339 lines
7.7 KiB
Python
Executable File
339 lines
7.7 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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"""
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Create the pseudo potential for a given atom
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Usage:
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put_pseudo_in_ezfio.py <ezfio_path>
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Help:
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atom is the Abreviation of the atom
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"""
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import os
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import sys
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from docopt import docopt
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from subprocess import Popen, PIPE
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qpackage_root = os.environ['QP_ROOT']
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EZFIO = "{0}/EZFIO".format(qpackage_root)
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sys.path = [EZFIO + "/Python"] + sys.path
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from ezfio import ezfio
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import re
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p = re.compile(ur'\|(\d+)><\d+\|')
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def get_pseudo_str(l_atom):
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"""
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Run EMSL_local for geting the str of the speudo potential
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str_ele :
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Element Symbol: Na
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Number of replaced protons: 10
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Number of projectors: 2
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Pseudopotential data:
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Local component:
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Coeff. r^n Exp.
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1.00000000 -1 5.35838717
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5.35838717 1 3.67918975
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-2.07764789 0 1.60507673
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Non-local component:
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Coeff. r^n Exp. Proj.
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10.69640234 0 1.32389367 |0><0|
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10.11238853 0 1.14052020 |1><1|
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"""
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EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root)
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EMSL_path = "{0}/EMSL_api.py".format(EMSL_root)
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db_path = "{0}/db/Pseudo.db".format(EMSL_root)
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str_ = ""
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for a in l_atom:
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l_cmd_atom = ["--atom", a]
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l_cmd_head = [EMSL_path, "get_basis_data",
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"--db_path", db_path,
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"--basis", "BFD-Pseudo"]
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process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
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stdout, _ = process.communicate()
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str_ += stdout.strip() + "\n"
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return str_
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def get_v_n_dz_local(str_ele):
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"""
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From a str_ele of the pseudo (aka only one ele in the str)
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get the list ussefull for the Local potential : v_k n_k and dz_k
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"""
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l_v_k = []
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l_n_k = []
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l_dz_k = []
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for l in str_ele.splitlines():
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try:
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v, n, dz = l.split()
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v = float(v)
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n = int(n)
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dz = float(dz)
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except ValueError:
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pass
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else:
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l_v_k.append(v)
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l_n_k.append(n)
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l_dz_k.append(dz)
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return l_v_k, l_n_k, l_dz_k
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def get_v_n_dz_l_nonlocal(str_ele):
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"""
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From a str_ele of the pseudo (aka only one ele in the str)
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get the list ussefull for the non Local potential
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v_kl (v, l)
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n_k (v, l)
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dz_k (dz ,l)
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"""
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l_v_kl = []
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l_n_kl = []
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l_dz_kl = []
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for l in str_ele.splitlines():
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try:
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v, n, dz, proj = l.split()
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v = float(v)
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n = int(n)
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dz = float(dz)
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l = int(p.match(proj).group(1))
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except ValueError:
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pass
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else:
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l_v_kl.append([v])
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l_n_kl.append([n])
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l_dz_kl.append([dz])
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if not l_v_kl:
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l_v_kl.append([0.])
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l_n_kl.append([0])
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l_dz_kl.append([0.])
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return l_v_kl, l_n_kl, l_dz_kl
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def get_zeff_alpha_beta(str_ele):
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"""
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Return the the zeff, alpha num elec and beta num elec
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Assert ezfio_set_file alredy defined
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"""
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import re
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# ___
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# | ._ o _|_
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# _|_ | | | |_
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#
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# ~#~#~#~#~#~#~ #
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# s t r _ e l e #
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# ~#~#~#~#~#~#~ #
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# m = re.search('Element Symbol: ([a-zA-Z]+)', str_ele)
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# name = m.group(1).capitalize()
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name = str_ele.split("\n")[0].strip().capitalize()
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m = re.search('Number of replaced protons: (\d+)', str_ele)
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z_remove = int(m.group(1))
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# _
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# |_) _. ._ _ _
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# | (_| | _> (/_
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#
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from elts_num_ele import name_to_elec
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z = name_to_elec[name]
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z_eff = z - z_remove
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alpha = (z_remove / 2)
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beta = (z_remove / 2)
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# _
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# |_) _ _|_ ._ ._
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# | \ (/_ |_ |_| | | |
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#
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return [z_eff, alpha, beta]
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def add_zero(array, size, type):
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for add in xrange(len(array), size):
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array.append([type(0)])
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return array
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def make_it_square(matrix, dim, type=float):
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"""
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matix the matrix to square
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dim array [lmax, kmax]
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type the null value you want
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[[[28.59107316], [19.37583724]], [[50.25646328]]]
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=>
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[[[28.59107316], [19.37583724]], [[50.25646328], [0.0]]]
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"""
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lmax = dim[0]
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kmax = dim[1]
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for l_list in matrix:
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l_list = add_zero(l_list, lmax, type)
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for k_list in list_:
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k_list = add_zero(k_list, kmax, type)
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return matrix
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if __name__ == "__main__":
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arguments = docopt(__doc__)
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# ___
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# | ._ o _|_
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# _|_ | | | |_
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#
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# ~#~#~#~#~ #
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# E Z F I O #
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# ~#~#~#~#~ #
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ezfio_path = arguments["<ezfio_path>"]
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ezfio_path = os.path.expanduser(ezfio_path)
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ezfio_path = os.path.expandvars(ezfio_path)
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ezfio_path = os.path.abspath(ezfio_path)
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ezfio.set_file("{0}".format(ezfio_path))
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# ~#~#~#~#~#~#~#~#~#~#~ #
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# P s e u d o _ d a t a #
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# ~#~#~#~#~#~#~#~#~#~#~ #
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l_ele = ezfio.get_nuclei_nucl_label()
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str_ = get_pseudo_str(l_ele)
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# _
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# |_) _. ._ _ _
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# | (_| | _> (/_
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#
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l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ")
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if str_ele]
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for i in "l_zeff v_k n_k dz_k v_kl n_kl dz_kl".split():
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exec("{0} = []".format(i))
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alpha_tot = 0
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beta_tot = 0
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for str_ele in l_str_ele:
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# ~#~#~#~#~ #
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# S p l i t #
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# ~#~#~#~#~ #
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l = str_ele.find("Local component:")
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nl = str_ele.find("Non-local component")
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# ~#~#~#~#~ #
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# L o c a l #
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# ~#~#~#~#~ #
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l_v, l_n, l_dz = get_v_n_dz_local(str_ele[l:nl])
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v_k.append(l_v)
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n_k.append(l_n)
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dz_k.append(l_dz)
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# ~#~#~#~#~#~#~#~#~ #
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# N o n _ L o c a l #
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# ~#~#~#~#~#~#~#~#~ #
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l_v_kl, l_n_kl, l_dz_kl = get_v_n_dz_l_nonlocal(str_ele[nl:])
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v_kl.append(l_v_kl)
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n_kl.append(l_n_kl)
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dz_kl.append(l_dz_kl)
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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# Z _ e f f , a l p h a / b e t a _ e l e c #
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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zeff, alpha, beta = get_zeff_alpha_beta(str_ele)
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alpha_tot += alpha
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beta_tot += beta
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l_zeff.append(zeff)
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# _
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# /\ _| _| _|_ _ _ _ _|_ o _
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# /--\ (_| (_| |_ (_) (/_ /_ | | (_)
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#
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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# Z _ e f f , a l p h a / b e t a _ e l e c #
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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ezfio.nuclei_nucl_charge = l_zeff
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alpha_tot = ezfio.get_electrons_elec_alpha_num() - alpha_tot
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beta_tot = ezfio.get_electrons_elec_beta_num() - beta_tot
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ezfio.electrons_elec_alpha_num = alpha_tot
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ezfio.electrons_elec_beta_num = beta_tot
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# Change all the array 'cause EZFIO
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# v_kl (v, l) => v_kl(l,v)
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# v_kl => zip(*_v_kl)
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# [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]]
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# [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)]
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# ~#~#~#~#~ #
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# L o c a l #
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# ~#~#~#~#~ #
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klocmax = max([len(i) for i in v_k])
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ezfio.pseudo_pseudo_klocmax = klocmax
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ezfio.pseudo_pseudo_v_k = zip(*v_k)
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ezfio.pseudo_pseudo_n_k = zip(*n_k)
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ezfio.pseudo_pseudo_dz_k = zip(*dz_k)
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# ~#~#~#~#~#~#~#~#~ #
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# N o n _ L o c a l #
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# ~#~#~#~#~#~#~#~#~ #
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lmax = max([len(i) for i in v_kl])
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kmax = max([len(sublist) for list_ in v_kl for sublist in list_])
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ezfio.pseudo_pseudo_lmax = lmax - 1
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ezfio.pseudo_pseudo_kmax = kmax
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v_kl = make_it_square(v_kl, [lmax, kmax])
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n_kl = make_it_square(n_kl, [lmax, kmax], int)
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dz_kl = make_it_square(dz_kl, [lmax, kmax])
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ezfio.pseudo_pseudo_v_kl = zip(*v_kl)
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ezfio.pseudo_pseudo_n_kl = zip(*n_kl)
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ezfio.pseudo_pseudo_dz_kl = zip(*dz_kl)
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ezfio.pseudo_do_pseudo = True
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