mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-22 12:23:43 +01:00
369 lines
9.7 KiB
Python
Executable File
369 lines
9.7 KiB
Python
Executable File
#!/usr/bin/env python2
|
|
"""
|
|
convert output of GAMESS/GAU$$IAN to ezfio
|
|
|
|
Usage:
|
|
qp_convert_output_to_ezfio [-o EZFIO_DIR] FILE
|
|
|
|
Options:
|
|
-o --output=EZFIO_DIR Produced directory
|
|
by default is FILE.ezfio
|
|
|
|
"""
|
|
|
|
import sys
|
|
import os
|
|
from functools import reduce
|
|
from ezfio import ezfio
|
|
from docopt import docopt
|
|
|
|
|
|
try:
|
|
QP_ROOT = os.environ["QP_ROOT"]
|
|
QP_EZFIO = os.environ["QP_EZFIO"]
|
|
except KeyError:
|
|
print "Error: QP_ROOT environment variable not found."
|
|
sys.exit(1)
|
|
else:
|
|
sys.path = [QP_EZFIO + "/Python",
|
|
QP_ROOT + "/install/resultsFile",
|
|
QP_ROOT + "/install",
|
|
QP_ROOT + "/scripts"] + sys.path
|
|
|
|
try:
|
|
from resultsFile import *
|
|
except:
|
|
print "Error: resultsFile Python library not installed"
|
|
sys.exit(1)
|
|
|
|
|
|
|
|
|
|
def write_ezfio(res, filename):
|
|
|
|
res.clean_uncontractions()
|
|
ezfio.set_file(filename)
|
|
|
|
# _
|
|
# |_ | _ _ _|_ ._ _ ._ _
|
|
# |_ | (/_ (_ |_ | (_) | | _>
|
|
#
|
|
print "Electrons\t...\t",
|
|
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
|
|
ezfio.set_electrons_elec_beta_num(res.num_beta)
|
|
print "OK"
|
|
|
|
#
|
|
# |\ | _ | _ o
|
|
# | \| |_| (_ | (/_ |
|
|
#
|
|
|
|
print "Nuclei\t\t...\t",
|
|
# ~#~#~#~ #
|
|
# 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)
|
|
print "OK"
|
|
|
|
# _
|
|
# /\ _ _ |_) _. _ o _
|
|
# /--\ (_) _> |_) (_| _> | _>
|
|
#
|
|
|
|
print "AOS\t\t...\t",
|
|
# ~#~#~#~ #
|
|
# I n i t #
|
|
# ~#~#~#~ #
|
|
|
|
import string
|
|
at = []
|
|
num_prim = []
|
|
power_x = []
|
|
power_y = []
|
|
power_z = []
|
|
coefficient = []
|
|
exponent = []
|
|
|
|
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")
|
|
|
|
print "OK"
|
|
|
|
# _
|
|
# |\/| _ _ |_) _. _ o _
|
|
# | | (_) _> |_) (_| _> | _>
|
|
#
|
|
|
|
print "MOS\t\t...\t",
|
|
# ~#~#~#~ #
|
|
# 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_num = len(MOs)
|
|
while len(MOindices) < mo_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_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_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_num(mo_num)
|
|
ezfio.set_mo_basis_mo_occ(OccNum)
|
|
ezfio.set_mo_basis_mo_coef(MoMatrix)
|
|
print "OK"
|
|
|
|
|
|
print "Pseudos\t\t...\t",
|
|
try:
|
|
lmax = 0
|
|
nucl_charge_remove = []
|
|
klocmax = 0
|
|
kmax = 0
|
|
nucl_num = len(res.geometry)
|
|
for ecp in res.pseudo:
|
|
lmax_local = ecp['lmax']
|
|
lmax = max(lmax_local, lmax)
|
|
nucl_charge_remove.append(ecp['zcore'])
|
|
klocmax = max(klocmax, len(ecp[str(lmax_local)]))
|
|
for l in range(lmax_local):
|
|
kmax = max(kmax, len(ecp[str(l)]))
|
|
lmax = lmax-1
|
|
ezfio.set_pseudo_pseudo_lmax(lmax)
|
|
ezfio.set_pseudo_nucl_charge_remove(nucl_charge_remove)
|
|
ezfio.set_pseudo_pseudo_klocmax(klocmax)
|
|
ezfio.set_pseudo_pseudo_kmax(kmax)
|
|
pseudo_n_k = [[0 for _ in range(nucl_num)] for _ in range(klocmax)]
|
|
pseudo_v_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
|
|
pseudo_dz_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
|
|
pseudo_n_kl = [[[0 for _ in range(nucl_num)] for _ in range(kmax)] for _ in range(lmax+1)]
|
|
pseudo_v_kl = [[[0. for _ in range(nucl_num)] for _ in range(kmax)] for _ in range(lmax+1)]
|
|
pseudo_dz_kl = [[[0. for _ in range(nucl_num)] for _ in range(kmax)] for _ in range(lmax+1)]
|
|
for ecp in res.pseudo:
|
|
lmax_local = ecp['lmax']
|
|
klocmax = len(ecp[str(lmax_local)])
|
|
atom = ecp['atom']-1
|
|
for kloc in range(klocmax):
|
|
try:
|
|
v, n, dz = ecp[str(lmax_local)][kloc]
|
|
pseudo_n_k[kloc][atom] = n-2
|
|
pseudo_v_k[kloc][atom] = v
|
|
pseudo_dz_k[kloc][atom] = dz
|
|
except:
|
|
pass
|
|
for l in range(lmax_local):
|
|
for k in range(kmax):
|
|
try:
|
|
v, n, dz = ecp[str(l)][k]
|
|
pseudo_n_kl[l][k][atom] = n-2
|
|
pseudo_v_kl[l][k][atom] = v
|
|
pseudo_dz_kl[l][k][atom] = dz
|
|
except:
|
|
pass
|
|
ezfio.set_pseudo_pseudo_n_k(pseudo_n_k)
|
|
ezfio.set_pseudo_pseudo_v_k(pseudo_v_k)
|
|
ezfio.set_pseudo_pseudo_dz_k(pseudo_dz_k)
|
|
ezfio.set_pseudo_pseudo_n_kl(pseudo_n_kl)
|
|
ezfio.set_pseudo_pseudo_v_kl(pseudo_v_kl)
|
|
ezfio.set_pseudo_pseudo_dz_kl(pseudo_dz_kl)
|
|
|
|
n_alpha = res.num_alpha
|
|
n_beta = res.num_beta
|
|
for i in range(nucl_num):
|
|
charge[i] -= nucl_charge_remove[i]
|
|
n_alpha -= nucl_charge_remove[i]/2
|
|
n_beta -= nucl_charge_remove[i]/2
|
|
ezfio.set_nuclei_nucl_charge(charge)
|
|
ezfio.set_electrons_elec_alpha_num(n_alpha)
|
|
ezfio.set_electrons_elec_beta_num(n_beta)
|
|
|
|
except:
|
|
ezfio.set_pseudo_do_pseudo(False)
|
|
else:
|
|
ezfio.set_pseudo_do_pseudo(True)
|
|
|
|
print "OK"
|
|
|
|
|
|
|
|
|
|
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'])
|
|
|
|
if ARGUMENTS["--output"]:
|
|
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
|
|
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)
|
|
sys.stdout.flush()
|
|
if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
|
|
print """Warning: You need to run
|
|
|
|
qp run save_ortho_mos
|
|
|
|
to be sure your MOs will be orthogonal, which is not the case when
|
|
the MOs are read from output files (not enough precision in output)."""
|
|
|