#355 Bq ghost atom gaussian 98

[Anonymous]

I am :
Enguerran Vanquelef
enguerran.vanquelef@q4md-forcefieldtools.org

I work with:
Opensuse 10.2 64 bits
Openbabel 2.1.1

The bug I have noted:
I have noted a problem with some gaussian log files.
When a gaussian log file contain a ghost atom (named Bq in the log file) no translation is possible. Openbabel give the following message : segmentation fault.

other files work fine

regards

Enguerran Vanquelef

[Nobody/Anonymous]

gaussian 98 output file

[Nobody/Anonymous]

Logged In: NO

Hello, I'm working on a tcl script which will translate le Log file to xyz file. Another path is an option in Gaussian : Punch=(coord) will copy in a text files optimized coordinates in atomic units, which is easier to translate in .xyz file than a log file.
I will inform you...

thanks

Enguerran Vanquelef

[Nobody/Anonymous]

Logged In: NO

Hello,

I have wrote a smal Tcl script. When Gaussian uses Bq atoms, it generates a coordinate table with center number starting "2" instead of "1". Maybe this is the origin of the bug.

regards

PS : The Tcl script if you are interessting :

!/usr/bin/tclsh

set path [pwd]
puts $path

set liste_log [lsort -dictionary [glob $path/*.log]]
set nb_log [llength $liste_log]
puts "il y a $nb_log fichiers .log"

find the last standard orientation :

for {set n 0} {$n<$nb_log} {incr n} {
set nom_fich_log [lindex $liste_log $n]
puts "\nnom du fichier en cours :[file tail $nom_fich_log]"
set log_courant [open $nom_fich_log r]
set hfichxyz [file rootname [file tail $nom_fich_log]].xyz
set fichxyz [open $hfichxyz w]
set ligne [gets $log_courant]
while {$ligne!=" -- Stationary point found."} {
set ligne [gets $log_courant]
}
# I'm just after "Stationnary point found"
set mot1 [lindex $ligne 0]
set mot2 [lindex $ligne 1]
set phrase $mot1$mot2
while {$phrase!="Standardorientation:"} {
set ligne [gets $log_courant]
set mot1 [lindex $ligne 0]
set mot2 [lindex $ligne 1]
set phrase $mot1$mot2
}
#I'm just after the line "Standard orientation"
#puts $ligne
set ligne [gets $log_courant]
#puts $ligne
set ligne [gets $log_courant]
#puts $ligne
set ligne [gets $log_courant]
#puts $ligne
set ligne [gets $log_courant]
#puts $ligne
set ligne [gets $log_courant]
#puts "coorodos:"
#Next line is the start of coordinates block
set i 1
while {[lindex $ligne 0]!="---------------------------------------------------------------------"} {
switch [lindex $ligne 1] {
6 {set tab(nom,$i) "C"}
1 {set tab(nom,$i) "H"}
8 {set tab(nom,$i) "O"}
7 {set tab(nom,$i) "N"}
16 {set tab(nom,$i) "S"}
default {set tab($i,nom) "*"}
}
set tab(X,$i) [lindex $ligne 3]
set tab(Y,$i) [lindex $ligne 4]
set tab(Z,$i) [lindex $ligne 5]
#puts "[lindex $ligne 1]\t [lindex $ligne 3]\t [lindex $ligne 4]\t [lindex $ligne 5]"
set ligne [gets $log_courant]
incr i
}
puts $fichxyz "[expr $i-1]"
puts $fichxyz "[file tail $nom_fich_log]"
for {set m 1} {$m<$i} {incr m} {
puts $fichxyz "$tab(nom,$m)\t[format %+8.6f $tab(X,$m)]\t[format %+8.6f $tab(Y,$m)]\t[format %+8.6f $tab(Z,$m)]"
}
}
close $fichxyz
close $log_courant

I must unset all variables

[Nobody/Anonymous]

Logged In: NO

Hello,

a problem occurs with my tcl script with another Gaussian 98 output file which contain a Bq atom.
I have found a small solution but not very "regular" :
I had to replace "Input orientation" by "Standrad orientation" few lines under "Stationary point found" and I have modified the Tcl script (find it below, I have added Bq case in the switch block).

regards

Enguerran Vanquelef

!/usr/bin/tclsh

set path [pwd]
puts $path
set liste_log [lsort -dictionary [glob $path/*.log]]
set nb_log [llength $liste_log]
puts "il y a $nb_log fichiers .log"

find the last standard orientation :

for {set n 0} {$n<$nb_log} {incr n} {
set nom_fich_log [lindex $liste_log $n]
puts "nom du fichier en cours : [file tail $nom_fich_log]"
set log_courant [open $nom_fich_log r]
set hfichxyz [file rootname [file tail $nom_fich_log]]_opt.xyz
set fichxyz [open $hfichxyz w]
set ligne [gets $log_courant]
while {$ligne!=" -- Stationary point found."} {
set ligne [gets $log_courant]
}
# I'm just after "Stationnary point found"
set mot1 [lindex $ligne 0]
set mot2 [lindex $ligne 1]
set phrase $mot1$mot2
while {$phrase!="Standardorientation:"} {
set ligne [gets $log_courant]
set mot1 [lindex $ligne 0]
set mot2 [lindex $ligne 1]
set phrase $mot1$mot2
}
#I'm just after the line "Standard orientation"
set ligne [gets $log_courant]
set ligne [gets $log_courant]
set ligne [gets $log_courant]
set ligne [gets $log_courant]
set ligne [gets $log_courant]
#Next line is the start of coordinates block
set i 1
while {[lindex $ligne 0]!="---------------------------------------------------------------------"} {
switch [lindex $ligne 1] {
6 {set tab(nom,$i) "C"}
1 {set tab(nom,$i) "H"}
8 {set tab(nom,$i) "O"}
7 {set tab(nom,$i) "N"}
16 {set tab(nom,$i) "S"}
0 {set tab(nom,$i) "Bq"}
default {set tab($i,nom) "*"}
}
set tab(X,$i) [lindex $ligne 3]
set tab(Y,$i) [lindex $ligne 4]
set tab(Z,$i) [lindex $ligne 5]
set ligne [gets $log_courant]
incr i
}
puts $fichxyz "[expr $i-1]"
puts $fichxyz "[file tail $nom_fich_log]"
for {set m 1} {$m<$i} {incr m} {
puts $fichxyz "$tab(nom,$m)\t[format %+8.6f $tab(X,$m)]\t[format %+8.6f $tab(Y,$m)]\t[format %+8.6f $tab(Z,$m)]"
}
}
close $fichxyz
close $log_courant

I must unset all variables

[Geoff Hutchison]

Logged In: YES
user_id=21420
Originator: NO

This works just fine with the 2.2 development code in SVN. I would be happy to send you a source snapshot if you wish.