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https://github.com/LCPQ/quantum_package
synced 2024-08-24 21:41:46 +02:00
qmcpack No phase reorder and only one basis by atom
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commit
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@ -35,6 +35,11 @@ else:
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# |\/| o _ _
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# |\/| o _ _
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# | | | _> (_
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# | | | _> (_
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#
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#
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def list_to_string(l):
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return " ".join(map(str, l))
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ao_num = ezfio.get_ao_basis_ao_num()
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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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print "ao_num", ao_num
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@ -52,7 +57,7 @@ l_label = ezfio.get_nuclei_nucl_label()
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l_charge = ezfio.get_nuclei_nucl_charge()
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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 = 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 = [list_to_string(i) for i in zip(*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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@ -67,7 +72,7 @@ for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
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l = (t[0], t[1] + zcore[i], t[2])
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l = (t[0], t[1] + zcore[i], t[2])
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except NameError:
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except NameError:
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l = t
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l = t
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print " ".join(map(str, l))
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print list_to_string(l)
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#
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#
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# Call externet process to get the sysmetry
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# Call externet process to get the sysmetry
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@ -85,22 +90,34 @@ basis_raw, sym_raw, _ = out.split("\n\n\n")
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# |_) (_| _> | _> __) (/_ |_
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# |_) (_| _> | _> __) (/_ |_
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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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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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print "BEGIN_BASIS_SET"
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import re
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print ""
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l_basis_raw = re.split('\n\s*\n', basis_without_header)
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print basis_without_header
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a_already_print = []
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l_basis_clean = []
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for i, (a,b) in enumerate(zip(l_label,l_basis_raw)):
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if a not in a_already_print:
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l_basis_clean.append(b.replace('Atom {0}'.format(i + 1), a))
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a_already_print.append(a)
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else:
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continue
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print "BEGIN_BASIS_SET\n"
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print "\n\n".join(l_basis_clean)
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print "END_BASIS_SET"
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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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#
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#
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#
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#
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# Function
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# Function
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#
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#
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@ -126,8 +143,9 @@ def compare_gamess_style(item1, item2):
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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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def expend_sym_str(str_):
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#Expend
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#Expend x2 -> xx
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# yx2 -> xxy
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for i, c in enumerate(str_):
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for i, c in enumerate(str_):
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try:
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try:
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n = int(c)
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n = int(c)
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@ -140,6 +158,13 @@ def expend_and_order_sym(str_):
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return "".join(sorted(str_, key=str_.count, reverse=True))
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return "".join(sorted(str_, key=str_.count, reverse=True))
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def expend_sym_l(l_l_sym):
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for l in l_l_sym:
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l[2] = expend_sym_str(l[2])
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return l_l_sym
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def get_nb_permutation(str_):
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def get_nb_permutation(str_):
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l = len(str_) - 1
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l = len(str_) - 1
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@ -148,17 +173,8 @@ def get_nb_permutation(str_):
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else:
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else:
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return 2 * (2 * l + 1)
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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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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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def order_l_l_sym(l_l_sym):
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l_l_sym_iter = iter(l_l_sym)
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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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for i, l in enumerate(l_l_sym_iter):
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n = get_nb_permutation(l[2])
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n = get_nb_permutation(l[2])
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@ -168,6 +184,18 @@ for i, l in enumerate(l_l_sym_iter):
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cmp=compare_gamess_style)
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cmp=compare_gamess_style)
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for next_ in range(n - 1):
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for next_ in range(n - 1):
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next(l_l_sym_iter)
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next(l_l_sym_iter)
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return l_l_sym
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#==========================
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# We will order the symetry
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#==========================
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l_sym_without_header = sym_raw.split("\n")[3:-2]
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l_l_sym_raw = [i.split() for i in l_sym_without_header]
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l_l_sym_expend_sym = expend_sym_l(l_l_sym_raw)
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l_l_sym_ordered = order_l_l_sym(l_l_sym_expend_sym)
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#========
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#========
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@ -200,12 +228,12 @@ def order_by_sim(mo_coef, l_l_sym):
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return mo_coef_order
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return mo_coef_order
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def chunked(mo_coef, chunks_size):
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def chunked(l, chunks_size):
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mo_coef_block = []
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l_block = []
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for i in mo_coef:
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for i in l:
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chunks = [i[x:x + chunks_size] for x in xrange(0, len(i), chunks_size)]
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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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l_block.append(chunks)
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return mo_coef_block
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return l_block
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def print_mo_coef(mo_coef_block, l_l_sym):
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def print_mo_coef(mo_coef_block, l_l_sym):
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@ -216,10 +244,8 @@ def print_mo_coef(mo_coef_block, l_l_sym):
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nb_block = len(mo_coef_block[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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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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a = [i[i_block] for i in mo_coef_block]
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r_ = range(len_block_curent, len_block_curent + len(a[0]))
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print " ".join([str(
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print " ".join([str(i + 1) for i in r_])
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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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len_block_curent += len(a[0])
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@ -238,11 +264,12 @@ def print_mo_coef(mo_coef_block, l_l_sym):
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mo_coef = ezfio.get_mo_basis_mo_coef()
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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_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_phase = mo_coef
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mo_coef_phase_order = order_by_sim(mo_coef_phase, l_l_sym_ordered)
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mo_coef_transp = zip(*mo_coef_phase_order)
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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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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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print_mo_coef(mo_coef_block, l_l_sym_ordered)
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# _
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# _
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# |_) _ _ _| _
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# |_) _ _ _| _
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@ -263,13 +290,11 @@ if do_pseudo:
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v_kl = ezfio.get_pseudo_pseudo_v_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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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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for i, a in enumerate(l_label):
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l_str = []
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l_str = []
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#Local
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l_dump = []
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l_dump = []
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for k in range(klocmax):
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for k in range(klocmax):
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if v_k[k][i]:
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if v_k[k][i]:
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@ -277,6 +302,8 @@ if do_pseudo:
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l_dump.append(l_)
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l_dump.append(l_)
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l_str.append(l_dump)
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l_str.append(l_dump)
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#Non local
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for l in range(lmax + 1):
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for l in range(lmax + 1):
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l_dump = []
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l_dump = []
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for k in range(kmax):
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for k in range(kmax):
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