mirror of
https://gitlab.com/scemama/qp_plugins_scemama.git
synced 2024-06-02 03:15:25 +02:00
392 lines
8.8 KiB
Python
Executable File
392 lines
8.8 KiB
Python
Executable File
#!/usr/bin/env python3
|
|
#
|
|
# Modified from the QMCPACK interface developed by @tapplencourt and @abenali
|
|
|
|
print("#QP -> CHAMP")
|
|
|
|
# ___
|
|
# | ._ o _|_
|
|
# _|_ | | | |_
|
|
#
|
|
|
|
from ezfio import ezfio
|
|
|
|
import os
|
|
import sys
|
|
ezfio_path = sys.argv[1]
|
|
|
|
ezfio.set_file(ezfio_path)
|
|
|
|
do_pseudo = ezfio.get_pseudo_do_pseudo()
|
|
if do_pseudo:
|
|
print("do_pseudo True")
|
|
from qp_path import QP_ROOT
|
|
|
|
l_ele_path = os.path.join(QP_ROOT,"data","list_element.txt")
|
|
with open(l_ele_path, "r") as f:
|
|
data_raw = f.read()
|
|
|
|
l_element_raw = data_raw.split("\n")
|
|
l_element = [element_raw.split() for element_raw in l_element_raw]
|
|
d_z = dict((abr, z) for (z, abr, ele, _) in [x for x in l_element if x != []] )
|
|
else:
|
|
print("do_pseudo False")
|
|
|
|
try:
|
|
n_det = ezfio.get_determinants_n_det()
|
|
except IOError:
|
|
n_det = 1
|
|
|
|
if n_det == 1:
|
|
print("multi_det False")
|
|
else:
|
|
print("multi_det True")
|
|
|
|
#
|
|
# |\/| o _ _
|
|
# | | | _> (_
|
|
#
|
|
|
|
def list_to_string(l):
|
|
return " ".join(map(str, l))
|
|
|
|
|
|
ao_num = ezfio.get_ao_basis_ao_num()
|
|
print("ao_num", ao_num)
|
|
|
|
mo_num = ezfio.get_mo_basis_mo_num()
|
|
print("mo_num", mo_num)
|
|
|
|
alpha = ezfio.get_electrons_elec_alpha_num()
|
|
beta = ezfio.get_electrons_elec_beta_num()
|
|
print("elec_alpha_num", alpha)
|
|
print("elec_beta_num", beta)
|
|
print("elec_tot_num", alpha + beta)
|
|
print("spin_multiplicity", (alpha - beta) + 1)
|
|
|
|
l_label = ezfio.get_nuclei_nucl_label()
|
|
l_charge = ezfio.get_nuclei_nucl_charge()
|
|
l_coord = ezfio.get_nuclei_nucl_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)):
|
|
t_1 = d_z[t[0]] if do_pseudo else t[1]
|
|
|
|
t_new = [t[0],t_1,t[2]]
|
|
print(list_to_string(t_new))
|
|
|
|
#
|
|
# Call externet process to get the sysmetry
|
|
#
|
|
import subprocess
|
|
process = subprocess.Popen(
|
|
['qp_print_basis', ezfio_path],
|
|
stdout=subprocess.PIPE)
|
|
out, err = process.communicate()
|
|
|
|
basis_raw, sym_raw, _ = out.decode().split("\n\n\n")
|
|
basis_split = basis_raw.split('\n')
|
|
|
|
# _ __
|
|
# |_) _. _ o _ (_ _ _|_
|
|
# |_) (_| _> | _> __) (/_ |_
|
|
#
|
|
|
|
beginning = 0
|
|
for x in basis_split:
|
|
if x.startswith("Basis set"):
|
|
break
|
|
beginning += 1
|
|
|
|
beginning+=2
|
|
basis_without_header = "\n".join(basis_split[beginning:])
|
|
|
|
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
|
|
#
|
|
d_gms_order = ["s",
|
|
"x", "y", "z" ,
|
|
"xx", "yy", "zz", "xy", "xz", "yz" ,
|
|
"xxx", "yyy", "zzz", "xxy", "xxz", "yyx", "yyz", "zzx", "zzy", "xyz",
|
|
"xxxx", "yyyy", "zzzz", "xxxy", "xxxz", "yyyx", "yyyz", "zzzx", "zzzy", "xxyy", "xxzz", "yyzz", "xxyz", "yyxz", "zzxy"]
|
|
|
|
def key_gamess_style(item1):
|
|
try:
|
|
l = d_gms_order.index(item1)
|
|
except ValueError:
|
|
return 0
|
|
else:
|
|
result = d_gms_order.index(item1)
|
|
return result
|
|
|
|
def expend_sym_str(str_):
|
|
#Expend x2 -> xx
|
|
# yx2 -> xxy
|
|
for i, c in enumerate(str_):
|
|
try:
|
|
n = int(c)
|
|
except ValueError:
|
|
pass
|
|
else:
|
|
str_ = str_[:i - 1] + str_[i - 1] * n + str_[i + 1:]
|
|
|
|
#Order by frequency
|
|
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 n_orbital(n):
|
|
if n==0:
|
|
return 1
|
|
elif n==1:
|
|
return 3
|
|
else:
|
|
return 2*n_orbital(n-1)-n_orbital(n-2)+1
|
|
|
|
def get_nb_permutation(str_):
|
|
if (str_) == 's': return 1
|
|
else: return n_orbital(len(str_))
|
|
|
|
import functools
|
|
def order_l_l_sym(l_l_sym):
|
|
n = 1
|
|
iter_ = list(range(len(l_l_sym)))
|
|
for i in iter_:
|
|
if n != 1:
|
|
n += -1
|
|
continue
|
|
|
|
l = l_l_sym[i]
|
|
n = get_nb_permutation(l[2])
|
|
|
|
def local_key(x):
|
|
return key_gamess_style(x[2])
|
|
|
|
l_l_sym[i:i + n] = sorted(l_l_sym[i:i + n],
|
|
key=local_key)
|
|
|
|
|
|
return l_l_sym
|
|
|
|
|
|
#==========================
|
|
# We will order the symetry
|
|
#==========================
|
|
|
|
l_sym_without_header = sym_raw.split("\n")[3:-2]
|
|
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)
|
|
l_l_sym_ordered = order_l_l_sym(l_l_sym_expend_sym)
|
|
|
|
#========
|
|
#MO COEF
|
|
#========
|
|
def order_phase(mo_coef):
|
|
#Order
|
|
mo_coef_phase = []
|
|
import math
|
|
|
|
for i in mo_coef:
|
|
if abs(max(i)) > abs(min(i)):
|
|
sign_max = math.copysign(1, max(i))
|
|
else:
|
|
sign_max = math.copysign(1, min(i))
|
|
|
|
if sign_max == -1:
|
|
ii = [-1 * l for l in i]
|
|
else:
|
|
ii = i
|
|
|
|
mo_coef_phase.append(ii)
|
|
return mo_coef_phase
|
|
|
|
def chunked(l, chunks_size):
|
|
l_block = []
|
|
for i in l:
|
|
chunks = [i[x:x + chunks_size] for x in range(0, len(i), chunks_size)]
|
|
l_block.append(chunks)
|
|
return l_block
|
|
|
|
|
|
def print_mo_coef(mo_coef_block, l_l_sym):
|
|
print("")
|
|
print("BEGIN_MO")
|
|
print("")
|
|
len_block_curent = 0
|
|
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]
|
|
r_ = list(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])
|
|
|
|
for l in l_l_sym:
|
|
i = int(l[0]) - 1
|
|
i_a = int(l[1]) - 1
|
|
sym = l[2]
|
|
|
|
print(l_label[i_a], sym, " ".join('%20.15e'%i
|
|
for i in a[i]))
|
|
|
|
if i_block != nb_block - 1:
|
|
print("")
|
|
else:
|
|
print("END_MO")
|
|
|
|
|
|
mo_coef = ezfio.get_mo_basis_mo_coef()
|
|
mo_coef_transp = list(zip(*mo_coef))
|
|
mo_coef_block = chunked(mo_coef_transp, 4)
|
|
print_mo_coef(mo_coef_block, l_l_sym_ordered)
|
|
|
|
# _
|
|
# |_) _ _ _| _
|
|
# | _> (/_ |_| (_| (_)
|
|
#
|
|
if do_pseudo:
|
|
print("")
|
|
print("BEGIN_PSEUDO")
|
|
klocmax = ezfio.get_pseudo_pseudo_klocmax()
|
|
kmax = ezfio.get_pseudo_pseudo_kmax()
|
|
lmax = ezfio.get_pseudo_pseudo_lmax()
|
|
|
|
n_k = ezfio.get_pseudo_pseudo_n_k()
|
|
v_k = ezfio.get_pseudo_pseudo_v_k()
|
|
dz_k = ezfio.get_pseudo_pseudo_dz_k()
|
|
|
|
n_kl = ezfio.get_pseudo_pseudo_n_kl()
|
|
v_kl = ezfio.get_pseudo_pseudo_v_kl()
|
|
dz_kl = ezfio.get_pseudo_pseudo_dz_kl()
|
|
|
|
for i, a in enumerate(l_label):
|
|
|
|
l_str = []
|
|
|
|
#Local
|
|
l_dump = []
|
|
for k in range(klocmax):
|
|
if v_k[k][i]:
|
|
l_ = list_to_string([v_k[k][i], n_k[k][i] + 2, dz_k[k][i]])
|
|
l_dump.append(l_)
|
|
|
|
l_str.append(l_dump)
|
|
|
|
#Non local
|
|
for l in range(lmax + 1):
|
|
l_dump = []
|
|
for k in range(kmax):
|
|
if v_kl[l][k][i]:
|
|
l_ = list_to_string([v_kl[l][k][i], n_kl[l][k][i] + 2,
|
|
dz_kl[l][k][i]])
|
|
l_dump.append(l_)
|
|
if l_dump:
|
|
l_str.append(l_dump)
|
|
|
|
str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
|
|
print(str_.format(a, i + 1, int(d_z[a])-int(l_charge[i]), int(len(l_str) - 1)))
|
|
|
|
for i, l in enumerate(l_str):
|
|
str_ = "FOR L= {0} COEFF N ZETA"
|
|
print(str_.format(int(len(l_str) - i - 1)))
|
|
for ii, ll in enumerate(l):
|
|
print(" ", ii + 1, ll)
|
|
|
|
str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
|
|
print(str_.format(sum([int(d_z[a])-int(l_charge[i]) for i,a in enumerate(l_label)])))
|
|
print("END_PSEUDO")
|
|
|
|
# _
|
|
# | \ _ _|_
|
|
# |_/ (/_ |_
|
|
#
|
|
|
|
|
|
psi_coef = ezfio.get_determinants_psi_coef()
|
|
psi_det = ezfio.get_determinants_psi_det()
|
|
bit_kind = ezfio.get_determinants_bit_kind()
|
|
|
|
|
|
nexcitedstate = ezfio.get_determinants_n_states()
|
|
|
|
print("")
|
|
print("BEGIN_DET")
|
|
print("")
|
|
print("mo_num", mo_num)
|
|
print("det_num", n_det)
|
|
print("")
|
|
|
|
if "QP_STATE" in os.environ:
|
|
state = int(os.environ["QP_STATE"])-1
|
|
else:
|
|
state = 0
|
|
|
|
psi_coef_small = psi_coef[state]
|
|
|
|
|
|
|
|
|
|
encode = 8*bit_kind
|
|
|
|
def bindigits(n, bits):
|
|
s = bin(n & int("1"*bits, 2))[2:]
|
|
return ("{0:0>%s}" % (bits)).format(s)
|
|
|
|
decode = lambda det: ''.join(bindigits(i,encode)[::-1] for i in det)[:mo_num]
|
|
|
|
MultiDetAlpha = []
|
|
MultiDetBeta = []
|
|
for coef, (det_a, det_b) in zip(psi_coef_small, psi_det):
|
|
|
|
print(coef)
|
|
MyDetA=decode(det_a)
|
|
MyDetB=decode(det_b)
|
|
print(MyDetA)
|
|
print(MyDetB)
|
|
print('')
|
|
MultiDetAlpha.append( det_a )
|
|
MultiDetBeta.append( det_b )
|
|
print("END_DET")
|
|
|