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qmcpack No phase reorder and only one basis by atom

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This commit is contained in:
TApplencourt 2016-02-02 16:20:12 +01:00
parent 99a9ba01e1
commit 7453b47f14
1 changed files with 71 additions and 44 deletions
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115
plugins/qmcpack/qp_convert_qmcpack_from_ezfio.py
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@ -5,7 +5,7 @@ print "#QP -> QMCPACK"
# ___
# | ._ o _|_
# _|_ | | | |_
#
#
from ezfio import ezfio
@ -34,7 +34,12 @@ else:
#
# |\/| o _ _
# | | | _> (_
#
#
def list_to_string(l):
return " ".join(map(str, l))
ao_num = ezfio.get_ao_basis_ao_num()
print "ao_num", ao_num
@ -52,14 +57,14 @@ l_label = ezfio.get_nuclei_nucl_label()
l_charge = ezfio.get_nuclei_nucl_charge()
l_coord = ezfio.get_nuclei_nucl_coord()
l_coord_str = [" ".join(map(str, i)) for i in l_coord]
l_coord_str = [list_to_string(i) for i in zip(*l_coord)]
print "nucl_num", len(l_label)
# _
# / _ _ ._ _|
# \_ (_) (_) | (_|
#
#
print "Atomic coord in Bohr"
for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
@ -67,7 +72,7 @@ for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
l = (t[0], t[1] + zcore[i], t[2])
except NameError:
l = t
print " ".join(map(str, l))
print list_to_string(l)
#
# Call externet process to get the sysmetry
@ -78,29 +83,41 @@ process = subprocess.Popen(
stdout=subprocess.PIPE)
out, err = process.communicate()
basis_raw, sym_raw, _ = out.split("\n\n\n")
basis_raw, sym_raw, _= out.split("\n\n\n")
# _ __
# |_) _. _ o _ (_ _ _|_
# |_) (_| _> | _> __) (/_ |_
#
#
basis_without_header = "\n".join(basis_raw.split("\n")[7:])
for i, l in enumerate(l_label):
basis_without_header = basis_without_header.replace('Atom {0}'.format(i + 1), l)
print "BEGIN_BASIS_SET"
print ""
print basis_without_header
import re
l_basis_raw = re.split('\n\s*\n', basis_without_header)
a_already_print = []
l_basis_clean = []
for i, (a,b) in enumerate(zip(l_label,l_basis_raw)):
if a not in a_already_print:
l_basis_clean.append(b.replace('Atom {0}'.format(i + 1), a))
a_already_print.append(a)
else:
continue
print "BEGIN_BASIS_SET\n"
print "\n\n".join(l_basis_clean)
print "END_BASIS_SET"
# _
# |\/| / \ _
# | | \_/ _>
#
#
# Function
#
@ -126,8 +143,9 @@ def compare_gamess_style(item1, item2):
return compare_gamess_style(item1[:-1], item2[:-1])
def expend_and_order_sym(str_):
#Expend
def expend_sym_str(str_):
#Expend x2 -> xx
# yx2 -> xxy
for i, c in enumerate(str_):
try:
n = int(c)
@ -140,6 +158,13 @@ def expend_and_order_sym(str_):
return "".join(sorted(str_, key=str_.count, reverse=True))
def expend_sym_l(l_l_sym):
for l in l_l_sym:
l[2] = expend_sym_str(l[2])
return l_l_sym
def get_nb_permutation(str_):
l = len(str_) - 1
@ -148,26 +173,29 @@ def get_nb_permutation(str_):
else:
return 2 * (2 * l + 1)
def order_l_l_sym(l_l_sym):
l_l_sym_iter = iter(l_l_sym)
for i, l in enumerate(l_l_sym_iter):
n = get_nb_permutation(l[2])
if n != 1:
l_l_sym[i:i + n] = sorted(l_l_sym[i:i + n],
key=lambda x: x[2],
cmp=compare_gamess_style)
for next_ in range(n - 1):
next(l_l_sym_iter)
return l_l_sym
#==========================
# We will order the symetry
#==========================
l_sym_without_header = sym_raw.split("\n")[3:-2]
l_l_sym = [i.split() for i in l_sym_without_header]
l_l_sym_raw = [i.split() for i in l_sym_without_header]
l_l_sym_expend_sym = expend_sym_l(l_l_sym_raw)
for l in l_l_sym:
l[2] = expend_and_order_sym(l[2])
l_l_sym_iter = iter(l_l_sym)
for i, l in enumerate(l_l_sym_iter):
n = get_nb_permutation(l[2])
if n != 1:
l_l_sym[i:i + n] = sorted(l_l_sym[i:i + n],
key=lambda x: x[2],
cmp=compare_gamess_style)
for next_ in range(n - 1):
next(l_l_sym_iter)
l_l_sym_ordered = order_l_l_sym(l_l_sym_expend_sym)
#========
@ -200,12 +228,12 @@ def order_by_sim(mo_coef, l_l_sym):
return mo_coef_order
def chunked(mo_coef, chunks_size):
mo_coef_block = []
for i in mo_coef:
def chunked(l, chunks_size):
l_block = []
for i in l:
chunks = [i[x:x + chunks_size] for x in xrange(0, len(i), chunks_size)]
mo_coef_block.append(chunks)
return mo_coef_block
l_block.append(chunks)
return l_block
def print_mo_coef(mo_coef_block, l_l_sym):
@ -216,10 +244,8 @@ def print_mo_coef(mo_coef_block, l_l_sym):
nb_block = len(mo_coef_block[0])
for i_block in range(0, nb_block):
a = [i[i_block] for i in mo_coef_block]
print " ".join([str(
i + 1) for i in range(len_block_curent, len_block_curent + len(a[
0]))])
r_ = range(len_block_curent, len_block_curent + len(a[0]))
print " ".join([str(i + 1) for i in r_])
len_block_curent += len(a[0])
@ -238,11 +264,12 @@ def print_mo_coef(mo_coef_block, l_l_sym):
mo_coef = ezfio.get_mo_basis_mo_coef()
mo_coef_phase = order_phase(mo_coef)
mo_coef_phase_order = order_by_sim(mo_coef_phase, l_l_sym)
#mo_coef_phase = order_phase(mo_coef)
mo_coef_phase = mo_coef
mo_coef_phase_order = order_by_sim(mo_coef_phase, l_l_sym_ordered)
mo_coef_transp = zip(*mo_coef_phase_order)
mo_coef_block = chunked(mo_coef_transp, 4)
print_mo_coef(mo_coef_block, l_l_sym)
print_mo_coef(mo_coef_block, l_l_sym_ordered)
# _
# |_) _ _ _| _
@ -263,13 +290,11 @@ if do_pseudo:
v_kl = ezfio.get_pseudo_pseudo_v_kl()
dz_kl = ezfio.get_pseudo_pseudo_dz_kl()
def list_to_string(l):
return " ".join(map(str, l))
for i, a in enumerate(l_label):
l_str = []
#Local
l_dump = []
for k in range(klocmax):
if v_k[k][i]:
@ -277,6 +302,8 @@ if do_pseudo:
l_dump.append(l_)
l_str.append(l_dump)
#Non local
for l in range(lmax + 1):
l_dump = []
for k in range(kmax):