mirror of
https://github.com/LCPQ/quantum_package
synced 2024-11-14 01:53:55 +01:00
293 lines
6.7 KiB
Python
Executable File
293 lines
6.7 KiB
Python
Executable File
#!/usr/bin/env python
|
|
"""
|
|
This function acceep
|
|
|
|
Usage:
|
|
qp_convert_output_to_ezfio.py <file.out> [--ezfio=<folder.ezfio>]
|
|
|
|
Option:
|
|
file.out is the file to check (like gamess.out)
|
|
folder.ezfio is the name you whant for the ezfio
|
|
(by default is file.out.ezfio)
|
|
|
|
"""
|
|
|
|
|
|
import sys
|
|
import os
|
|
from functools import reduce
|
|
|
|
|
|
# ~#~#~#~#~#~#~#~ #
|
|
# Add to the path #
|
|
# ~#~#~#~#~#~#~#~ #
|
|
|
|
|
|
try:
|
|
QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
|
|
except:
|
|
print "Error: QPACKAGE_ROOT environment variable not found."
|
|
sys.exit(1)
|
|
else:
|
|
sys.path = [QPACKAGE_ROOT + "/EZFIO/Python",
|
|
QPACKAGE_ROOT + "/resultsFile",
|
|
QPACKAGE_ROOT + "/scripts"] + sys.path
|
|
|
|
# ~#~#~#~#~#~ #
|
|
# I m p o r t #
|
|
# ~#~#~#~#~#~ #
|
|
|
|
from ezfio import ezfio
|
|
|
|
|
|
try:
|
|
from resultsFile import *
|
|
except:
|
|
print "Error: resultsFile Python library not installed"
|
|
sys.exit(1)
|
|
|
|
from docopt import docopt
|
|
|
|
# _
|
|
# |_ ._ _ _|_ o _ ._
|
|
# | |_| | | (_ |_ | (_) | |
|
|
#
|
|
|
|
|
|
def write_ezfio(res, filename):
|
|
|
|
res.clean_uncontractions()
|
|
ezfio.set_file(filename)
|
|
|
|
# _
|
|
# |_ | _ _ _|_ ._ _ ._ _
|
|
# |_ | (/_ (_ |_ | (_) | | _>
|
|
#
|
|
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
|
|
ezfio.set_electrons_elec_beta_num(res.num_beta)
|
|
|
|
#
|
|
# |\ | _ | _ o
|
|
# | \| |_| (_ | (/_ |
|
|
#
|
|
|
|
# ~#~#~#~ #
|
|
# I n i t #
|
|
# ~#~#~#~ #
|
|
|
|
charge = []
|
|
coord_x = []
|
|
coord_y = []
|
|
coord_z = []
|
|
|
|
# ~#~#~#~#~#~#~ #
|
|
# P a r s i n g #
|
|
# ~#~#~#~#~#~#~ #
|
|
|
|
for a in res.geometry:
|
|
charge.append(a.charge)
|
|
if res.units == 'BOHR':
|
|
coord_x.append(a.coord[0])
|
|
coord_y.append(a.coord[1])
|
|
coord_z.append(a.coord[2])
|
|
else:
|
|
coord_x.append(a.coord[0] / a0)
|
|
coord_y.append(a.coord[1] / a0)
|
|
coord_z.append(a.coord[2] / a0)
|
|
|
|
# ~#~#~#~#~ #
|
|
# W r i t e #
|
|
# ~#~#~#~#~ #
|
|
|
|
ezfio.set_nuclei_nucl_num(len(res.geometry))
|
|
ezfio.set_nuclei_nucl_charge(charge)
|
|
|
|
# Transformt H1 into H
|
|
import re
|
|
p = re.compile(ur'(\d*)$')
|
|
label = [p.sub("", x.name).capitalize() for x in res.geometry]
|
|
ezfio.set_nuclei_nucl_label(label)
|
|
|
|
ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
|
|
|
|
# _
|
|
# /\ _ _ |_) _. _ o _
|
|
# /--\ (_) _> |_) (_| _> | _>
|
|
#
|
|
|
|
# ~#~#~#~ #
|
|
# I n i t #
|
|
# ~#~#~#~ #
|
|
|
|
import string
|
|
at = []
|
|
num_prim = []
|
|
power_x = []
|
|
power_y = []
|
|
power_z = []
|
|
coefficient = []
|
|
exponent = []
|
|
|
|
res.clean_contractions()
|
|
res.convert_to_cartesian()
|
|
|
|
# ~#~#~#~#~#~#~ #
|
|
# P a r s i n g #
|
|
# ~#~#~#~#~#~#~ #
|
|
|
|
for b in res.basis:
|
|
c = b.center
|
|
for i, atom in enumerate(res.geometry):
|
|
if atom.coord == c:
|
|
at.append(i + 1)
|
|
num_prim.append(len(b.prim))
|
|
s = b.sym
|
|
power_x.append(string.count(s, "x"))
|
|
power_y.append(string.count(s, "y"))
|
|
power_z.append(string.count(s, "z"))
|
|
coefficient.append(b.coef)
|
|
exponent.append([p.expo for p in b.prim])
|
|
|
|
# ~#~#~#~#~ #
|
|
# W r i t e #
|
|
# ~#~#~#~#~ #
|
|
|
|
ezfio.set_ao_basis_ao_num(len(res.basis))
|
|
ezfio.set_ao_basis_ao_nucl(at)
|
|
ezfio.set_ao_basis_ao_prim_num(num_prim)
|
|
ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
|
|
|
|
# ~#~#~#~#~#~#~ #
|
|
# P a r s i n g #
|
|
# ~#~#~#~#~#~#~ #
|
|
|
|
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
|
|
|
|
for i in range(len(res.basis)):
|
|
coefficient[
|
|
i] += [0. for j in range(len(coefficient[i]), prim_num_max)]
|
|
exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)]
|
|
|
|
coefficient = reduce(lambda x, y: x + y, coefficient, [])
|
|
exponent = reduce(lambda x, y: x + y, exponent, [])
|
|
|
|
coef = []
|
|
expo = []
|
|
for i in range(prim_num_max):
|
|
for j in range(i, len(coefficient), prim_num_max):
|
|
coef.append(coefficient[j])
|
|
expo.append(exponent[j])
|
|
|
|
# ~#~#~#~#~ #
|
|
# W r i t e #
|
|
# ~#~#~#~#~ #
|
|
|
|
ezfio.set_ao_basis_ao_coef(coef)
|
|
ezfio.set_ao_basis_ao_expo(expo)
|
|
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
|
|
|
|
# _
|
|
# |\/| _ _ |_) _. _ o _
|
|
# | | (_) _> |_) (_| _> | _>
|
|
#
|
|
|
|
# ~#~#~#~ #
|
|
# I n i t #
|
|
# ~#~#~#~ #
|
|
|
|
MoTag = res.determinants_mo_type
|
|
ezfio.set_mo_basis_mo_label('Orthonormalized')
|
|
MO_type = MoTag
|
|
allMOs = res.mo_sets[MO_type]
|
|
|
|
# ~#~#~#~#~#~#~ #
|
|
# P a r s i n g #
|
|
# ~#~#~#~#~#~#~ #
|
|
|
|
try:
|
|
closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos]
|
|
active = [(allMOs[i].eigenvalue, i) for i in res.active_mos]
|
|
virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos]
|
|
except:
|
|
closed = []
|
|
virtual = []
|
|
active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
|
|
|
|
closed = map(lambda x: x[1], closed)
|
|
active = map(lambda x: x[1], active)
|
|
virtual = map(lambda x: x[1], virtual)
|
|
MOindices = closed + active + virtual
|
|
|
|
MOs = []
|
|
for i in MOindices:
|
|
MOs.append(allMOs[i])
|
|
|
|
mo_tot_num = len(MOs)
|
|
while len(MOindices) < mo_tot_num:
|
|
MOindices.append(len(MOindices))
|
|
|
|
MOmap = list(MOindices)
|
|
for i in range(len(MOindices)):
|
|
MOmap[i] = MOindices.index(i)
|
|
|
|
energies = []
|
|
for i in xrange(mo_tot_num):
|
|
energies.append(MOs[i].eigenvalue)
|
|
|
|
if res.occ_num is not None:
|
|
OccNum = []
|
|
for i in MOindices:
|
|
OccNum.append(res.occ_num[MO_type][i])
|
|
|
|
while len(OccNum) < mo_tot_num:
|
|
OccNum.append(0.)
|
|
|
|
MoMatrix = []
|
|
sym0 = [i.sym for i in res.mo_sets[MO_type]]
|
|
sym = [i.sym for i in res.mo_sets[MO_type]]
|
|
for i in xrange(len(sym)):
|
|
sym[MOmap[i]] = sym0[i]
|
|
|
|
MoMatrix = []
|
|
for i in xrange(len(MOs)):
|
|
m = MOs[i]
|
|
for coef in m.vector:
|
|
MoMatrix.append(coef)
|
|
|
|
while len(MoMatrix) < len(MOs[0].vector) ** 2:
|
|
MoMatrix.append(0.)
|
|
|
|
# ~#~#~#~#~ #
|
|
# W r i t e #
|
|
# ~#~#~#~#~ #
|
|
|
|
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
|
|
ezfio.set_mo_basis_mo_occ(OccNum)
|
|
ezfio.set_mo_basis_mo_coef(MoMatrix)
|
|
|
|
|
|
def get_full_path(file_path):
|
|
file_path = os.path.expanduser(file_path)
|
|
file_path = os.path.expandvars(file_path)
|
|
file_path = os.path.abspath(file_path)
|
|
return file_path
|
|
|
|
if __name__ == '__main__':
|
|
arguments = docopt(__doc__)
|
|
|
|
file_ = get_full_path(arguments['<file.out>'])
|
|
|
|
if arguments["--ezfio"]:
|
|
ezfio_file = get_full_path(arguments["--ezfio"])
|
|
else:
|
|
ezfio_file = "{0}.ezfio".format(file_)
|
|
|
|
try:
|
|
res_file = getFile(file_)
|
|
except:
|
|
raise
|
|
else:
|
|
print file_, 'recognized as', str(res_file).split('.')[-1].split()[0]
|
|
|
|
write_ezfio(res_file, ezfio_file)
|