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code to parse the first atom of a dalton input file along with its basis set
Raw
assemble.py
#!/usr/bin/env python
import sys
import numpy
from atom import Atom
from read_log import read_log_file
from read_mol import read_mol_file
if len(sys.argv) != 6:
print "usage: assemble mol log Ns Np Nd"
sys.exit()
mol_file = sys.argv[1]
log_file = sys.argv[2]
ns = int(sys.argv[3])
np = int(sys.argv[4])
nd = int(sys.argv[5])
atom = read_mol_file(mol_file)
orbitals = read_log_file(log_file)
atom.add_mos(orbitals)
atom.generate_mos(ns,np,nd,0)
print atom
Raw
atom.py
from numpy import *
from generator import generate_mos
class Atom(object):
def __init__(self, Z):
self.Z = Z
self.S = []
self.P = []
self.D = []
self.F = []
def add_mos(self, orbitals):
self.org_SMO = orbitals['1']
self.org_PMO = orbitals['2']
self.org_DMO = orbitals['4']
self.org_FMO = identity(len(self.F))
def generate_mos(self, ns, np, nd, nf):
if ns > 0:
# the following line is for C2v symmetry.
smos = column_stack((self.org_SMO[:,0:2],self.org_SMO[:,3])) # 1,2 and 4th makes the S-orbitals
# the following line is for D2 symmetry.
#smos = self.org_SMO[:,0:3]
smos = smos[:ns]
self.SMO = generate_mos(len(self.S), smos)
else:
self.SMO = identity(len(self.S))
if np > 0:
# the following line is the same for C2v and D2 symmetry
pmos = self.org_PMO[:,0:2]
pmos = pmos[:np]
self.PMO = generate_mos(len(self.P), pmos)
else:
self.PMO = identity(len(self.P))
if nd > 0:
# the following line is for C2v symmetry
dmos = self.org_DMO[:,0:1]
# the following line is for D2 symmetry
#dmos = self.org_DMO[:,2:3]
dmos = dmos[:nd]
self.DMO = generate_mos(len(self.D), dmos)
else:
self.DMO = identity(len(self.D))
self.FMO = generate_mos(len(self.F), self.org_FMO)
def set_shells(self,ns,np,nd,nf):
self.Lmax = 0
self.Ns = ns
self.Np = np
self.Nd = nd
self.Nf = nf
if ns > 0: self.Lmax += 1
if np > 0: self.Lmax += 1
if nd > 0: self.Lmax += 1
if nf > 0: self.Lmax += 1
def set_coords(self,x,y,z):
self.x = x
self.y = y
self.z = z
def set_label(self,label):
self.label = label
def get_row(self,i_row,MO):
return MO[i_row]
def format_row(self,row,n_col=3,n_max=-1,format="%20.8e",separator="\n", separator2="%20s" % ""):
# format is
# "" + 3 x 20.8f # first line
# "%20s" + 3 x 20.8f # following lines
s = ""
first = True
for i,value in enumerate(row):
idx = i + 1
s += format % (value)
if idx % n_col == 0:
s += separator + separator2
if idx%n_col == 0: s = s[:-(len(separator2)+1)]
return s
def build_coeff_string(self, exponents, mocoeffs, n_col=3):
(n_max,k_max) = shape(mocoeffs)
s = "H%4i%5i\n" % (len(exponents),k_max)
for i,alpha in enumerate(exponents):
row = self.get_row(i,mocoeffs)
s += "%20.8f%s\n" % (alpha, self.format_row(row,n_col,k_max))
return s
def __str__(self):
self.Ns = 1
s = "%10.1f 1%5i%5i%5i%5i%5i\n" % (self.Z,self.Lmax,self.Ns,self.Np,self.Nd,self.Nf)
s += "%s%9.5f%20.5f%20.5f\n" % (self.label, self.x, self.y, self.z)
s += self.build_coeff_string(self.S, self.SMO, 3)
s += self.build_coeff_string(self.P, self.PMO, 3)
s += self.build_coeff_string(self.D, self.DMO, 3)
s += self.build_coeff_string(self.F, self.FMO, 3)
return s[:-1]
Raw
GaH.log
****************************************************************************
*************** DALTON2011 - An electronic structure program ***************
****************************************************************************
This is output from DALTON Release Dalton2011 (Rev. 0, July 2011)
----------------------------------------------------------------------------
NOTE:
DALTON is an experimental code for the evaluation of molecular
properties using (MC)SCF, DFT, CI, and CC wave functions.
The authors accept no responsibility for the performance of
the code or for the correctness of the results.
The code (in whole or part) is provided under a licence and
is not to be reproduced for further distribution without
the written permission of the authors or their representatives.
See the home page "http://daltonprogram.org" for further information.
If results obtained with this code are published,
an appropriate citation would be:
"Dalton, a molecular electronic structure program,
Release Dalton2011 (2011), see http://daltonprogram.org"
----------------------------------------------------------------------------
Authors in alphabetical order (major contribution(s) in parenthesis):
Celestino Angeli, University of Ferrara, Italy (NEVPT2)
Keld L. Bak, UNI-C, Denmark (AOSOPPA, non-adiabatic coupling, magnetic properties)
Vebjoern Bakken, University of Oslo, Norway (DALTON; geometry optimizer, symmetry detection)
Gao Bin, University of Tromsoe, Norway (ECP with Gen1Int)
Ove Christiansen, Aarhus University, Denmark (CC module)
Renzo Cimiraglia, University of Ferrara, Italy (NEVPT2)
Sonia Coriani, University of Trieste, Italy (CC module, MCD in RESPONS)
Paal Dahle, University of Oslo, Norway (Parallelization)
Erik K. Dalskov, UNI-C, Denmark (SOPPA)
Thomas Enevoldsen, SDU - Odense University, Denmark (SOPPA)
Berta Fernandez, U. of Santiago de Compostela, Spain (doublet spin, ESR in RESPONS)
Lara Ferrighi, Aarhus University, Denmark (PCM Cubic response)
Heike Fliegl, University of Helsinki, Finland (CCSD(R12))
Luca Frediani, University of Tromsoe, Norway (PCM)
Christof Haettig, Ruhr University Bochum, Germany (CC module)
Kasper Hald, Aarhus University, Denmark (CC module)
Asger Halkier, Aarhus University, Denmark (CC module)
Hanne Heiberg, University of Oslo, Norway (geometry analysis, selected one-electron integrals)
Trygve Helgaker, University of Oslo, Norway (DALTON; ABACUS, ERI, DFT modules, London, and much more)
Hinne Hettema, University of Auckland, New Zealand (quadratic response in RESPONS; SIRIUS supersymmetry)
Brano Jansik University of Aarhus Denmark (DFT cubic response)
Hans Joergen Aa. Jensen, Univ. of Southern Denmark, Denmark (DALTON; SIRIUS, RESPONS, ABACUS modules, London, and much more)
Dan Jonsson, University of Tromsoe, Norway (cubic response in RESPONS module)
Poul Joergensen, Aarhus University, Denmark (RESPONS, ABACUS, and CC modules)
Sheela Kirpekar, SDU - Odense University, Denmark (Mass-velocity & Darwin integrals)
Wim Klopper, University of Karlsruhe, Germany (R12 code in CC, SIRIUS, and ABACUS modules)
Stefan Knecht, Univ. of Southern Denmark, Denmark (Parallel CI)
Rika Kobayashi, ANU Supercomputer Facility, Australia (DIIS in CC, London in MCSCF)
Jacob Kongsted, Univ. of Southern Denmark, Denmark (QM/MM code)
Henrik Koch, University of Trondheim, Norway (CC module, Cholesky decomposition)
Andrea Ligabue, University of Modena, Italy (CTOCD, AOSOPPA)
Ola B. Lutnaes, University of Oslo, Norway (DFT Hessian)
Kurt V. Mikkelsen, University of Copenhagen, Denmark (MC-SCRF and QM/MM code)
Christian Neiss, Univ. Erlangen-Nürnberg, Germany (CCSD(R12))
Christian B. Nielsen, University of Copenhagen, Denmark (QM/MM code)
Patrick Norman, University of Linkoeping, Sweden (cubic response and complex response in RESPONS)
Jeppe Olsen, Aarhus University, Denmark (SIRIUS CI/density modules)
Anders Osted, Copenhagen University, Denmark (QM/MM code)
Martin J. Packer, University of Sheffield, UK (SOPPA)
Thomas B. Pedersen, University of Oslo, Norway (Cholesky decomposition)
Zilvinas Rinkevicius, KTH Stockholm, Sweden (open-shell DFT, ESR)
Elias Rudberg, KTH Stockholm, Sweden (DFT grid and basis info)
Torgeir A. Ruden, University of Oslo, Norway (Numerical derivatives in ABACUS)
Kenneth Ruud, University of Tromsoe, Norway (DALTON; ABACUS magnetic properties and much more)
Pawel Salek, KTH Stockholm, Sweden (DALTON; DFT code)
Claire C.M. Samson University of Karlsruhe Germany (Boys localization, r12 integrals in ERI)
Alfredo Sanchez de Meras, University of Valencia, Spain (CC module, Cholesky decomposition)
Trond Saue, CNRS/ULP Toulouse, France (direct Fock matrix construction)
Stephan P. A. Sauer, University of Copenhagen, Denmark (SOPPA(CCSD), SOPPA prop., AOSOPPA, vibrational g-factors)
Bernd Schimmelpfennig, Forschungszentrum Karlsruhe, Germany (AMFI module)
Arnfinn H. Steindal, University of Tromsoe, Norway (parallel QM/MM)
K. O. Sylvester-Hvid, University of Copenhagen, Denmark (MC-SCRF)
Peter R. Taylor, VLSCI/Univ. of Melbourne, Australia (Symmetry handling ABACUS, integral transformation)
David P. Tew, University of Bristol, England (CCSD(R12))
Olav Vahtras, KTH Stockholm, Sweden (triplet response, spin-orbit, ESR, TDDFT, open-shell DFT)
David J. Wilson, La Trobe University, Australia (DFT Hessian and DFT magnetizabilities)
Hans Agren, KTH Stockholm, Sweden (SIRIUS module, MC-SCRF solvation model)
--------------------------------------------------------------------------------
Date and time (Linux) : Fri Mar 30 09:32:26 2012
Host name : sunray
* Work memory size : 524288000 = 3.906 gigabytes.
* Directories for basis set searches:
1) /home/cstein/projects/sauer/spin-spin/GaH
2) /home/cstein/development/fortran/DALTON/Dalton2011_release/basis
*******************************************************************
*********** Output from DALTON general input processing ***********
*******************************************************************
--------------------------------------------------------------------------------
Overall default print level: 0
Print level for DALTON.STAT: 1
HERMIT 1- and 2-electron integral sections will be executed
"Old" integral transformation used (limited to max 255 basis functions)
Wave function sections will be executed (SIRIUS module)
--------------------------------------------------------------------------------
****************************************************************************
*************** Output of molecule and basis set information ***************
****************************************************************************
The two title cards from your ".mol" input:
------------------------------------------------------------------------
1: GaH : Coupling Constants : R = 3.1061 au
2: second title line
------------------------------------------------------------------------
INFO from READIN: Threshold for discarding integrals was 1.00D-16
INFO from READIN: Threshold is reset to minimum value 1.00D-15
Atomic type no. 1
--------------------
Nuclear charge: 31.00000
Number of symmetry independent centers: 1
Number of basis sets to read; 2
Atomic type no. 2
--------------------
Nuclear charge: 1.00000
Number of symmetry independent centers: 1
Number of basis sets to read; 2
SYMGRP: Point group information
-------------------------------
Point group: C2v
* The point group was generated by:
Reflection in the yz-plane
Reflection in the xz-plane
* Group multiplication table
| E C2z Oxz Oyz
-----+--------------------
E | E C2z Oxz Oyz
C2z | C2z E Oyz Oxz
Oxz | Oxz Oyz E C2z
Oyz | Oyz Oxz C2z E
* Character table
| E C2z Oxz Oyz
-----+--------------------
A1 | 1 1 1 1
B1 | 1 -1 1 -1
B2 | 1 -1 -1 1
A2 | 1 1 -1 -1
* Direct product table
| A1 B1 B2 A2
-----+--------------------
A1 | A1 B1 B2 A2
B1 | B1 A1 A2 B2
B2 | B2 A2 A1 B1
A2 | A2 B2 B1 A1
Isotopic Masses
---------------
Ga 68.925581
H 1.007825
Total mass: 69.933406 amu
Natural abundance: 60.099 %
Center-of-mass coordinates (a.u.): 0.000000 0.000000 3.061337
Atoms and basis sets
--------------------
Number of atom types : 2
Total number of atoms: 2
label atoms charge prim cont basis
----------------------------------------------------------------------
Ga 1 31.0000 131 131 [25s14p10d2f|25s14p10d2f]
H 1 1.0000 24 24 [10s3p1d|10s3p1d]
----------------------------------------------------------------------
total: 2 32.0000 155 155
----------------------------------------------------------------------
Spherical harmonic basis used.
Threshold for integrals: 1.00D-15
Cartesian Coordinates (a.u.)
----------------------------
Total number of coordinates: 6
Ga : 1 x 0.0000000000 2 y 0.0000000000 3 z 3.1061000000
H : 4 x 0.0000000000 5 y 0.0000000000 6 z 0.0000000000
Symmetry Coordinates
--------------------
Number of coordinates in each symmetry: 2 2 2 0
Symmetry A1 ( 1)
1 Ga z 3
2 H z 6
Symmetry B1 ( 2)
3 Ga x 1
4 H x 4
Symmetry B2 ( 3)
5 Ga y 2
6 H y 5
Interatomic separations (in Angstrom):
--------------------------------------
Ga H
------ ------
Ga : 0.000000
H : 1.643677 0.000000
Max interatomic separation is 1.6437 Angstrom ( 3.1061 Bohr)
between atoms 2 and 1, "H " and "Ga ".
Bond distances (Angstrom):
--------------------------
atom 1 atom 2 distance
------ ------ --------
bond distance: H Ga 1.643677
Principal moments of inertia (u*A**2) and principal axes
--------------------------------------------------------
IA 0.000000 0.000000 0.000000 1.000000
IB 2.683577 0.000000 1.000000 0.000000
IC 2.683577 1.000000 0.000000 0.000000
Rotational constants
--------------------
The molecule is linear.
B = 188322.92 MHz ( 6.281776 cm-1)
@ Nuclear repulsion energy : 9.980361224687 Hartree
Symmetry Orbitals
-----------------
Number of orbitals in each symmetry: 78 32 32 13
Symmetry A1 ( 1)
1 Ga 1s 1
2 Ga 1s 2
3 Ga 1s 3
4 Ga 1s 4
5 Ga 1s 5
6 Ga 1s 6
7 Ga 1s 7
8 Ga 1s 8
9 Ga 1s 9
10 Ga 1s 10
11 Ga 1s 11
12 Ga 1s 12
13 Ga 1s 13
14 Ga 1s 14
15 Ga 1s 15
16 Ga 1s 16
17 Ga 1s 17
18 Ga 1s 18
19 Ga 1s 19
20 Ga 1s 20
21 Ga 1s 21
22 Ga 1s 22
23 Ga 1s 23
24 Ga 1s 24
25 Ga 1s 25
26 Ga 2pz 28
27 Ga 2pz 31
28 Ga 2pz 34
29 Ga 2pz 37
30 Ga 2pz 40
31 Ga 2pz 43
32 Ga 2pz 46
33 Ga 2pz 49
34 Ga 2pz 52
35 Ga 2pz 55
36 Ga 2pz 58
37 Ga 2pz 61
38 Ga 2pz 64
39 Ga 2pz 67
40 Ga 3d0 70
41 Ga 3d2+ 72
42 Ga 3d0 75
43 Ga 3d2+ 77
44 Ga 3d0 80
45 Ga 3d2+ 82
46 Ga 3d0 85
47 Ga 3d2+ 87
48 Ga 3d0 90
49 Ga 3d2+ 92
50 Ga 3d0 95
51 Ga 3d2+ 97
52 Ga 3d0 100
53 Ga 3d2+ 102
54 Ga 3d0 105
55 Ga 3d2+ 107
56 Ga 3d0 110
57 Ga 3d2+ 112
58 Ga 3d0 115
59 Ga 3d2+ 117
60 Ga 4f0 121
61 Ga 4f2+ 123
62 Ga 4f0 128
63 Ga 4f2+ 130
64 H 1s 132
65 H 1s 133
66 H 1s 134
67 H 1s 135
68 H 1s 136
69 H 1s 137
70 H 1s 138
71 H 1s 139
72 H 1s 140
73 H 1s 141
74 H 2pz 144
75 H 2pz 147
76 H 2pz 150
77 H 3d0 153
78 H 3d2+ 155
Symmetry B1 ( 2)
79 Ga 2px 26
80 Ga 2px 29
81 Ga 2px 32
82 Ga 2px 35
83 Ga 2px 38
84 Ga 2px 41
85 Ga 2px 44
86 Ga 2px 47
87 Ga 2px 50
88 Ga 2px 53
89 Ga 2px 56
90 Ga 2px 59
91 Ga 2px 62
92 Ga 2px 65
93 Ga 3d1+ 71
94 Ga 3d1+ 76
95 Ga 3d1+ 81
96 Ga 3d1+ 86
97 Ga 3d1+ 91
98 Ga 3d1+ 96
99 Ga 3d1+ 101
100 Ga 3d1+ 106
101 Ga 3d1+ 111
102 Ga 3d1+ 116
103 Ga 4f1+ 122
104 Ga 4f3+ 124
105 Ga 4f1+ 129
106 Ga 4f3+ 131
107 H 2px 142
108 H 2px 145
109 H 2px 148
110 H 3d1+ 154
Symmetry B2 ( 3)
111 Ga 2py 27
112 Ga 2py 30
113 Ga 2py 33
114 Ga 2py 36
115 Ga 2py 39
116 Ga 2py 42
117 Ga 2py 45
118 Ga 2py 48
119 Ga 2py 51
120 Ga 2py 54
121 Ga 2py 57
122 Ga 2py 60
123 Ga 2py 63
124 Ga 2py 66
125 Ga 3d1- 69
126 Ga 3d1- 74
127 Ga 3d1- 79
128 Ga 3d1- 84
129 Ga 3d1- 89
130 Ga 3d1- 94
131 Ga 3d1- 99
132 Ga 3d1- 104
133 Ga 3d1- 109
134 Ga 3d1- 114
135 Ga 4f3- 118
136 Ga 4f1- 120
137 Ga 4f3- 125
138 Ga 4f1- 127
139 H 2py 143
140 H 2py 146
141 H 2py 149
142 H 3d1- 152
Symmetry A2 ( 4)
143 Ga 3d2- 68
144 Ga 3d2- 73
145 Ga 3d2- 78
146 Ga 3d2- 83
147 Ga 3d2- 88
148 Ga 3d2- 93
149 Ga 3d2- 98
150 Ga 3d2- 103
151 Ga 3d2- 108
152 Ga 3d2- 113
153 Ga 4f2- 119
154 Ga 4f2- 126
155 H 3d2- 151
Symmetries of electric field: B1 (2) B2 (3) A1 (1)
Symmetries of magnetic field: B2 (3) B1 (2) A2 (4)
.---------------------------------------.
| Starting in Integral Section (HERMIT) |
`---------------------------------------'
*************************************************************************
****************** Output from HERMIT input processing ******************
*************************************************************************
************************************************************************
************************** Output from HERINT **************************
************************************************************************
Threshold for neglecting two-electron integrals: 1.00D-15
Number of two-electron integrals written: 9666321 ( 13.2% )
Megabytes written: 110.687
>>> Time used in TWOINT is 1.52 seconds
>>>> Total CPU time used in HERMIT: 1.65 seconds
>>>> Total wall time used in HERMIT: 1.65 seconds
.----------------------------------.
| End of Integral Section (HERMIT) |
`----------------------------------'
.--------------------------------------------.
| Starting in Wave Function Section (SIRIUS) |
`--------------------------------------------'
*** Output from Huckel module :
Using EWMO model: T
Using EHT model: F
Number of Huckel orbitals each symmetry: 10 4 4 1
EWMO - Energy Weighted Maximum Overlap - is a Huckel type method,
which normally is better than Extended Huckel Theory.
Reference: Linderberg and Ohrn, Propagators in Quantum Chemistry (Wiley, 1973)
Huckel EWMO eigenvalues for symmetry : 1
-378.818107 -48.168558 -42.493905 -6.397103 -4.483742
-1.197078 -1.193400 -0.691420 -0.332282 -0.101504
Huckel EWMO eigenvalues for symmetry : 2
-42.493900 -4.482300 -1.193400 -0.208500
Huckel EWMO eigenvalues for symmetry : 3
-42.493900 -4.482300 -1.193400 -0.208500
Huckel EWMO eigenvalues for symmetry : 4
-1.193400
**********************************************************************
*SIRIUS* a direct, restricted step, second order MCSCF program *
**********************************************************************
Date and time (Linux) : Fri Mar 30 09:32:27 2012
Host name : sunray
Title lines from ".mol" input file:
GaH : Coupling Constants : R = 3.1061 au
second title line
Print level on unit LUPRI = 2 is 0
Print level on unit LUW4 = 2 is 5
Restricted, closed shell Hartree-Fock calculation.
Initial molecular orbitals are obtained according to
".MOSTART EWMO " input option.
Wave function specification
============================
For the wave function of type : >>> HF <<<
Number of closed shell electrons 32
Number of electrons in active shells 0
Total charge of the molecule 0
Spin multiplicity 1
Total number of symmetries 4
Reference state symmetry 1
Orbital specifications
======================
Abelian symmetry species All | 1 2 3 4
--- | --- --- --- ---
Total number of orbitals 155 | 78 32 32 13
Number of basis functions 155 | 78 32 32 13
** Automatic occupation of RHF orbitals **
-- Initial occupation of symmetries is determined from extended Huckel guess.
-- Initial occupation of symmetries is :
Occupied SCF orbitals 16 | 9 3 3 1
Maximum number of Fock iterations 0
Maximum number of DIIS iterations 60
Maximum number of QC-SCF iterations 60
Threshold for SCF convergence 1.00D-05
>>>>> DIIS optimization of Hartree-Fock <<<<<
C1-DIIS algorithm; max error vectors = 10
Automatic occupation of symmetries with 32 electrons.
Iter Total energy Error norm Delta(E) HF occupation
-----------------------------------------------------------------------------
(Precalculated two-electron integrals are transformed to P-supermatrix elements.
Threshold for discarding integrals : 1.00D-15 )
>>> Time used in FORMSUP is 0.55 seconds
1 -1923.77790617 1.19D+04 -1.92D+03 9 3 3 1
Virial theorem: -V/T = 1.999985
MULPOP Ga 0.52; H -0.52;
-----------------------------------------------------------------------------
2 -1923.83507752 1.39D-01 -5.72D-02 9 3 3 1
Virial theorem: -V/T = 1.999838
MULPOP Ga 0.24; H -0.24;
-----------------------------------------------------------------------------
3 -1923.83736668 9.89D-02 -2.29D-03 9 3 3 1
Virial theorem: -V/T = 2.000163
MULPOP Ga 0.20; H -0.20;
-----------------------------------------------------------------------------
4 -1923.83766248 3.17D-02 -2.96D-04 9 3 3 1
Virial theorem: -V/T = 1.999947
MULPOP Ga 0.19; H -0.19;
-----------------------------------------------------------------------------
5 -1923.83779655 5.47D-03 -1.34D-04 9 3 3 1
Virial theorem: -V/T = 1.999989
MULPOP Ga 0.18; H -0.18;
-----------------------------------------------------------------------------
6 -1923.83780417 1.03D-03 -7.62D-06 9 3 3 1
Virial theorem: -V/T = 1.999994
MULPOP Ga 0.18; H -0.18;
-----------------------------------------------------------------------------
7 -1923.83780458 1.86D-04 -4.14D-07 9 3 3 1
Virial theorem: -V/T = 1.999994
MULPOP Ga 0.18; H -0.18;
-----------------------------------------------------------------------------
8 -1923.83780460 2.50D-05 -1.06D-08 9 3 3 1
Virial theorem: -V/T = 1.999994
MULPOP Ga 0.18; H -0.18;
-----------------------------------------------------------------------------
9 -1923.83780460 3.40D-06 -1.83D-10 9 3 3 1
*** DIIS converged in 9 iterations !
- total time used in SIRFCK : 0.00 seconds
*** SCF orbital energy analysis ***
Only the five lowest virtual orbital energies printed in each symmetry.
Number of electrons : 32
Orbital occupations : 9 3 3 1
Sym Hartree-Fock orbital energies
1 -378.81225001 -48.16253977 -42.48693324 -6.38923540 -4.47322965
-1.19429596 -1.18548051 -0.51646242 -0.29503426 0.02202752
0.05172481 0.08758810 0.11481477 0.11902999
2 -42.48900287 -4.47983426 -1.18514901 0.01651996 0.08021816
0.11601662 0.31868306 0.38253363
3 -42.48900287 -4.47983426 -1.18514901 0.01651996 0.08021816
0.11601662 0.31868306 0.38253363
4 -1.19429596 0.11481477 0.38279196 0.39986164 1.17348623
1.22267494
E(LUMO) : 0.01651996 au (symmetry 3)
- E(HOMO) : -0.29503426 au (symmetry 1)
------------------------------------------
gap : 0.31155422 au
>>> Writing SIRIFC interface file <<<
>>>> CPU and wall time for SCF : 0.920 0.923
.-----------------------------------.
| >>> Final results from SIRIUS <<< |
`-----------------------------------'
@ Spin multiplicity: 1
@ Spatial symmetry: 1
@ Total charge of molecule: 0
@ Final HF energy: -1923.837804595280
@ Nuclear repulsion: 9.980361224687
@ Electronic energy: -1933.818165819967
@ Final gradient norm: 0.000003399088
Date and time (Linux) : Fri Mar 30 09:32:28 2012
Host name : sunray
(Only coefficients > 0.000000001 are printed.)
Molecular orbitals for symmetry species 1
------------------------------------------
Orbital 1 2 3 4 5 6 7
1 Ga :1s -0.0000000006270 -0.0000000001944 0.0000000000001 0.0000000000741 -0.0000000000004 0.0000000000000 -0.0000000000002
2 Ga :1s -0.0000000046861 -0.0000000014519 0.0000000000010 0.0000000005538 -0.0000000000031 0.0000000000000 -0.0000000000014
3 Ga :1s -0.0000000652174 -0.0000000202160 0.0000000000136 0.0000000077080 -0.0000000000430 0.0000000000000 -0.0000000000181
4 Ga :1s -0.0000005626617 -0.0000001743371 0.0000000001171 0.0000000664978 -0.0000000003727 0.0000000000000 -0.0000000001627
5 Ga :1s -0.0000073647622 -0.0000022828624 0.0000000015326 0.0000008704435 -0.0000000048596 0.0000000000000 -0.0000000020493
6 Ga :1s -0.0000627474392 -0.0000194442349 0.0000000130592 0.0000074166725 -0.0000000415671 0.0000000000000 -0.0000000181259
7 Ga :1s -0.0003263639593 -0.0001012236584 0.0000000679459 0.0000385936947 -0.0000002151817 0.0000000000000 -0.0000000896939
8 Ga :1s -0.0013801234873 -0.0004282862927 0.0000002877159 0.0001634190762 -0.0000009174209 0.0000000000000 -0.0000004056662
9 Ga :1s -0.0049984175670 -0.0015579285426 0.0000010457088 0.0005942442204 -0.0000033075077 0.0000000000000 -0.0000013568243
10 Ga :1s -0.0160614920756 -0.0050471871016 0.0000033927885 0.0019291981480 -0.0000108530408 0.0000000000000 -0.0000048783881
11 Ga :1s -0.0460112294654 -0.0148049775631 0.0000099452701 0.0056679418854 -0.0000314849627 0.0000000000000 -0.0000126517377
12 Ga :1s -0.1152237755510 -0.0389484024274 0.0000262552270 0.0150273068225 -0.0000848424355 0.0000000000000 -0.0000390560165
13 Ga :1s -0.2373902774191 -0.0896810635923 0.0000605587806 0.0350159360772 -0.0001940266502 0.0000000000000 -0.0000751021688
14 Ga :1s -0.3532002206851 -0.1664072513144 0.0001134320139 0.0671110871533 -0.0003829667171 0.0000000000000 -0.0001873151228
15 Ga :1s -0.2915476635011 -0.2003937774209 0.0001360191407 0.0849908433743 -0.0004633005933 0.0000000000000 -0.0001443317624
16 Ga :1s -0.0812171173030 0.0114809978792 -0.0000098611654 -0.0046847145298 -0.0000115256550 0.0000000000000 -0.0001454497686
17 Ga :1s -0.0007610557795 0.4958185903728 -0.0003732381394 -0.3017025159847 0.0018351255081 0.0000000000000 0.0011535910125
18 Ga :1s -0.0016185237220 0.5295222069411 -0.0003418569628 -0.4823181956553 0.0026796772011 0.0000000000000 0.0006295038369
19 Ga :1s 0.0007613718655 0.1110858178173 -0.0000302998241 0.0887793886241 -0.0004495700386 0.0000000000000 0.0011063301107
20 Ga :1s -0.0003231801228 -0.0007702678006 0.0000146989043 0.7290695016271 -0.0057879518115 0.0000000000000 -0.0062722962132
21 Ga :1s 0.0001395206951 0.0023016772724 -0.0000012209237 0.4284874391054 -0.0002837217850 0.0000000000000 0.0023164166524
22 Ga :1s -0.0000614286936 -0.0005962936553 -0.0000152040605 0.0220360466226 0.0003485678580 0.0000000000000 0.0148803129213
23 Ga :1s 0.0000474178598 0.0004663089362 0.0000292839339 -0.0111815921379 0.0006176047762 0.0000000000000 -0.0210936941120
24 Ga :1s -0.0000268765540 -0.0002597987259 0.0000252855426 0.0043740651187 0.0048467746033 0.0000000000003 0.0099759694160
25 Ga :1s -0.0000050010624 -0.0000485064274 0.0000045219835 0.0007584818097 0.0009805666376 0.0000000000001 0.0021851230659
26 Ga :2pz 0.0000000062868 -0.0000001849712 -0.0003169276262 0.0000005156392 0.0001204723705 0.0000000000000 0.0000005823157
27 Ga :2pz 0.0000000607298 -0.0000016000046 -0.0027650322030 0.0000044354196 0.0010505482037 0.0000000000000 0.0000051902599
28 Ga :2pz 0.0000003786033 -0.0000087800494 -0.0151213871940 0.0000248733385 0.0058180869837 0.0000000000000 0.0000281225269
29 Ga :2pz 0.0000022335773 -0.0000338489109 -0.0599632601392 0.0000985115332 0.0234650478528 0.0000000000000 0.0001161126122
30 Ga :2pz 0.0000033147992 -0.0000978975784 -0.1733251294682 0.0003015692485 0.0709257162074 0.0000000000000 0.0003420303758
31 Ga :2pz -0.0000000548427 -0.0001982612781 -0.3411127690071 0.0006124755178 0.1467458447691 0.0000000000000 0.0007335445407
32 Ga :2pz 0.0000003932139 -0.0002497692630 -0.3896886382457 0.0007701816963 0.1772262059068 0.0000000000000 0.0008347287714
33 Ga :2pz -0.0000005040805 -0.0001612404448 -0.1839363917841 -0.0000973210164 -0.0366298928089 0.0000000000000 -0.0000738818859
34 Ga :2pz 0.0000007802880 -0.0000218909823 -0.0218902688003 -0.0014531702544 -0.4240243021489 0.0000000000000 -0.0023890586706
35 Ga :2pz -0.0000006180587 -0.0000076713263 -0.0011652147326 -0.0026403315312 -0.4962502317641 0.0000000000000 -0.0022136596412
36 Ga :2pz -0.0000006396659 -0.0000079551744 -0.0002613391005 -0.0012934839699 -0.1773768727226 0.0000000000000 -0.0022271368399
37 Ga :2pz 0.0000079852692 0.0000691939706 -0.0000338740147 0.0001294394410 -0.0071652804362 0.0000000000000 0.0061467250602
38 Ga :2pz 0.0000022751534 0.0000203117294 -0.0000169782630 -0.0002217731710 -0.0021641054474 -0.0000000000002 -0.0044605791538
39 Ga :2pz 0.0000055373859 0.0000538027648 -0.0000015595188 -0.0008502033867 -0.0006367036978 -0.0000000000001 -0.0015702628692
40 Ga :3d0 0.0000003273328 -0.0000002224465 0.0000005903863 -0.0000007654164 0.0000074118280 0.0000000000000 -0.0020215947238
41 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.0020251983513 0.0000000000000
42 Ga :3d0 -0.0000004686852 -0.0000025275372 0.0000060874882 -0.0000095156234 0.0000571675641 0.0000000000000 -0.0164648213786
43 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.0164862209177 0.0000000000000
44 Ga :3d0 0.0000002710117 -0.0000310787323 0.0000151282544 -0.0000165014549 0.0002586843137 0.0000000000000 -0.0701960683178
45 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.0703202581960 0.0000000000000
46 Ga :3d0 0.0000001781694 -0.0000518002224 0.0000287517986 -0.0000663651854 0.0006956194769 0.0000000000001 -0.1906450195374
47 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.1908573980729 -0.0000000000001
48 Ga :3d0 0.0000006882760 0.0000134755870 0.0000199247050 -0.0001666784387 0.0012911560587 0.0000000000001 -0.3245321965608
49 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.3252343360082 -0.0000000000001
50 Ga :3d0 -0.0000009145653 -0.0000121939584 0.0000016748266 -0.0006596159217 0.0015716326387 0.0000000000001 -0.3667844846208
51 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.3671462213480 -0.0000000000001
52 Ga :3d0 0.0000019970039 0.0000141929913 -0.0000055765348 -0.0008264394148 0.0009814527984 0.0000000000001 -0.2721714584005
53 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.2762702459588 -0.0000000000001
54 Ga :3d0 -0.0000065009381 -0.0000615169993 0.0000028325371 0.0003018200877 -0.0005203073321 0.0000000000000 -0.0983536678025
55 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.0940852178196 0.0000000000000
56 Ga :3d0 -0.0000009144553 -0.0000073172334 0.0000116533716 -0.0001062214139 0.0011972512189 0.0000000000000 -0.0048018337366
57 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.0017761993521 0.0000000000000
58 Ga :3d0 -0.0000025809400 -0.0000247693972 0.0000021956489 0.0003990556453 0.0005185813842 0.0000000000001 0.0014076788484
59 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.0008736642126 0.0000000000000
60 Ga :4f0 0.0000031315972 0.0000294720465 -0.0000017670837 0.0000096849647 0.0004240313449 0.0000000000000 0.0055421860097
61 Ga :4f2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0016099660312 0.0000000000000
62 Ga :4f0 0.0000003964607 0.0000032084760 -0.0000029608034 -0.0000978915869 -0.0005594961316 0.0000000000000 -0.0015525233859
63 Ga :4f2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 -0.0006618611923 0.0000000000000
64 H :1s -0.0000000000057 -0.0000000000125 -0.0000000000091 0.0000000005431 0.0000000020709 0.0000000000000 -0.0000000333174
65 H :1s 0.0000000000578 0.0000000000581 0.0000000000586 0.0000000002921 0.0000000049667 0.0000000000000 -0.0000002158941
66 H :1s -0.0000000005350 -0.0000000012409 -0.0000000008999 0.0000000549719 0.0000002105747 0.0000000000000 -0.0000034199782
67 H :1s 0.0000000038874 0.0000000039916 0.0000000044858 0.0000000990338 0.0000007628009 0.0000000000000 -0.0000260966852
68 H :1s -0.0000000213762 -0.0000001088496 -0.0000000723375 0.0000054725872 0.0000217976715 0.0000000000000 -0.0003731845176
69 H :1s 0.0000001298639 0.0000003617073 0.0000000180325 0.0000136640606 0.0000517034914 0.0000000000000 -0.0025463007491
70 H :1s -0.0000017338039 -0.0000152092356 -0.0000002961325 0.0000709424341 0.0007547411105 0.0000000000000 -0.0114521337408
71 H :1s 0.0000097622277 0.0000816897915 -0.0000138548892 0.0001444831860 0.0005698307000 0.0000000000000 -0.0087373058889
72 H :1s 0.0000032049615 0.0000269091505 -0.0000448896842 0.0000549450917 -0.0060374341466 -0.0000000000002 -0.0074099412406
73 H :1s 0.0000138546171 0.0001344533393 -0.0000107075265 -0.0021309258135 -0.0023546407489 -0.0000000000003 -0.0053139181624
74 H :2pz -0.0000000118619 0.0000002947378 -0.0000002759152 0.0000589909428 0.0004911203731 0.0000000000000 -0.0023948461227
75 H :2pz 0.0000073769494 0.0000638053423 -0.0000083566555 -0.0001110416919 -0.0000012354508 0.0000000000000 0.0014349101062
76 H :2pz -0.0000014766488 -0.0000139724593 -0.0000122991897 0.0003092281577 -0.0016419236591 0.0000000000000 0.0008826043382
77 H :3d0 0.0000017959682 0.0000146140574 -0.0000009600507 0.0000981338292 0.0000207228385 0.0000000000000 -0.0009951021479
78 H :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000462033457 0.0000000000000
Orbital 8 9 10 11
1 Ga :1s -0.0000000000134 0.0000000000099 -0.0000000000023 0.0000000000020
2 Ga :1s -0.0000000001005 0.0000000000738 -0.0000000000169 0.0000000000142
3 Ga :1s -0.0000000013984 0.0000000010264 -0.0000000002346 0.0000000002050
4 Ga :1s -0.0000000120693 0.0000000088587 -0.0000000020274 0.0000000017105
5 Ga :1s -0.0000001579292 0.0000001159182 -0.0000000265015 0.0000000230812
6 Ga :1s -0.0000013461065 0.0000009880187 -0.0000002261128 0.0000001909745
7 Ga :1s -0.0000070015087 0.0000051390382 -0.0000011744968 0.0000010333663
8 Ga :1s -0.0000296651978 0.0000217736886 -0.0000049851765 0.0000041544396
9 Ga :1s -0.0001077966477 0.0000791221892 -0.0000180745098 0.0000161210623
10 Ga :1s -0.0003503358535 0.0002571409493 -0.0000589040107 0.0000483012106
11 Ga :1s -0.0010284823713 0.0007549194784 -0.0001723501007 0.0001564033826
12 Ga :1s -0.0027328090190 0.0020059232919 -0.0004598518037 0.0003682058351
13 Ga :1s -0.0063680189732 0.0046747344669 -0.0010661332706 0.0009975123523
14 Ga :1s -0.0122820035939 0.0090171286000 -0.0020712576312 0.0015558875590
15 Ga :1s -0.0155982094580 0.0114557745940 -0.0025989514008 0.0027984559774
16 Ga :1s 0.0007355714957 -0.0005404343757 0.0000706041868 -0.0014379248119
17 Ga :1s 0.0585767226034 -0.0431047642740 0.0099879282110 -0.0054283435049
18 Ga :1s 0.0976916923807 -0.0720132183072 0.0162551199140 -0.0203748574134
19 Ga :1s -0.0228657318835 0.0169158964314 -0.0034002797168 0.0159172743624
20 Ga :1s -0.1932626320495 0.1445818785392 -0.0340181777380 0.0057398539584
21 Ga :1s -0.2165084734727 0.1657051863018 -0.0376804151770 0.0676991606244
22 Ga :1s 0.2381306346457 -0.1749134585432 0.0264398206989 -0.2514744470615
23 Ga :1s 0.4066817925769 -0.4037987240974 0.1759462947883 0.5351966375558
24 Ga :1s 0.1399623670774 -0.3234208037210 -0.7898574456096 -0.0313291341065
25 Ga :1s 0.0053160292924 -0.0202428571263 -3.5011903301970 -0.3110808833107
26 Ga :2pz -0.0000069126494 -0.0000149391644 -0.0000001110062 -0.0000021351185
27 Ga :2pz -0.0000575580448 -0.0001254245113 -0.0000000353826 -0.0000199320571
28 Ga :2pz -0.0003343571622 -0.0007226003730 -0.0000054172559 -0.0001031702343
29 Ga :2pz -0.0012865230608 -0.0028052078138 0.0000000892230 -0.0004477881678
30 Ga :2pz -0.0041239066080 -0.0089073316560 -0.0000748524324 -0.0012538107711
31 Ga :2pz -0.0079653708948 -0.0174403057274 0.0000534863987 -0.0029038417230
32 Ga :2pz -0.0110800966274 -0.0237025973030 -0.0004141051410 -0.0028533393135
33 Ga :2pz 0.0052583276667 0.0107916798073 0.0007544716754 0.0000244905032
34 Ga :2pz 0.0233037540415 0.0530736182217 -0.0013041474107 0.0115335269288
35 Ga :2pz 0.0453553051795 0.0966893254141 0.0033222617362 0.0074713435866
36 Ga :2pz -0.0088670678509 -0.0177038482226 -0.0046435618476 0.0111983581351
37 Ga :2pz -0.1154728375199 -0.3195026141425 0.0294533973363 -0.1477315015932
38 Ga :2pz -0.0268706827689 -0.1984082256096 0.5006815058002 -1.0298917328364
39 Ga :2pz -0.0012450011010 0.0038307368495 1.4263812017234 1.7276185678753
40 Ga :3d0 -0.0001391382112 -0.0001346089942 -0.0000054221177 -0.0000391688779
41 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
42 Ga :3d0 -0.0011389340942 -0.0010880118494 -0.0000457701419 -0.0003479729826
43 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
44 Ga :3d0 -0.0048432175806 -0.0046852843141 -0.0001893268216 -0.0013668529321
45 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
46 Ga :3d0 -0.0132575987267 -0.0126284898746 -0.0005372068468 -0.0041062888570
47 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
48 Ga :3d0 -0.0222221000860 -0.0216296045784 -0.0008522697338 -0.0059523199456
49 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
50 Ga :3d0 -0.0253413466185 -0.0232557760406 -0.0010287446649 -0.0087347308304
51 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
52 Ga :3d0 -0.0157117568512 -0.0173420312275 -0.0006844173061 -0.0016975253652
53 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
54 Ga :3d0 0.0112721332830 0.0253061785029 0.0023815382122 -0.0007066592235
55 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
56 Ga :3d0 0.0277435204550 0.0381609267460 -0.0482130974131 0.2368132935880
57 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
58 Ga :3d0 0.0029188277518 0.0088190416347 -0.3334230991935 0.0359263913276
59 Ga :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
60 Ga :4f0 -0.0076929190453 -0.0064379838700 -0.0086348603105 -0.0123174427111
61 Ga :4f2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
62 Ga :4f0 -0.0045299772972 0.0011053331990 0.0487350911378 -0.0663379253967
63 Ga :4f2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
64 H :1s 0.0000003028380 0.0000002488048 0.0000000149419 0.0000000535603
65 H :1s 0.0000022912006 0.0000018994261 0.0000000114370 0.0000004183115
66 H :1s 0.0000311635616 0.0000256078135 0.0000015145524 0.0000055148958
67 H :1s 0.0002707534824 0.0002242131171 0.0000030520546 0.0000492294351
68 H :1s 0.0034494523489 0.0028395878412 0.0001566901692 0.0006133798402
69 H :1s 0.0276238575244 0.0230642795932 0.0002887930805 0.0050879419093
70 H :1s 0.1081494452608 0.0908631293574 0.0078602850760 0.0207388688265
71 H :1s 0.2486350714375 0.2136141972823 -0.0241670226471 0.0372750685598
72 H :1s 0.1362183797766 0.2702626645437 0.5220620024264 -0.8686138635093
73 H :1s -0.0091928922459 0.0384625752726 3.4881051996779 0.8467300496835
74 H :2pz 0.0058147204091 0.0011812298069 0.0011938503241 0.0020911780418
75 H :2pz 0.0233768038097 0.0083364179842 -0.0007131664738 -0.0232362366550
76 H :2pz -0.0034893162880 0.0211846165397 0.1242180696094 -0.2730254527116
77 H :3d0 0.0038228791895 0.0026527611182 0.0003898009118 -0.0010973702282
78 H :3d2+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
Molecular orbitals for symmetry species 2
------------------------------------------
Orbital 1 2 3 4 5
1 Ga :2px -0.0003168972189 0.0001202437545 0.0000004778171 0.0000112034919 -0.0000133215850
2 Ga :2px -0.0027647322397 0.0010485723645 0.0000039921614 0.0000956634741 -0.0001081616548
3 Ga :2px -0.0151198574046 0.0058069825514 0.0000231123742 0.0005418049064 -0.0006445570146
4 Ga :2px -0.0599558470164 0.0234202618257 0.0000892635301 0.0021409577352 -0.0024155027516
5 Ga :2px -0.1733045830111 0.0707869453790 0.0002848977485 0.0066632026835 -0.0079786088154
6 Ga :2px -0.3410658571626 0.1464564347682 0.0005539168184 0.0134030299916 -0.0148004714583
7 Ga :2px -0.3897000941868 0.1768761677705 0.0007675325513 0.0173433863966 -0.0221158410377
8 Ga :2px -0.1840075683782 -0.0363245414573 -0.0003575172650 -0.0068176960622 0.0123859539970
9 Ga :2px -0.0218866082126 -0.4228125778100 -0.0017206953271 -0.0427368166177 0.0404292495586
10 Ga :2px -0.0011623099450 -0.4951325154857 -0.0029050666103 -0.0673062126373 0.0969580335761
11 Ga :2px -0.0002756096609 -0.1804439254310 0.0022968850454 0.0023703987511 -0.0338150349108
12 Ga :2px -0.0000151064247 -0.0063743995732 0.0012339540683 0.2649326012207 -0.1960136299455
13 Ga :2px 0.0000045256624 0.0008396716656 -0.0033038280692 0.2251970561752 -1.1931598395609
14 Ga :2px -0.0000018913257 -0.0003840870034 0.0005682301710 0.6852283638262 1.2278268836432
15 Ga :3d1+ 0.0000010816789 0.0000029383096 -0.0020272758070 0.0000054789406 -0.0000071467388
16 Ga :3d1+ 0.0000092514946 0.0000247127223 -0.0165073206438 0.0000407177519 -0.0000752547163
17 Ga :3d1+ 0.0000315936626 0.0001039425395 -0.0703928258477 0.0001907655993 -0.0002508842434
18 Ga :3d1+ 0.0000367559974 0.0002983467113 -0.1911247011621 0.0004657330784 -0.0009122652079
19 Ga :3d1+ 0.0000012910751 0.0005495567771 -0.3255011090097 0.0009241030733 -0.0009541881322
20 Ga :3d1+ 0.0000024628408 0.0010701615471 -0.3676549275650 0.0007111022756 -0.0024223359422
21 Ga :3d1+ 0.0000034669730 0.0010558422284 -0.2743395475822 0.0012955595273 0.0013175268791
22 Ga :3d1+ 0.0000028581360 -0.0002169869308 -0.0948493527666 -0.0026813178444 -0.0056118465146
23 Ga :3d1+ 0.0000019472140 0.0002355510758 -0.0019205201816 0.0064457053605 0.0506558344785
24 Ga :3d1+ 0.0000004726638 0.0001373431699 0.0001565513394 0.0029059685062 0.0490108985184
25 Ga :4f1+ 0.0000005570173 0.0003788123460 0.0029822961434 -0.0011373757531 0.0080198942051
26 Ga :4f3+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
27 Ga :4f1+ -0.0000013706024 -0.0003846638169 -0.0016593247948 -0.0216300418586 -0.0338553846209
28 Ga :4f3+ 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
29 H :2px -0.0000001131106 -0.0000615181209 0.0008446401890 0.0021218240721 -0.0024118235457
30 H :2px 0.0000003471201 -0.0002015601982 -0.0003070758650 0.0095598790667 -0.0091877704707
31 H :2px 0.0000021844388 0.0006310476141 0.0038255081265 0.0211686133309 0.1079560015178
32 H :3d1+ 0.0000001519426 -0.0001437513152 0.0001483031154 0.0003170908673 -0.0014310119302
Molecular orbitals for symmetry species 3
------------------------------------------
Orbital 1 2 3 4 5
1 Ga :2py -0.0003168972189 0.0001202437545 0.0000004778171 0.0000112034919 -0.0000133215850
2 Ga :2py -0.0027647322397 0.0010485723645 0.0000039921614 0.0000956634741 -0.0001081616548
3 Ga :2py -0.0151198574046 0.0058069825514 0.0000231123742 0.0005418049064 -0.0006445570146
4 Ga :2py -0.0599558470164 0.0234202618257 0.0000892635301 0.0021409577352 -0.0024155027516
5 Ga :2py -0.1733045830111 0.0707869453790 0.0002848977485 0.0066632026835 -0.0079786088154
6 Ga :2py -0.3410658571626 0.1464564347682 0.0005539168184 0.0134030299916 -0.0148004714583
7 Ga :2py -0.3897000941867 0.1768761677704 0.0007675325513 0.0173433863966 -0.0221158410377
8 Ga :2py -0.1840075683782 -0.0363245414572 -0.0003575172650 -0.0068176960622 0.0123859539970
9 Ga :2py -0.0218866082126 -0.4228125778101 -0.0017206953271 -0.0427368166177 0.0404292495586
10 Ga :2py -0.0011623099450 -0.4951325154857 -0.0029050666103 -0.0673062126373 0.0969580335761
11 Ga :2py -0.0002756096609 -0.1804439254310 0.0022968850454 0.0023703987511 -0.0338150349109
12 Ga :2py -0.0000151064247 -0.0063743995732 0.0012339540683 0.2649326012207 -0.1960136299454
13 Ga :2py 0.0000045256624 0.0008396716656 -0.0033038280692 0.2251970561749 -1.1931598395612
14 Ga :2py -0.0000018913257 -0.0003840870034 0.0005682301710 0.6852283638263 1.2278268836432
15 Ga :3d1- 0.0000010816789 0.0000029383096 -0.0020272758070 0.0000054789406 -0.0000071467388
16 Ga :3d1- 0.0000092514946 0.0000247127223 -0.0165073206438 0.0000407177519 -0.0000752547163
17 Ga :3d1- 0.0000315936626 0.0001039425395 -0.0703928258477 0.0001907655993 -0.0002508842434
18 Ga :3d1- 0.0000367559974 0.0002983467113 -0.1911247011621 0.0004657330784 -0.0009122652079
19 Ga :3d1- 0.0000012910751 0.0005495567771 -0.3255011090097 0.0009241030733 -0.0009541881322
20 Ga :3d1- 0.0000024628408 0.0010701615471 -0.3676549275650 0.0007111022756 -0.0024223359422
21 Ga :3d1- 0.0000034669730 0.0010558422284 -0.2743395475822 0.0012955595273 0.0013175268791
22 Ga :3d1- 0.0000028581360 -0.0002169869308 -0.0948493527666 -0.0026813178444 -0.0056118465146
23 Ga :3d1- 0.0000019472140 0.0002355510758 -0.0019205201816 0.0064457053606 0.0506558344786
24 Ga :3d1- 0.0000004726638 0.0001373431699 0.0001565513394 0.0029059685063 0.0490108985185
25 Ga :4f3- 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
26 Ga :4f1- 0.0000005570173 0.0003788123460 0.0029822961434 -0.0011373757531 0.0080198942051
27 Ga :4f3- 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000 0.0000000000000
28 Ga :4f1- -0.0000013706024 -0.0003846638169 -0.0016593247948 -0.0216300418587 -0.0338553846210
29 H :2py -0.0000001131106 -0.0000615181209 0.0008446401890 0.0021218240721 -0.0024118235457
30 H :2py 0.0000003471201 -0.0002015601982 -0.0003070758651 0.0095598790667 -0.0091877704708
31 H :2py 0.0000021844388 0.0006310476141 0.0038255081265 0.0211686133311 0.1079560015180
32 H :3d1- 0.0000001519426 -0.0001437513152 0.0001483031154 0.0003170908673 -0.0014310119302
Molecular orbitals for symmetry species 4
------------------------------------------
Orbital 1 2 3
1 Ga :3d2- 0.0020251983513 0.0000763348443 -0.0002676777404
2 Ga :3d2- 0.0164862209177 0.0004626561533 -0.0027099804665
3 Ga :3d2- 0.0703202581960 0.0026436892461 -0.0093805081663
4 Ga :3d2- 0.1908573980729 0.0050418656700 -0.0326781032997
5 Ga :3d2- 0.3252343360082 0.0139964688955 -0.0367056945523
6 Ga :3d2- 0.3671462213480 0.0027843695641 -0.0823986426221
7 Ga :3d2- 0.2762702459588 0.0297177161710 0.0425542038594
8 Ga :3d2- 0.0940852178196 -0.0709223003815 -0.1747705710953
9 Ga :3d2- 0.0017761993521 0.1720133066681 1.3394244751884
10 Ga :3d2- 0.0008736642126 -1.0862344671322 -0.6805944112640
11 Ga :4f2- -0.0016099660312 -0.0005495480951 0.0146780715331
12 Ga :4f2- 0.0006618611923 0.0068694625664 -0.2018540183644
13 H :3d2- -0.0000462033457 -0.0005825501904 -0.0011712721483
>>>> Total CPU time used in SIRIUS : 1.02 seconds
>>>> Total wall time used in SIRIUS : 1.02 seconds
Date and time (Linux) : Fri Mar 30 09:32:28 2012
Host name : sunray
.---------------------------------------.
| End of Wave Function Section (SIRIUS) |
`---------------------------------------'
>>>> Total CPU time used in DALTON: 2.68 seconds
>>>> Total wall time used in DALTON: 2.69 seconds
Date and time (Linux) : Fri Mar 30 09:32:28 2012
Host name : sunray
Raw
GaH.mol
INTGRL
GaH : Coupling Constants : R = 3.1061 au
second title line
s 2 2 X Y 0.10D-15 0.10D-15
31.0 1 4 2 1 1 1
Ga 0.00000 0.00000 3.1061
H 4 0
13044227613.8
1953256299.2
292482643.2
43796657.2
H 21 0
6558157.30000000 0.00000800 -0.00000250 0.00000090
982025.34000000 0.00006220 -0.00001930 0.00000740
223467.69000000 0.00032700 -0.00010140 0.00003870
63288.29100000 0.00137940 -0.00042810 0.00016330
20642.94000000 0.00499930 -0.00155820 0.00059440
7450.52240000 0.01606050 -0.00504690 0.00192920
2905.07440000 0.04601240 -0.01480560 0.00566890
1204.21000000 0.11522240 -0.03894820 0.01502820
524.30454000 0.23739210 -0.08968320 0.03502220
237.46563000 0.35319890 -0.16640760 0.06711350
110.57866000 0.29155000 -0.20040100 0.08501560
51.37462400 0.08121290 0.01149430 -0.00472120
24.44084600 0.00076550 0.49581340 -0.30167370
11.76859100 0.00161240 0.52955500 -0.48254890
5.34211900 -0.00075300 0.11101850 0.08916950
2.49503600 0.00031340 -0.00070000 0.72878300
1.09877300 -0.00013060 0.00222830 0.42885420
0.26018000 0.00005130 -0.00050140 0.02072490
0.12707900 0.00000000 0.00000000 0.00000000
0.05440800 0.00000000 0.00000000 0.00000000
0.01439800 0.00000000 0.00000000 0.00000000
H 14 0
8050.16740000 0.00031690 -0.00012030 0.00002000
1907.53610000 0.00276480 -0.00104920 0.00016890
618.62746000 0.01512040 -0.00581020 0.00096680
235.32417000 0.05995830 -0.02343450 0.00377970
98.89964600 0.17331200 -0.07082700 0.01190820
44.24821500 0.34108200 -0.14655110 0.02356930
20.61742900 0.38969670 -0.17696600 0.03142330
9.78051600 0.18398170 0.03638210 -0.01361880
4.44123800 0.02188960 0.42328480 -0.07340030
1.96404500 0.00116080 0.49525860 -0.12647850
0.83357800 0.00027350 0.17974280 0.01585790
0.19344500 0.00000000 0.00000000 0.00000000
0.05611700 0.00000000 0.00000000 0.00000000
0.01930000 0.00000000 0.00000000 0.00000000
H 10 0
244.14741000 0.00202700 0.00000000 0.00000000
73.06759500 0.01650880 0.00000000 0.00000000
27.59208100 0.07038230 0.00000000 0.00000000
11.54651800 0.19114300 0.00000000 0.00000000
5.04862800 0.32540920 0.00000000 0.00000000
2.17846500 0.36781990 0.00000000 0.00000000
0.90025300 0.27446850 0.00000000 0.00000000
0.33732700 0.00000000 1.00000000 0.00000000
0.11690000 0.00000000 0.00000000 1.00000000
0.03870000 0.00000000 0.00000000 0.00000000
H 2 0
0.28810000 1.00000000 0.00000000
0.09800000 0.00000000 1.00000000
1.0 1 3 2 1 1
H 0.00000 0.00000 0.000
F 4 0
66145.0
9950.0
1496.0
225.0
F 6 0
33.87000000 0.00606800 0.00000000 0.00000000 0.00000000
5.09500000 0.04530800 0.00000000 0.00000000 0.00000000
1.15900000 0.20282200 0.00000000 0.00000000 0.00000000
0.32580000 0.50390300 1.00000000 0.00000000 0.00000000
0.10270000 0.38342100 0.00000000 1.00000000 0.00000000
0.02526000 0.00000000 0.00000000 0.00000000 1.00000000
F 3 0
1.407000 1.0000 0.0000
0.388000 0.0000 1.0000
0.102000
F 1 0
1.057000
FINISH
Raw
generators.py
from numpy import *
from numpy.random import random
def gen_mos_mask(n_dim,n,m):
# this assumes we are in the upper left corner of the matrix
i = array([True]*n + [False]*(n_dim-n))
j = array([True]*m + [False]*(n_dim-m))
return outer(i,j)
def gen_iden_mask(n,m,ns,ndim):
# generate smaller lower right corner of the matrix
i = array([False]*n + [True]*ns)
j = array([False]*m + [True]*ns + [False]*(ndim-m-ns))
return outer(i,j)
def generate_mos(n_dim,mos):
C = zeros((n_dim,n_dim))
(n,m) = shape(mos) # rows, cols
i = n_dim - n # get minor dimension
mos_mask = gen_mos_mask(n_dim,n,m) # generate mask for molecular orbitals
iden_mask = gen_iden_mask(n,m,i,n_dim) # generate mask for identity matrix
C[mos_mask] = mos.ravel()
C[iden_mask] = identity(i).ravel()
# make the transpose
Ct = C.transpose()
# delete what we do not need
Dt = Ct[:i+m]
# transpose back
C = Dt.transpose()
# get dimensions
return C
if __name__ == '__main__':
mos = random((3,2))
print generate_mos(6,mos)
Raw
read_log.py
import numpy
def parse_mos(data,ext_count,norb_count):
symbols = ['Ga','Ge','As','Se','Br']
if len(data) == 0:
if ext_count < 0: return (None,2) # only return updated counter for space between multiple lines of MOs
else: return (None,ext_count) # just return the nothing
if data[0] == 'Molecular': ext_count = 4 # counter for space between finding line and first MO
ext_count -= 1
if len(data) > 1 and norb_count + ext_count >= 1:
# from here, parse each line as an MO, first index is 0.
# only parse if it contains XX MO in a H_n XX complex
if data[1] in symbols:
data = map(float, data[3:])
return (data,ext_count)
return (None,ext_count)
parse_keys = {'Molecular orbitals for symmetry species': parse_mos
}
reset_keys = {'------------------------------------------':True}
ncount = {'1':25,'2':14,'3':0,'4':10}
orbitals = {'1':[],'2':[],'3':[],'4':[]}
def read_log_file(filename):
f = open(filename, 'r')
pFunc = None
ext_count = 0
norb_count = 0
O_CNT = 0
for line in f:
data = line.split()
#if pFunc is not None and len(data) ==0 and ext_count == 0: pFunc = None
for key in parse_keys:
if key in line:
norb_count = ncount[data[5]]
orb_list = orbitals[data[5]]
pFunc = parse_keys[key]
O_CNT = -1
if len(data) > 0:
if data[0] == 'Orbital': O_CNT += 1
if pFunc is not None:
# parse the data according to pFunc
(r,ext_count) = pFunc(data,ext_count,norb_count)
if r is not None: # we have valid data
#print "%4i, %4i, %s" % (ext_count,O_CNT,r)
if O_CNT == 0: orb_list.append(r) # add it to the list of MOs
else:
orb_list[-1*ext_count].extend(r) # or extend current MOs
f.close()
# convert to numpy arrays
for key in orbitals:
orbitals[key] = numpy.array(orbitals[key])
return orbitals
if __name__ == '__main__':
import sys
orbitals = read_log_file(sys.argv[1])
print orbitals
Raw
read_mol.py
from numpy import identity, s_, delete
from atom import Atom
# format is something like
#0 INTGRL
#1 title
#2 title
#3 keywords, some strange format a la [s, n_atoms, symmetry stuff]
#4 1st atom [Z, number of atoms, Lmax, n_L0, n_L1, ... n_Lmax]
#5 atom coordinate
#6 atom basis set
def read_mol_file(filename):
Natoms = 0
Ns = 0
Np = 0
Nd = 0
Nf = 0
Nlmax = 0
atom = None
ln_cnt_basis = 0
basis_lines = 0
reading_atom_properties = False
reading_basis = False
parsing_atom = False
f = open(filename, 'r')
for i,line in enumerate(f):
data = line.split()
if i == 3: Natoms = int(data[1])
if i > 3 and not parsing_atom and not reading_atom_properties and not reading_basis:
# this is the first read of an atom, parse stuff such as
# angular momentum shells
parsing_atom = True
reading_atom_properties = True
if reading_atom_properties:
ln_cnt_basis = 3
Z = float(data[0])
if atom is None:
atom = Atom(Z)
Nlmax = int(data[2])
Ns = int(data[3])
if Nlmax > 1: Np = int(data[4])
if Nlmax > 2: Nd = int(data[5])
if Nlmax > 3: Nf = int(data[6])
atom.set_shells(Ns,Np,Nd,Nf)
reading_atom_properties = False
if parsing_atom and i>3 and ln_cnt_basis == 2:
# parse label and coordinates
atom.set_label(data[0])
data = data[1:]
data = map(float, data)
atom.set_coords(data[0],data[1],data[2])
if not reading_atom_properties and ln_cnt_basis > 0: ln_cnt_basis -= 1
if ln_cnt_basis == 0 and parsing_atom and not reading_atom_properties: reading_basis = True
if reading_basis and basis_lines == 0:
# read the line specifying number of primitives
basis_lines = int(data[1])
if Ns >= 0: Ns -= 1
if Ns == -1 and Np >=0: Np -= 1
if Ns == -1 and Np == -1 and Nd >= 0: Nd -= 1
if Ns == -1 and Np == -1 and Nd == -1 and Nf >= 0: Nf -= 1
continue
if reading_basis and basis_lines > 0:
try:
a = float(data[0])
except ValueError:
break # finish when we've read the entire first atom
basis_lines -= 1
if Ns >=0:
atom.S.append(float(data[0]))
continue
if Np >=0:
atom.P.append(float(data[0]))
continue
if Nd >=0:
atom.D.append(float(data[0]))
continue
if Nf >=0:
atom.F.append(float(data[0]))
continue
f.close()
return atom
if __name__ == '__main__':
import sys
atom = read_mol_file(sys.argv[1])
# does not work here. oh well
#print atom
@cstein
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Author

cstein commented Apr 21, 2012

I think all the relevant files are here now.

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