qp_run full_ci {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_var = ezfio.get_full_ci_energy()
cur_pt2 = ezfio.get_full_ci_energy_pt2()
ref_var = ref_energy_var[basis][geo]
ref_pt2 = ref_energy_pt2[basis][geo]
if pseudo:
ref_var = ref_var.with_pseudo
ref_pt2 = ref_pt2.with_pseudo
else:
ref_var = ref_var.without_pseudo
ref_pt2 = ref_pt2.without_pseudo
t = [abs(cur_var - ref_var) <= precision,
abs(cur_pt2 - ref_pt2) <= precision]
if all(t):
return True
else:
raise ValueError(get_error_message([ref_var, ref_pt2],
[cur_var, cur_pt2]))
def run_hf(geo, basis, mult=1, pseudo=False, remove_after_sucess=True):
"""
Run a simle by default hf
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy = defaultdict(defaultdict)
ref_energy["sto-3g"]["methane"] = Energy(-39.7267433402, None)
ref_energy["vdz"]["SO2"] = Energy(None, -41.48912297776174)
# ref_energy["vdz"]["HBO"] = Energy(None, -19.1198231418)
ref_energy["vdz"]["HBO"] = Energy(None, -19.1198254041)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# G l o b a l _ v a r i a b l e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
global has_hf_alredy
has_hf_alredy = True
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, pseudo)
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.integrals_bielec_direct = False
ezfio.integrals_bielec_threshold_ao = 1.e-15
ezfio.integrals_bielec_disk_access_ao_integrals = "None"
ezfio.integrals_bielec_threshold_mo = 1.e-15
ezfio.integrals_bielec_disk_access_mo_integrals = "None"
ezfio.hartree_fock_mo_guess_type = "Huckel"
ezfio.hartree_fock_thresh_scf = 1.e-10
ezfio.hartree_fock_n_it_scf_max = 100
ezfio.pseudo_do_pseudo = pseudo
# ~#~#~ #
# R u n #
# ~#~#~ #
# cmd = "{0}/Hartree_Fock/SCF {1}.ezfio/".format(QP_src,geo)
cmd = "qp_run SCF {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_e = ezfio.get_hartree_fock_energy()
ref_e = ref_energy[basis][geo]
if pseudo:
ref_e = ref_e.with_pseudo
else:
ref_e = ref_e.without_pseudo
if abs(cur_e - ref_e) <= precision:
if remove_after_sucess:
subprocess.call(["rm -R {0}.ezfio".format(geo)], shell=True)
return True
else:
raise ValueError(get_error_message([ref_e], [cur_e]))
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.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)
try:
lmax = 0
nucl_charge_remove = []
klocmax = 0
kmax = 0
nucl_num = len(res.geometry)
for ecp in res.pseudo:
lmax_local = ecp['lmax']
lmax = max(lmax_local, lmax)
nucl_charge_remove.append(ecp['zcore'])
klocmax = max(klocmax, len(ecp[str(lmax_local)]))
for l in range(lmax_local):
kmax = max(kmax, len(ecp[str(l)]))
lmax = lmax - 1
ezfio.set_pseudo_pseudo_lmax(lmax)
ezfio.set_pseudo_nucl_charge_remove(nucl_charge_remove)
ezfio.set_pseudo_pseudo_klocmax(klocmax)
ezfio.set_pseudo_pseudo_kmax(kmax)
pseudo_n_k = [[0 for _ in range(nucl_num)] for _ in range(klocmax)]
pseudo_v_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
pseudo_dz_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
pseudo_n_kl = [[[0 for _ in range(nucl_num)] for _ in range(kmax)]
for _ in range(lmax + 1)]
pseudo_v_kl = [[[0. for _ in range(nucl_num)] for _ in range(kmax)]
for _ in range(lmax + 1)]
pseudo_dz_kl = [[[0. for _ in range(nucl_num)] for _ in range(kmax)]
for _ in range(lmax + 1)]
for ecp in res.pseudo:
lmax_local = ecp['lmax']
klocmax = len(ecp[str(lmax_local)])
atom = ecp['atom'] - 1
for kloc in range(klocmax):
try:
v, n, dz = ecp[str(lmax_local)][kloc]
pseudo_n_k[kloc][atom] = n - 2
pseudo_v_k[kloc][atom] = v
pseudo_dz_k[kloc][atom] = dz
except:
pass
for l in range(lmax_local):
for k in range(kmax):
try:
v, n, dz = ecp[str(l)][k]
pseudo_n_kl[l][k][atom] = n - 2
pseudo_v_kl[l][k][atom] = v
pseudo_dz_kl[l][k][atom] = dz
except:
pass
ezfio.set_pseudo_pseudo_n_k(pseudo_n_k)
ezfio.set_pseudo_pseudo_v_k(pseudo_v_k)
ezfio.set_pseudo_pseudo_dz_k(pseudo_dz_k)
ezfio.set_pseudo_pseudo_n_kl(pseudo_n_kl)
ezfio.set_pseudo_pseudo_v_kl(pseudo_v_kl)
ezfio.set_pseudo_pseudo_dz_kl(pseudo_dz_kl)
n_alpha = res.num_alpha
n_beta = res.num_beta
for i in range(nucl_num):
charge[i] -= nucl_charge_remove[i]
n_alpha -= nucl_charge_remove[i] / 2
n_beta -= nucl_charge_remove[i] / 2
ezfio.set_nuclei_nucl_charge(charge)
ezfio.set_electrons_elec_alpha_num(n_alpha)
ezfio.set_electrons_elec_beta_num(n_beta)
except:
ezfio.set_pseudo_do_pseudo(False)
else:
ezfio.set_pseudo_do_pseudo(True)
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)
#!/usr/bin/env python from ezfio import ezfio import sys filename = sys.argv[1] num_elec, nucl_num, mo_tot_num = map(int, sys.argv[2:5]) nuclear_repulsion = float(sys.argv[5]) ao_num = int(sys.argv[6]) n_kpts = int(sys.argv[7]) n_aux = int(sys.argv[8]) ezfio.set_file(filename) #ao_num = mo_tot_num #Important ! import math nelec_per_kpt = num_elec // n_kpts nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.)) nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.)) ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts) ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts) #ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.)) #ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.)) ezfio.set_utils_num_kpts(n_kpts) ezfio.set_integrals_bielec_df_num(n_aux) #Important ezfio.set_nuclei_nucl_num(nucl_num)
def run_full_ci_10k_pt2_end(geo, basis, pseudo):
"""
Run a Full_ci with 10k with the TruePT2
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy_var = defaultdict(dict)
ref_energy_pt2 = defaultdict(dict)
ref_energy_var["sto-3g"]["methane"] = Energy(-39.8058687211, None)
ref_energy_pt2["sto-3g"]["methane"] = Energy(-39.8059180427, None)
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.determinants_n_det_max = 10000
ezfio.determinants_n_det_max_jacobi = 10000
ezfio.determinants_n_states = 1
ezfio.determinants_read_wf = 1
ezfio.determinants_s2_eig = False
ezfio.determinants_threshold_generators = 0.99
ezfio.determinants_threshold_selectors = 0.999
ezfio.perturbation_do_pt2_end = True
ezfio.perturbation_pt2_max = 1.e-4
# ~#~#~ #
# R u n #
# ~#~#~ #
# cmd = "{0}/Full_CI/full_ci {1}.ezfio/".format(QP_src,geo)
cmd = "qp_run full_ci {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_var = ezfio.get_full_ci_energy()
cur_pt2 = ezfio.get_full_ci_energy_pt2()
ref_var = ref_energy_var[basis][geo]
ref_pt2 = ref_energy_pt2[basis][geo]
if pseudo:
ref_var = ref_var.with_pseudo
ref_pt2 = ref_pt2.with_pseudo
else:
ref_var = ref_var.without_pseudo
ref_pt2 = ref_pt2.without_pseudo
t = [abs(cur_var - ref_var) <= precision,
abs(cur_pt2 - ref_pt2) <= precision]
if all(t):
return True
else:
raise ValueError(get_error_message([ref_var, ref_pt2],
[cur_var, cur_pt2]))