mirror of
https://github.com/LCPQ/quantum_package
synced 2024-12-23 04:43:50 +01:00
Rename qp_convert and major cleaning in it
This commit is contained in:
parent
989fd4bc07
commit
374c2c003c
@ -1,7 +1,13 @@
|
||||
#!/usr/bin/env python
|
||||
"""
|
||||
This programme generate all the
|
||||
ocaml template needed by qp_edit
|
||||
|
||||
You can see `ezfio_generate_provider.py`
|
||||
for an example of utilisation
|
||||
"""
|
||||
|
||||
import sys
|
||||
import os
|
||||
|
||||
# If type in **kwargs
|
||||
from ei_handler import Type
|
||||
|
292
scripts/ezfio_interface/qp_convert_output_to_ezfio.py
Executable file
292
scripts/ezfio_interface/qp_convert_output_to_ezfio.py
Executable file
@ -0,0 +1,292 @@
|
||||
#!/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) 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)
|
@ -1,210 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
import sys,os
|
||||
try:
|
||||
QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
|
||||
except:
|
||||
print "Error: QPACKAGE_ROOT environment variable not found."
|
||||
sys.exit(1)
|
||||
|
||||
sys.path = [ QPACKAGE_ROOT+"/EZFIO/Python", QPACKAGE_ROOT+"/resultsFile" ]+sys.path
|
||||
from ezfio import ezfio
|
||||
import ezfio as ez
|
||||
print "EZFIO: ", os.path.dirname(ez.__file__)
|
||||
|
||||
try:
|
||||
from resultsFile import *
|
||||
except:
|
||||
print "Error: resultsFile Python library not installed"
|
||||
sys.exit(1)
|
||||
|
||||
|
||||
def write_ezfioFile(res,filename):
|
||||
res.clean_uncontractions()
|
||||
ezfio.set_file(filename)
|
||||
|
||||
# Electrons
|
||||
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
|
||||
ezfio.set_electrons_elec_beta_num(res.num_beta)
|
||||
|
||||
# Nuclei
|
||||
ezfio.set_nuclei_nucl_num(len(res.geometry))
|
||||
charge = []
|
||||
coord = []
|
||||
coord_x = []
|
||||
coord_y = []
|
||||
coord_z = []
|
||||
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)
|
||||
ezfio.set_nuclei_nucl_charge(charge)
|
||||
label = map(lambda x: x.name, res.geometry)
|
||||
ezfio.set_nuclei_nucl_label(label)
|
||||
ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
|
||||
|
||||
# Basis
|
||||
basis = res.uncontracted_basis
|
||||
geom = res.geometry
|
||||
|
||||
res.clean_contractions()
|
||||
# AO Basis
|
||||
import string
|
||||
at = []
|
||||
num_prim = []
|
||||
magnetic_number = []
|
||||
angular_number = []
|
||||
power_x = []
|
||||
power_y = []
|
||||
power_z = []
|
||||
coefficient = []
|
||||
exponent = []
|
||||
res.convert_to_cartesian()
|
||||
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 ] )
|
||||
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)
|
||||
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
|
||||
len_res_basis = len(res.basis)
|
||||
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] )
|
||||
ezfio.set_ao_basis_ao_coef(coef)
|
||||
ezfio.set_ao_basis_ao_expo(expo)
|
||||
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
|
||||
|
||||
|
||||
# MO
|
||||
MoTag = res.determinants_mo_type
|
||||
ezfio.set_mo_basis_mo_label('Orthonormalized')
|
||||
MO_type = MoTag
|
||||
allMOs = res.mo_sets[MO_type]
|
||||
|
||||
|
||||
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.sort()
|
||||
# active.sort()
|
||||
# virtual.sort()
|
||||
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.)
|
||||
|
||||
mo = []
|
||||
for i in MOindices:
|
||||
mo.append(res.mo_sets[MoTag][i])
|
||||
|
||||
if len(mo) < mo_tot_num:
|
||||
newmo = orbital()
|
||||
newmo.eigenvalue = 0.
|
||||
newmo.vector = [0. for i in range(mo_tot_num)]
|
||||
newmo.vector[len(mo)] = 1.
|
||||
while len(mo) < mo_tot_num:
|
||||
mo.append(newmo)
|
||||
Energies = [ m.eigenvalue for m in mo ]
|
||||
|
||||
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
|
||||
ezfio.set_mo_basis_mo_occ(OccNum)
|
||||
ezfio.set_mo_basis_mo_coef(MoMatrix)
|
||||
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
# Check command line
|
||||
|
||||
det_threshold = 0.
|
||||
|
||||
if len(sys.argv) == 2:
|
||||
State=0
|
||||
elif len(sys.argv) == 3:
|
||||
State=int(sys.argv[2])
|
||||
else:
|
||||
print "usage: "+sys.argv[0]+" file.out [state]"
|
||||
sys.exit(2)
|
||||
|
||||
firstArg = sys.argv[1]
|
||||
|
||||
file = getFile(firstArg)
|
||||
print firstArg, 'recognized as', str(file).split('.')[-1].split()[0]
|
||||
|
||||
filename = firstArg+".ezfio"
|
||||
write_ezfioFile(file,filename)
|
||||
|
||||
|
||||
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user