mirror of
https://github.com/LCPQ/quantum_package
synced 2024-12-22 20:35:19 +01:00
Rename qp_convert and major cleaning in it
This commit is contained in:
Thomas Applencourt
parent
989fd4bc07
commit
374c2c003c
@ -1,7 +1,13 @@
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#!/usr/bin/env python
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"""
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This programme generate all the
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ocaml template needed by qp_edit
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You can see `ezfio_generate_provider.py`
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for an example of utilisation
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"""
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import sys
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import os
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# If type in **kwargs
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from ei_handler import Type
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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 @@
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#!/usr/bin/env python
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"""
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This function acceep
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Usage:
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qp_convert_output_to_ezfio.py <file.out> [--ezfio=<folder.ezfio>]
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Option:
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file.out is the file to check (like gamess.out)
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folder.ezfio is the name you whant for the ezfio
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(by default is file.out.ezfio)
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"""
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import sys
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import os
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from functools import reduce
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# ~#~#~#~#~#~#~#~ #
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# Add to the path #
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# ~#~#~#~#~#~#~#~ #
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try:
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QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
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except:
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print "Error: QPACKAGE_ROOT environment variable not found."
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sys.exit(1)
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else:
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sys.path = [QPACKAGE_ROOT + "/EZFIO/Python",
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QPACKAGE_ROOT + "/resultsFile",
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QPACKAGE_ROOT + "/scripts"] + sys.path
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# ~#~#~#~#~#~ #
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# I m p o r t #
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# ~#~#~#~#~#~ #
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from ezfio import ezfio
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try:
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from resultsFile import *
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except:
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print "Error: resultsFile Python library not installed"
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sys.exit(1)
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from docopt import docopt
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# _
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# |_ ._ _ _|_ o _ ._
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# | |_| | | (_ |_ | (_) | |
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#
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def write_ezfio(res, filename):
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res.clean_uncontractions()
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ezfio.set_file(filename)
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# _
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# |_ | _ _ _|_ ._ _ ._ _
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# |_ | (/_ (_ |_ | (_) | | _>
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#
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ezfio.set_electrons_elec_alpha_num(res.num_alpha)
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ezfio.set_electrons_elec_beta_num(res.num_beta)
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#
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# |\ | _ | _ o
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# | \| |_| (_ | (/_ |
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#
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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charge = []
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coord_x = []
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coord_y = []
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coord_z = []
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# ~#~#~#~#~#~#~ #
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# P a r s i n g #
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# ~#~#~#~#~#~#~ #
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for a in res.geometry:
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charge.append(a.charge)
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if res.units == 'BOHR':
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coord_x.append(a.coord[0])
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coord_y.append(a.coord[1])
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coord_z.append(a.coord[2])
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else:
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coord_x.append(a.coord[0] / a0)
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coord_y.append(a.coord[1] / a0)
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coord_z.append(a.coord[2] / a0)
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# ~#~#~#~#~ #
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# W r i t e #
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# ~#~#~#~#~ #
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ezfio.set_nuclei_nucl_num(len(res.geometry))
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ezfio.set_nuclei_nucl_charge(charge)
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# Transformt H1 into H
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import re
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p = re.compile(ur'(\d*)$')
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label = [p.sub("", x.name) for x in res.geometry]
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ezfio.set_nuclei_nucl_label(label)
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ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
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# _
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# /\ _ _ |_) _. _ o _
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# /--\ (_) _> |_) (_| _> | _>
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#
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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import string
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at = []
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num_prim = []
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power_x = []
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power_y = []
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power_z = []
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coefficient = []
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exponent = []
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res.clean_contractions()
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res.convert_to_cartesian()
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# ~#~#~#~#~#~#~ #
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# P a r s i n g #
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# ~#~#~#~#~#~#~ #
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for b in res.basis:
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c = b.center
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for i, atom in enumerate(res.geometry):
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if atom.coord == c:
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at.append(i + 1)
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num_prim.append(len(b.prim))
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s = b.sym
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power_x.append(string.count(s, "x"))
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power_y.append(string.count(s, "y"))
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power_z.append(string.count(s, "z"))
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coefficient.append(b.coef)
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exponent.append([p.expo for p in b.prim])
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# ~#~#~#~#~ #
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# W r i t e #
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# ~#~#~#~#~ #
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ezfio.set_ao_basis_ao_num(len(res.basis))
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ezfio.set_ao_basis_ao_nucl(at)
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ezfio.set_ao_basis_ao_prim_num(num_prim)
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ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
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# ~#~#~#~#~#~#~ #
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# P a r s i n g #
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# ~#~#~#~#~#~#~ #
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prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
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for i in range(len(res.basis)):
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coefficient[
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i] += [0. for j in range(len(coefficient[i]), prim_num_max)]
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exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)]
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coefficient = reduce(lambda x, y: x + y, coefficient, [])
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exponent = reduce(lambda x, y: x + y, exponent, [])
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coef = []
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expo = []
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for i in range(prim_num_max):
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for j in range(i, len(coefficient), prim_num_max):
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coef.append(coefficient[j])
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expo.append(exponent[j])
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# ~#~#~#~#~ #
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# W r i t e #
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# ~#~#~#~#~ #
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ezfio.set_ao_basis_ao_coef(coef)
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ezfio.set_ao_basis_ao_expo(expo)
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ezfio.set_ao_basis_ao_basis("Read by resultsFile")
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# _
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# |\/| _ _ |_) _. _ o _
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# | | (_) _> |_) (_| _> | _>
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#
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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MoTag = res.determinants_mo_type
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ezfio.set_mo_basis_mo_label('Orthonormalized')
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MO_type = MoTag
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allMOs = res.mo_sets[MO_type]
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# ~#~#~#~#~#~#~ #
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# P a r s i n g #
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# ~#~#~#~#~#~#~ #
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try:
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closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos]
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active = [(allMOs[i].eigenvalue, i) for i in res.active_mos]
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virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos]
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except:
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closed = []
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virtual = []
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active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
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closed = map(lambda x: x[1], closed)
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active = map(lambda x: x[1], active)
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virtual = map(lambda x: x[1], virtual)
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MOindices = closed + active + virtual
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MOs = []
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for i in MOindices:
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MOs.append(allMOs[i])
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mo_tot_num = len(MOs)
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while len(MOindices) < mo_tot_num:
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MOindices.append(len(MOindices))
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MOmap = list(MOindices)
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for i in range(len(MOindices)):
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MOmap[i] = MOindices.index(i)
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energies = []
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for i in xrange(mo_tot_num):
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energies.append(MOs[i].eigenvalue)
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if res.occ_num is not None:
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OccNum = []
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for i in MOindices:
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OccNum.append(res.occ_num[MO_type][i])
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while len(OccNum) < mo_tot_num:
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OccNum.append(0.)
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MoMatrix = []
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sym0 = [i.sym for i in res.mo_sets[MO_type]]
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sym = [i.sym for i in res.mo_sets[MO_type]]
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for i in xrange(len(sym)):
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sym[MOmap[i]] = sym0[i]
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MoMatrix = []
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for i in xrange(len(MOs)):
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m = MOs[i]
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for coef in m.vector:
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MoMatrix.append(coef)
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while len(MoMatrix) < len(MOs[0].vector) ** 2:
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MoMatrix.append(0.)
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# ~#~#~#~#~ #
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# W r i t e #
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# ~#~#~#~#~ #
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ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
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ezfio.set_mo_basis_mo_occ(OccNum)
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ezfio.set_mo_basis_mo_coef(MoMatrix)
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def get_full_path(file_path):
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file_path = os.path.expanduser(file_path)
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file_path = os.path.expandvars(file_path)
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file_path = os.path.abspath(file_path)
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return file_path
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if __name__ == '__main__':
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arguments = docopt(__doc__)
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file_ = get_full_path(arguments['<file.out>'])
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if arguments["--ezfio"]:
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ezfio_file = get_full_path(arguments["--ezfio"])
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else:
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ezfio_file = "{0}.ezfio".format(file_)
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try:
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res_file = getFile(file_)
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except:
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raise
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else:
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print file_, 'recognized as', str(res_file).split('.')[-1].split()[0]
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write_ezfio(res_file, ezfio_file)
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@ -1,210 +0,0 @@
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#!/usr/bin/env python
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import sys,os
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try:
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QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
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except:
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print "Error: QPACKAGE_ROOT environment variable not found."
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sys.exit(1)
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sys.path = [ QPACKAGE_ROOT+"/EZFIO/Python", QPACKAGE_ROOT+"/resultsFile" ]+sys.path
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from ezfio import ezfio
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import ezfio as ez
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print "EZFIO: ", os.path.dirname(ez.__file__)
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try:
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from resultsFile import *
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except:
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print "Error: resultsFile Python library not installed"
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sys.exit(1)
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def write_ezfioFile(res,filename):
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res.clean_uncontractions()
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ezfio.set_file(filename)
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# Electrons
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ezfio.set_electrons_elec_alpha_num(res.num_alpha)
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ezfio.set_electrons_elec_beta_num(res.num_beta)
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# Nuclei
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ezfio.set_nuclei_nucl_num(len(res.geometry))
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charge = []
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coord = []
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coord_x = []
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coord_y = []
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coord_z = []
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for a in res.geometry:
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charge.append(a.charge)
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if res.units == 'BOHR':
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coord_x.append(a.coord[0])
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coord_y.append(a.coord[1])
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coord_z.append(a.coord[2])
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else:
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coord_x.append(a.coord[0]/a0)
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coord_y.append(a.coord[1]/a0)
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coord_z.append(a.coord[2]/a0)
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ezfio.set_nuclei_nucl_charge(charge)
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label = map(lambda x: x.name, res.geometry)
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ezfio.set_nuclei_nucl_label(label)
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ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
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# Basis
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basis = res.uncontracted_basis
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geom = res.geometry
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res.clean_contractions()
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# AO Basis
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import string
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at = []
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num_prim = []
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magnetic_number = []
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angular_number = []
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power_x = []
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power_y = []
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power_z = []
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coefficient = []
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exponent = []
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res.convert_to_cartesian()
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for b in res.basis:
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c = b.center
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for i,atom in enumerate(res.geometry):
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if atom.coord == c:
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at.append(i+1)
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num_prim.append(len(b.prim))
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s = b.sym
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power_x.append( string.count(s,"x") )
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power_y.append( string.count(s,"y") )
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power_z.append( string.count(s,"z") )
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coefficient.append( b.coef )
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exponent.append( [ p.expo for p in b.prim ] )
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ezfio.set_ao_basis_ao_num(len(res.basis))
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ezfio.set_ao_basis_ao_nucl(at)
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ezfio.set_ao_basis_ao_prim_num(num_prim)
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ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
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prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
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len_res_basis = len(res.basis)
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for i in range(len(res.basis)):
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coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
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exponent[i] += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
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coefficient = reduce(lambda x, y: x+y, coefficient, [])
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exponent = reduce(lambda x, y: x+y, exponent, [])
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coef = []
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expo = []
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for i in range(prim_num_max):
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for j in range(i,len(coefficient),prim_num_max):
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coef.append ( coefficient[j] )
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expo.append ( exponent[j] )
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ezfio.set_ao_basis_ao_coef(coef)
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ezfio.set_ao_basis_ao_expo(expo)
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ezfio.set_ao_basis_ao_basis("Read by resultsFile")
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# MO
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MoTag = res.determinants_mo_type
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ezfio.set_mo_basis_mo_label('Orthonormalized')
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MO_type = MoTag
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allMOs = res.mo_sets[MO_type]
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try:
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closed = [ (allMOs[i].eigenvalue,i) for i in res.closed_mos ]
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active = [ (allMOs[i].eigenvalue,i) for i in res.active_mos ]
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virtual =[ (allMOs[i].eigenvalue,i) for i in res.virtual_mos ]
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except:
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closed = []
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virtual = []
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active = [ (allMOs[i].eigenvalue,i) for i in range(len(allMOs)) ]
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# closed.sort()
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# active.sort()
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# virtual.sort()
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closed = map( lambda x: x[1], closed)
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active = map( lambda x: x[1], active)
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virtual = map( lambda x: x[1], virtual)
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MOindices = closed + active + virtual
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MOs = []
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for i in MOindices:
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MOs.append(allMOs[i])
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mo_tot_num = len(MOs)
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while len(MOindices) < mo_tot_num:
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MOindices.append(len(MOindices))
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MOmap = list(MOindices)
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for i in range(len(MOindices)):
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MOmap[i] = MOindices.index(i)
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energies = []
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for i in xrange(mo_tot_num):
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energies.append(MOs[i].eigenvalue)
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if res.occ_num is not None:
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OccNum = []
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for i in MOindices:
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OccNum.append(res.occ_num[MO_type][i])
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while len(OccNum) < mo_tot_num:
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OccNum.append(0.)
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MoMatrix = []
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sym0 = [ i.sym for i in res.mo_sets[MO_type] ]
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sym = [ i.sym for i in res.mo_sets[MO_type] ]
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for i in xrange(len(sym)):
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sym[MOmap[i]] = sym0[i]
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MoMatrix = []
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for i in xrange(len(MOs)):
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m = MOs[i]
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for coef in m.vector:
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MoMatrix.append(coef)
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|
||||
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