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Update qp_convert_output_to_ezfio.py

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Thomas Applencourt 2016-11-17 10:32:36 -06:00 committed by GitHub
parent 1b5166cecc
commit 2dc3eea92b
1 changed files with 129 additions and 8 deletions
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137
scripts/ezfio_interface/qp_convert_output_to_ezfio.py
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@ -12,12 +12,10 @@ Option:
"""
import sys
import os
from functools import reduce
# ~#~#~#~#~#~#~#~ #
# Add to the path #
# ~#~#~#~#~#~#~#~ #
@ -29,9 +27,9 @@ except:
print "Error: QP_ROOT environment variable not found."
sys.exit(1)
else:
sys.path = [QP_ROOT + "/install/EZFIO/Python",
QP_ROOT + "/resultsFile",
QP_ROOT + "/scripts"] + sys.path
sys.path = [ QP_ROOT + "/install/EZFIO/Python",
QP_ROOT + "/resultsFile",
QP_ROOT + "/scripts"] + sys.path
# ~#~#~#~#~#~ #
# I m p o r t #
@ -39,7 +37,6 @@ else:
from ezfio import ezfio
try:
from resultsFile import *
except:
@ -254,7 +251,7 @@ def write_ezfio(res, filename):
for coef in m.vector:
MoMatrix.append(coef)
while len(MoMatrix) < len(MOs[0].vector) ** 2:
while len(MoMatrix) < len(MOs[0].vector)**2:
MoMatrix.append(0.)
# ~#~#~#~#~ #
@ -273,7 +270,130 @@ def write_ezfio(res, filename):
# \_| |___/\___|\__,_|\__,_|\___/
#
ezfio.set_pseudo_do_pseudo(False)
# 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
#No 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)
matrix.append([[coef_n_zeta.split()[1:] for coef_n_zeta in l.split('\n')] for l in array_party[1:]])
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 = res_file.get_pseudo()
except:
ezfio.set_pseudo_do_pseudo(False)
else:
ezfio.set_pseudo_do_pseudo(True)
matrix, array_l_max_block, array_z_remove = parse_str(pseudo_str)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.pseudo_charge_remove = array_z_remove
ezfio.nuclei_nucl_charge = [
i - j for i, j in zip(ezfio.nuclei_nucl_charge, array_z_remove)
]
import math
num_elec = sum(ezfio.nuclei_nucl_charge)
ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
# 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)
def get_full_path(file_path):
@ -282,6 +402,7 @@ def get_full_path(file_path):
file_path = os.path.abspath(file_path)
return file_path
if __name__ == '__main__':
arguments = docopt(__doc__)