I'm using jmol to read some jaguar files. everything is good when I read
output file of optimization or single point to different level of theory. But when
I try to read vibrational output file jmol doesn't work and nothing appears on my
monitor. I'm using Jaguar version 4.2, release 77 and Jmol 6-1 version but I recorded
the same problem with other jmol distribution. I also attach one of my output file as example.
What can I do?
Kind regards,
Gianluca Croce
Job h2o_b3lyp_IR started on mila1 at Tue Jan 14 15:23:05 2003
+--------------------------------------------------------------------+
| Jaguar version 4.2, release 77 |
| |
| Copyright 1991-2000 Schrodinger, Inc. |
| All Rights Reserved. |
| |
| Use of this program should be acknowledged in publications as: |
| Jaguar 4.2, Schrodinger, Inc., Portland, Oregon, 2000. |
+--------------------------------------------------------------------+
start of program pre
Job name: h2o_b3lyp_IR
Executables used: /boot/schrodinger/jaguar-v42077/bin/Linux-x86
Temporary files : /tmp/davide/h2o_b3lyp_IR
Input file comments:
This JAGUAR input file generated by Babel 1.3
entry_name: h2o_b3lyp_631
basis set: 6-31g**
net molecular charge: 0
multiplicity: 1
number of basis functions.... 25
Input geometry:
angstroms
atom x y z
O1 0.0000000000 0.0000000000 -0.0639840000
H2 0.0000000000 0.7907550000 0.5077340000
H3 0.0000000000 -0.7907550000 0.5077340000
Molecular weight: 18.01 amu
Stoichiometry: H2O
Molecular Point Group: C2v
Point Group used: C1 (symmetry turned off)
nuclear repulsion energy....... 9.011557309 hartrees
Non-default options chosen:
SCF calculation type: DFT
DFT=Becke_3_Parameter/HF+Slater+Becke88+VWN+LYP (B3LYP)
Vibrational frequencies and related properties will be computed
from analytic second derivatives
J and K strips stored in core if nfb*nham < 1500
end of program pre
start of program onee
smallest eigenvalue of S: 2.084E-02
number of canonical orbitals..... 25
end of program onee
start of program hfig
initial wavefunction generated automatically from atomic wavefunctions
Irreducible Total no No of occupied orbitals
representation orbitals Shell_1 Shell_2 ...
No Symm 25 5
------------------------
Orbital occupation/shell 1.000
end of program hfig
start of program probe
end of program probe
start of program grid
number of gridpoints:
atom O1 H2 H3 total
grid # 1 105 74 74 253
grid # 2 117 107 107 331
grid # 3 232 208 208 648
grid # 4 428 225 225 878
grid # 5 4304 4304 4304 12912
grid # 6 1192 1192 1192 3576
grid # 7 5226 5226 5226 15678
end of program grid
start of program rwr
end of program rwr
start of program scf
number of electrons.......... 10
number of alpha electrons.... 5
number of beta electrons..... 5
number of orbitals, total.... 25
number of core orbitals...... 5
number of open shell orbs.... 0
number of occupied orbitals.. 5
number of virtual orbitals... 20
number of hamiltonians....... 1
number of shells............. 1
SCF type: DFT=Becke_3_Parameter/HF+Slater+Becke88+VWN+LYP (B3LYP)
i u d i g
t p i c r RMS maximum
e d i u i energy density DIIS
r t s t d total energy change change error
etot 1 N N 5 M -76.17924735665 8.1E-03 2.5E-01
etot 2 Y Y 6 M -76.36629248983 1.9E-01 9.3E-03 1.1E-01
etot 3 N Y 2 U -76.41279370412 4.7E-02 2.4E-03 3.2E-02
etot 4 Y Y 6 M -76.41854768066 5.8E-03 4.6E-04 7.6E-03
etot 5 N Y 2 U -76.41891913719 3.7E-04 3.3E-05 2.7E-04
etot 6 Y Y 6 M -76.41891879519 -3.4E-07 6.0E-06 2.4E-05
etot 7 Y Y 6 M -76.41891749477 -1.3E-06 1.5E-06 6.6E-06
etot 8 N N 2 U -76.41891977089 2.3E-06 0.0E+00 0.0E+00
Energy components, in hartrees:
(A) Nuclear repulsion............ 9.01155730939
(E) Total one-electron terms..... -122.84760126568
(I) Total two-electron terms..... 37.41712418540
(J) Coulomb.................... 46.75886509059
(K) Exchange+Correlation....... -9.34174090520
(L) Electronic energy............ -85.43047708028 (E+I)
(N) Total energy................. -76.41891977089 (A+L)
SCFE: SCF energy: DFT -76.41891977089 hartrees iterations: 8
HOMO energy: -0.28957
LUMO energy: 0.06255
Orbital energies:
-19.13716 -0.98898 -0.51840 -0.36107 -0.28957 0.06255
0.14864 0.76692 0.78767 0.88838 0.89257 1.01766
1.15823 1.51965 1.57018
end of program scf
start of program cutabab2
end of program cutabab2
start of program der2a
end of program der2a
start of program der2b
end of program der2b
start of program der2nda
end of program der2nda
start of program der2ndb
end of program der2ndb
start of program rwr
end of program rwr
start of program cphfa
1 vectors produced in CPHF
v i j k i g
e t c c c r
c e o o u i
t r r r t d RMS
1 1 1 1 4 M 1.1E-01
1 2 1 1 4 M 4.1E-03
1 3 1 1 4 M 5.9E-04
1 4 1 1 4 M 4.1E-05
end of program cphfa
start of program freq
harmonic frequencies in cm**-1 reduced masses and
normal modes in cartesian coordinates:
frequencies 1645.13 3635.81 3786.80
reduc. mass 0.52 0.49 0.52
O1 X 0.00000 0.00000 0.00000
O1 Y 0.00000 0.00000 0.06913
O1 Z -0.06922 0.04696 0.00000
H2 X 0.00000 0.00000 0.00000
H2 Y -0.39546 -0.58287 -0.54854
H2 Z 0.54928 -0.37267 -0.39660
H3 X 0.00000 0.00000 0.00000
H3 Y 0.39546 0.58286 -0.54855
H3 Z 0.54928 -0.37267 0.39660
Thermochemical Properties:
pressure: 1.0000 atm
rotational symmetry number: 2
zero point energy: 12.963 kcal/mol
temp(K) Cp (cal/mol K) S (cal/mol K) H (kcal/mol) G (kcal/mol)
0.00 7.9489 -0.1550 0.0000 0.0000
298.15 7.9936 45.1408 2.3716 -11.0871
end of program freq
Total cpu seconds user: 9.410 user+sys: 11.270
Job h2o_b3lyp_IR completed on mila1 at Tue Jan 14 15:23:20 2003
