Single Point Enrgy scan job not running

2 posts / 0 new
Last post
helloworld
Single Point Enrgy scan job not running

Hello everyone,

I am running this script which gives me this error:

**** error code 139 from /global/orca_4_0_1_2_linux_x86-64_openmpi202/orca orca1.inp > orca1.out ******
(My executable is located at this location = /global/orca_4_0_1_2_linux_x86-64_openmpi202/orca)

My script is :

#################################
# specify the name of the system
#################################
set control_input_settings [open SUMMARY.txt a]
puts $control_input_settings "Summary of scan."

global sys_name_id
set dir .
set sys_name_id rna
source ${dir}/hybrid2.tcl
source ${dir}/orca.tcl
#load the connectivity
load_connect_from_psf ${dir}/${sys_name_id}.c ${dir}/rna_solvated.psf
#define force field
set top { top_all36_na.rtf toppar_water_ions.rtf }
set prm ./par_mod.inp
source ${dir}/save_${sys_name_id}.chm

source qmatoms
source act
source pdbresidues

set A 147
set B 295

#scan parameters
set stepnum 10

set initdist [interatomic_distance coords= scan_0.c i=147 j=295 unit=angstrom ]

set incr -0.1

for {set i 0} { $i < $stepnum} {incr i} {
#1.89036 changes angstrom to bohr
set stepper [expr ($initdist + $incr*$i)*1.89036 ]

set atomA [ get_atom_entry atom_number=$A coords= scan_$i.c]
set atomB [ get_atom_entry atom_number=$B coords= scan_$i.c]
set symbol [ lindex $atomB 0]

set xa [ lindex $atomA 1]
set xb [ lindex $atomB 1]
set ya [ lindex $atomA 2]
set yb [ lindex $atomB 2]
set za [ lindex $atomA 3]
set zb [ lindex $atomB 3]

set xx [ expr $xb - $xa ]
set yy [ expr $yb - $ya ]
set zz [ expr $zb - $za ]

set length [ expr sqrt($xx*$xx + $yy*$yy + $zz*$zz) ]

set xxx [ expr $xx / $length ]
set yyy [ expr $yy / $length ]
set zzz [ expr $zz / $length ]

#displace atom along bond vector
set newx [ expr $xa + $xxx * $stepper ]
set newy [ expr $ya + $yyy * $stepper ]
set newz [ expr $za + $zzz * $stepper ]
set newat [subst {$symbol $newx $newy $newz}]

#-------------------------------------------------------------
# single point energy calculation with distance A-B fixed
set orca_args [ list \
hamiltonian=hf \
executable=/global/orca_4_0_1_2_linux_x86-64_openmpi202/orca ] \

energy coords= scan_${i}.c \
energy=e \
restraints= {{bond 147 295 3.43 30.0}} \
theory=orca : "$orca_args"

exec cp scan_$i.c scan_[expr ($i+1)].c
replace_atom_entry coords=scan_[expr ($i+1)].c atom_number=$B atom_entry= $newat

# write summary to file
puts $control_input_settings "======================================"
puts $control_input_settings "structure [expr ($i+1)]"

set energy [ get_matrix_element matrix=e indices= { 0 0 } ]
puts $control_input_settings [format "Energy:%14.6f" $energy]

set R1 [interatomic_distance coords= scan_$i.c i=$A j=$B unit=angstrom ]
puts $control_input_settings [format "Distance R1(A-B):%4.3f" $R1]

flush $control_input_settings

#---------------------------------------------------------------------------

}
# cleanup
catch {delete_object hybrid.orca.coords}
catch {file delete dummy.coords}
flush $control_input_settings
close $control_input_settings

exit
************************************************************************************************************

Can anyone help me with this ?
Thanking you in advance

tomkeal
tomkeal's picture
Hi,

Hi,

The error seems to suggest there has been a problem with running ORCA itself. The first thing to do is to check that the generated input orca1.inp looks OK, then check orca1.out for a more detailed error description. If it is not obvious from orca1.out what has gone wrong, try running ORCA as a standalone program on orca1.inp to see if any other error text is produced.

Tom

Log in or register to post comments