mirror of
https://github.com/LCPQ/quantum_package
synced 2024-06-20 04:02:16 +02:00
Same phase for the MOs than gamess
This commit is contained in:
TApplencourt
parent
263bdd0f6c
commit
99a9ba01e1
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@ -2,6 +2,11 @@
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print "#QP -> QMCPACK"
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# ___
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# | ._ o _|_
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# _|_ | | | |_
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#
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from ezfio import ezfio
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import sys
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@ -9,76 +14,99 @@ ezfio_path = sys.argv[1]
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ezfio.set_file(ezfio_path)
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do_pseudo = ezfio.get_pseudo_do_pseudo()
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if do_pseudo:
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print "do_pseudo True"
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zcore = ezfio.get_pseudo_nucl_charge_remove()
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print "do_pseudo True"
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zcore = ezfio.get_pseudo_nucl_charge_remove()
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else:
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print "do_pseudo False"
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print "do_pseudo False"
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try:
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n_det =ezfio.get_determinants_n_det()
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n_det = ezfio.get_determinants_n_det()
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except IOError:
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n_det = 1
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n_det = 1
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if n_det == 1:
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print "multi_det False"
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print "multi_det False"
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else:
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print "multi_det True"
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print "multi_det True"
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#
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# |\/| o _ _
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# | | | _> (_
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#
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ao_num = ezfio.get_ao_basis_ao_num()
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print "ao_num", ao_num
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mo_num = ezfio.get_mo_basis_mo_tot_num()
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print "mo_num", mo_num
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alpha = ezfio.get_electrons_elec_alpha_num()
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beta = ezfio.get_electrons_elec_beta_num()
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print "elec_alpha_num", alpha
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print "elec_beta_num", beta
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print "elec_tot_num", alpha + beta
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print "spin_multiplicity", 2*(alpha-beta)+1
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print "elec_tot_num", alpha + beta
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print "spin_multiplicity", 2 * (alpha - beta) + 1
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l_label = ezfio.get_nuclei_nucl_label()
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l_charge = ezfio.get_nuclei_nucl_charge()
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l_coord = ezfio.get_nuclei_nucl_coord()
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l_coord_str = [" ".join(map(str,i)) for i in l_coord]
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l_coord_str = [" ".join(map(str, i)) for i in l_coord]
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print "nucl_num",len(l_label)
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print "nucl_num", len(l_label)
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# _
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# / _ _ ._ _|
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# \_ (_) (_) | (_|
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#
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print "Atomic coord in Bohr"
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for i,t in enumerate(zip(l_label,l_charge,l_coord_str)):
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try :
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l = (t[0],t[1]+zcore[i],t[2])
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except NameError:
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l = t
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print " ".join(map(str,l))
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for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
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try:
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l = (t[0], t[1] + zcore[i], t[2])
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except NameError:
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l = t
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print " ".join(map(str, l))
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#
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# Call externet process to get the sysmetry
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#
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import subprocess
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process = subprocess.Popen(['qp_print_basis', ezfio_path], stdout=subprocess.PIPE)
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process = subprocess.Popen(
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['qp_print_basis', ezfio_path],
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stdout=subprocess.PIPE)
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out, err = process.communicate()
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basis_raw, sym_raw, mo_raw = out.split("\n\n\n")
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basis_raw, sym_raw, _ = out.split("\n\n\n")
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# _ __
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# |_) _. _ o _ (_ _ _|_
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# |_) (_| _> | _> __) (/_ |_
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#
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basis_without_header = "\n".join(basis_raw.split("\n")[7:])
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for i,l in enumerate(l_label):
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basis_without_header=basis_without_header.replace('Atom {0}'.format(i+1),l)
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for i, l in enumerate(l_label):
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basis_without_header = basis_without_header.replace('Atom {0}'.format(i + 1), l)
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print "BEGIN_BASIS_SET"
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print ""
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print basis_without_header
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print "END_BASIS_SET"
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# _
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# |\/| / \ _
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# | | \_/ _>
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#
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#
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#
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# Function
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#
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def same_character(item1):
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return item1==item1[0]* len(item1)
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return item1 == item1[0] * len(item1)
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def compare_gamess_style(item1, item2):
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if len(item1) < len(item2):
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@ -92,123 +120,190 @@ def compare_gamess_style(item1, item2):
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return 1
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elif same_character(item1) and not same_character(item2):
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return -1
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elif not same_character(item1) and same_character(item2):
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elif not same_character(item1) and same_character(item2):
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return 1
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else:
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return compare_gamess_style(item1[:-1],item2[:-1])
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return compare_gamess_style(item1[:-1], item2[:-1])
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def expend_and_order_sym(str_):
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#Expend
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for i,c in enumerate(str_):
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try:
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n = int(c)
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except ValueError:
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pass
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else:
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str_ = str_[:i-1] + str_[i-1]*n + str_[i+1:]
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#Expend
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for i, c in enumerate(str_):
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try:
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n = int(c)
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except ValueError:
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pass
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else:
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str_ = str_[:i - 1] + str_[i - 1] * n + str_[i + 1:]
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#Order by frequency
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return "".join(sorted(str_, key=str_.count, reverse=True))
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#Order by frequency
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return "".join(sorted(str_,key=str_.count,reverse=True))
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def get_nb_permutation(str_):
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l = len(str_)-1
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if l==0:
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return 1
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else:
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return 2*(2*l + 1)
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l = len(str_) - 1
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if l == 0:
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return 1
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else:
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return 2 * (2 * l + 1)
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#==========================
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# We will order the symetry
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#==========================
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## We will order the symetry
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l_sym_without_header = sym_raw.split("\n")[3:-2]
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l_l_sym = [i.split() for i in l_sym_without_header]
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for l in l_l_sym:
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l[2] = expend_and_order_sym(l[2])
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l[2] = expend_and_order_sym(l[2])
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l_l_sym_iter = iter(l_l_sym)
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for i,l in enumerate(l_l_sym_iter):
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n = get_nb_permutation(l[2])
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if n !=1:
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l_l_sym[i:i+n] = sorted(l_l_sym[i:i+n],key=lambda x : x[2], cmp=compare_gamess_style)
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for next_ in range(n-1):
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next(l_l_sym_iter)
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#Is orderd now
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l_block = mo_raw.split("\n\n")[5:-1]
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for i, l in enumerate(l_l_sym_iter):
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n = get_nb_permutation(l[2])
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if n != 1:
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l_l_sym[i:i + n] = sorted(l_l_sym[i:i + n],
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key=lambda x: x[2],
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cmp=compare_gamess_style)
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for next_ in range(n - 1):
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next(l_l_sym_iter)
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l_block_format=[]
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#========
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#MO COEF
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#========
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def order_phase(mo_coef):
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#Order
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mo_coef_phase = []
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import math
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print ""
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print "BEGIN_MO"
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for block in l_block:
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print ""
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l_ligne = block.split("\n")
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print l_ligne.pop(0)
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for i in mo_coef:
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if abs(max(i)) > abs(min(i)):
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sign_max = math.copysign(1, max(i))
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else:
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sign_max = math.copysign(1, min(i))
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for l in l_l_sym:
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i = int(l[0]) - 1
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i_a = int(l[1]) - 1
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sym = l[2]
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if sign_max == -1:
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ii = [-1 * l for l in i]
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else:
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ii = i
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print l_label[i_a],sym,l_ligne[i]
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mo_coef_phase.append(ii)
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return mo_coef_phase
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print "END_MO"
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def order_by_sim(mo_coef, l_l_sym):
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l_sym_oder = [int(l[0]) - 1 for l in l_l_sym]
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mo_coef_order = [[x for (y, x) in sorted(zip(l_sym_oder, i))]
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for i in mo_coef]
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return mo_coef_order
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def chunked(mo_coef, chunks_size):
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mo_coef_block = []
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for i in mo_coef:
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chunks = [i[x:x + chunks_size] for x in xrange(0, len(i), chunks_size)]
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mo_coef_block.append(chunks)
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return mo_coef_block
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def print_mo_coef(mo_coef_block, l_l_sym):
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print ""
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print "BEGIN_MO"
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print ""
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len_block_curent = 0
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nb_block = len(mo_coef_block[0])
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for i_block in range(0, nb_block):
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a = [i[i_block] for i in mo_coef_block]
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print " ".join([str(
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i + 1) for i in range(len_block_curent, len_block_curent + len(a[
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0]))])
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len_block_curent += len(a[0])
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for l in l_l_sym:
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i = int(l[0]) - 1
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i_a = int(l[1]) - 1
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sym = l[2]
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print l_label[i_a], sym, " ".join('{: 3.8f}'.format(i)
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for i in a[i])
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if i_block != nb_block - 1:
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print ""
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else:
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print "END_MO"
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mo_coef = ezfio.get_mo_basis_mo_coef()
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mo_coef_phase = order_phase(mo_coef)
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mo_coef_phase_order = order_by_sim(mo_coef_phase, l_l_sym)
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mo_coef_transp = zip(*mo_coef_phase_order)
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mo_coef_block = chunked(mo_coef_transp, 4)
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print_mo_coef(mo_coef_block, l_l_sym)
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# _
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# |_) _ _ _| _
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# | _> (/_ |_| (_| (_)
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#
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if do_pseudo:
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print ""
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print "BEGIN_PSEUDO"
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klocmax = ezfio.get_pseudo_pseudo_klocmax()
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kmax = ezfio.get_pseudo_pseudo_kmax()
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lmax = ezfio.get_pseudo_pseudo_lmax()
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n_k = ezfio.get_pseudo_pseudo_n_k()
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v_k = ezfio.get_pseudo_pseudo_v_k()
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dz_k = ezfio.get_pseudo_pseudo_dz_k()
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n_kl = ezfio.get_pseudo_pseudo_n_kl()
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v_kl = ezfio.get_pseudo_pseudo_v_kl()
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dz_kl = ezfio.get_pseudo_pseudo_dz_kl()
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def list_to_string(l):
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return " ".join(map(str,l))
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for i,a in enumerate(l_label):
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l_str = []
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l_dump = []
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for k in range(klocmax):
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if v_k[k][i]:
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l_ = list_to_string([v_k[k][i], n_k[k][i]+2, dz_k[k][i]])
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l_dump.append(l_)
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l_str.append(l_dump)
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for l in range(lmax+1):
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l_dump = []
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for k in range(kmax):
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if v_kl[l][k][i]:
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l_ = list_to_string([v_kl[l][k][i], n_kl[l][k][i]+2, dz_kl[l][k][i]])
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l_dump.append(l_)
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if l_dump:
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l_str.append(l_dump)
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str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
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print str_.format(a,i+1,int(zcore[i]),int(len(l_str)-1))
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for i, l in enumerate(l_str):
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str_ = "FOR L= {0} COEFF N ZETA"
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print str_.format(int(len(l_str)-i-1))
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for ii, ll in enumerate(l):
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print " ",ii+1, ll
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str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
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print str_.format(sum(zcore))
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print "END_PSEUDO"
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print ""
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print "BEGIN_PSEUDO"
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klocmax = ezfio.get_pseudo_pseudo_klocmax()
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kmax = ezfio.get_pseudo_pseudo_kmax()
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lmax = ezfio.get_pseudo_pseudo_lmax()
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n_k = ezfio.get_pseudo_pseudo_n_k()
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v_k = ezfio.get_pseudo_pseudo_v_k()
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dz_k = ezfio.get_pseudo_pseudo_dz_k()
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n_kl = ezfio.get_pseudo_pseudo_n_kl()
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v_kl = ezfio.get_pseudo_pseudo_v_kl()
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dz_kl = ezfio.get_pseudo_pseudo_dz_kl()
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def list_to_string(l):
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return " ".join(map(str, l))
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for i, a in enumerate(l_label):
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l_str = []
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l_dump = []
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for k in range(klocmax):
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if v_k[k][i]:
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l_ = list_to_string([v_k[k][i], n_k[k][i] + 2, dz_k[k][i]])
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l_dump.append(l_)
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l_str.append(l_dump)
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for l in range(lmax + 1):
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l_dump = []
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for k in range(kmax):
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if v_kl[l][k][i]:
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l_ = list_to_string([v_kl[l][k][i], n_kl[l][k][i] + 2,
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dz_kl[l][k][i]])
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l_dump.append(l_)
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if l_dump:
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l_str.append(l_dump)
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str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
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print str_.format(a, i + 1, int(zcore[i]), int(len(l_str) - 1))
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for i, l in enumerate(l_str):
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str_ = "FOR L= {0} COEFF N ZETA"
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print str_.format(int(len(l_str) - i - 1))
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for ii, ll in enumerate(l):
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print " ", ii + 1, ll
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str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
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print str_.format(sum(zcore))
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print "END_PSEUDO"
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# _
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# | \ _ _|_
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# |_/ (/_ |_
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#
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print ""
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print "BEGIN_DET"
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print ""
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@ -219,18 +314,17 @@ print ""
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psi_det = ezfio.get_determinants_psi_det()
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psi_coef = ezfio.get_determinants_psi_coef()[0]
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for c, (l_det_bit_alpha, l_det_bit_beta) in zip(psi_coef, psi_det):
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print c
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for det in l_det_bit_alpha:
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bin_det_raw = "{0:b}".format(det)[::-1]
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bin_det = bin_det_raw + "0" * (mo_num - len(bin_det_raw))
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print bin_det
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for c, (l_det_bit_alpha, l_det_bit_beta) in zip(psi_coef,psi_det):
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print c
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for det in l_det_bit_alpha:
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bin_det_raw = "{0:b}".format(det)[::-1]
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bin_det = bin_det_raw+"0"*(mo_num-len(bin_det_raw))
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print bin_det
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for det in l_det_bit_beta:
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bin_det_raw = "{0:b}".format(det)[::-1]
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bin_det = bin_det_raw+"0"*(mo_num-len(bin_det_raw))
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print bin_det
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print ""
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for det in l_det_bit_beta:
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bin_det_raw = "{0:b}".format(det)[::-1]
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bin_det = bin_det_raw + "0" * (mo_num - len(bin_det_raw))
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print bin_det
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print ""
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print "END_DET"
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