LCPQ/qp2
9
1
Fork 0
mirror of https://github.com/QuantumPackage/qp2.git synced 2024-12-22 03:23:29 +01:00
Code Releases Activity
89aaf30460
qp2/bin/qp_convert_output_to_ezfio

455 lines
12 KiB
Python
Executable File
Raw Blame History

#!/usr/bin/env python3
"""
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
from resultsFile import *
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", end=' ')
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", end=' ')
# ~#~#~#~ #
# 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(r'(\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", end=' ')
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
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(str.count(s, "x"))
power_y.append(str.count(s, "y"))
power_z.append(str.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("Basis\t\t...\t", end=' ')
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
coefficient = []
exponent = []
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
inucl = {}
for i, a in enumerate(res.geometry):
inucl[a.coord] = i
nbasis = 0
nucl_index = []
curr_center = -1
nucl_shell_num = []
ang_mom = []
nshell = 0
nshell_tot = 0
shell_index = []
shell_prim_num = []
for b in res.basis:
s = b.sym
if str.count(s, "y") + str.count(s, "x") == 0:
c = inucl[b.center]
nshell += 1
nshell_tot += 1
if c != curr_center:
curr_center = c
nucl_shell_num.append(nshell)
nshell = 0
nbasis += 1
nucl_index.append(c+1)
coefficient += b.coef[:len(b.prim)]
exponent += [p.expo for p in b.prim]
ang_mom.append(str.count(s, "z"))
shell_prim_num.append(len(b.prim))
shell_index += [nshell_tot] * len(b.prim)
shell_num = len(ang_mom)
assert(shell_index[0] = 1)
assert(shell_index[-1] = shell_num)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_basis_basis("Read from ResultsFile")
ezfio.set_basis_shell_num(shell_num)
ezfio.set_basis_basis_nucleus_index(nucl_index)
ezfio.set_basis_prim_num(len(coefficient))
ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
ezfio.set_basis_prim_coef(coefficient)
ezfio.set_basis_prim_expo(exponent)
ezfio.set_basis_shell_ang_mom(ang_mom)
ezfio.set_basis_shell_prim_num(shell_prim_num)
ezfio.set_basis_shell_index(shell_index)
print("OK")
# _
# |\/| _ _ |_) _. _ o _
# | | (_) _> |_) (_| _> | _>
#
print("MOS\t\t...\t", end=' ')
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
MoTag = res.determinants_mo_type
ezfio.set_mo_basis_mo_label('Orthonormalized')
ezfio.set_determinants_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 = [x[1] for x in closed]
active = [x[1] for x in active]
virtual = [x[1] for x in 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 range(mo_num):
energies.append(MOs[i].eigenvalue)
OccNum = []
if res.occ_num is not None:
for i in MOindices:
OccNum.append(res.occ_num[MO_type][i])
else:
for i in range(res.num_beta):
OccNum.append(2.)
for i in range(res.num_beta,res.num_alpha):
OccNum.append(1.)
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 range(len(sym)):
sym[MOmap[i]] = sym0[i]
irrep = {}
for i in sym:
irrep[i] = 0
for i, j in enumerate(irrep.keys()):
irrep[j] = i+1
sym = [ irrep[k] for k in sym ]
MoMatrix = []
for i in range(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_coef(MoMatrix)
ezfio.set_mo_basis_mo_occ(OccNum)
ezfio.set_mo_basis_mo_symmetry(sym)
print("OK")
print("Pseudos\t\t...\t", end=' ')
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]
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).""")
View Git Blame Copy Permalink