Ok this is the output:
+ [[ --debug = \-\-\h\e\l\p ]]
+ source /usr/local/share/votca/scripts/inverse/start_framework.sh
++ '[' --debug = --help ']'
++ [[ -n /usr/local/share/votca ]]
++ [[ -d /usr/local/share/votca ]]
++ [[ -d /usr/local/share/votca/scripts/inverse ]]
++ [[ -f /usr/local/share/votca/scripts/inverse/inverse.sh ]]
++ [[ -f /usr/local/share/votca/scripts/inverse/functions_common.sh ]]
++ source /usr/local/share/votca/scripts/inverse/functions_common.sh
+++ [[ --debug = \-\-\h\e\l\p ]]
+++ export BASH
+++ shopt -s extglob
+++ export -f msg
+++ export -f show_callstack
+++ unset -f die
+++ export -f die
+++ export -f cat_external
+++ export -f do_external
+++ export -f critical
+++ export -f for_all
+++ export -f csg_get_interaction_property
+++ export -f csg_get_property
+++ export -f trim_all
+++ export -f mark_done
+++ export -f is_done
+++ export -f is_int
+++ export -f to_int
+++ export -f is_part
+++ export -f has_duplicate
+++ export -f remove_duplicate
+++ export -f is_num
+++ export -f get_stepname
+++ export -f update_stepnames
+++ export -f get_current_step_dir
+++ export -f get_last_step_dir
+++ export -f get_main_dir
+++ export -f get_current_step_nr
+++ export -f get_step_nr
+++ export -f cp_from_main_dir
+++ export -f cp_from_last_step
+++ export -f get_time
+++ export -f get_number_tasks
+++ export -f get_table_comment
+++ export -f csg_inverse_clean
+++ export -f check_path_variable
+++ export -f add_to_csgshare
+++ export -f globalize_dir
+++ export -f globalize_file
+++ export -f source_function
+++ export -f csg_banner
+++ export -f csg_calc
+++ export -f show_csg_tables
+++ export -f get_command_from_csg_tables
+++ export -f source_wrapper
+++ export -f find_in_csgshare
++++ type -p mktemp
+++ '[' -z /bin/mktemp ']'
+++ export -f enable_logging
+++ export -f get_restart_file
+++ export -f check_for_obsolete_xml_options
+++ export -f command_not_found_handle
+++ for i in simulation_finish checkpoint_exist get_simulation_setting
+++ eval 'simulation_finish()' '{' command_not_found_handle
'simulation_finish;' '}'
+++ eval export -f simulation_finish
++++ export -f simulation_finish
+++ for i in simulation_finish checkpoint_exist get_simulation_setting
+++ eval 'checkpoint_exist()' '{' command_not_found_handle
'checkpoint_exist;' '}'
+++ eval export -f checkpoint_exist
++++ export -f checkpoint_exist
+++ for i in simulation_finish checkpoint_exist get_simulation_setting
+++ eval 'get_simulation_setting()' '{' command_not_found_handle
'get_simulation_setting;' '}'
+++ eval export -f get_simulation_setting
++++ export -f get_simulation_setting
+++ unset i
++ export CSG_MASTER_PID=7293
++ CSG_MASTER_PID=7293
++ export CSG_MAINDIR=/home/martin/votca/csg-tutorials/spce/ibi_lammps
++ CSG_MAINDIR=/home/martin/votca/csg-tutorials/spce/ibi_lammps
++ [[ -n '' ]]
++ export VOTCA_CSG_DEFAULTS=/usr/local/share/votca/xml/csg_defaults.xml
++ VOTCA_CSG_DEFAULTS=/usr/local/share/votca/xml/csg_defaults.xml
++ [[ -f /usr/local/share/votca/xml/csg_defaults.xml ]]
++ add_to_csgshare --at-the-end /usr/local/share/votca/scripts/inverse
++ local dir end=no
++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]]
++ end=yes
++ shift
++ [[ -z /usr/local/share/votca/scripts/inverse ]]
++ for dirlist in '"$@"'
++ old_IFS='
'
++ IFS=:
++ for dir in '$dirlist'
++ eval dir=/usr/local/share/votca/scripts/inverse
+++ dir=/usr/local/share/votca/scripts/inverse
++ [[ -d /usr/local/share/votca/scripts/inverse ]]
+++ globalize_dir /usr/local/share/votca/scripts/inverse
+++ [[ -z /usr/local/share/votca/scripts/inverse ]]
+++ [[ -d /usr/local/share/votca/scripts/inverse ]]
+++ cd /usr/local/share/votca/scripts/inverse
+++ pwd
++ dir=/usr/local/share/votca/scripts/inverse
++ [[ yes = \y\e\s ]]
++ export CSGSHARE=/usr/local/share/votca/scripts/inverse
++ CSGSHARE=/usr/local/share/votca/scripts/inverse
++ export PERL5LIB=/usr/local/share/votca/scripts/inverse
++ PERL5LIB=/usr/local/share/votca/scripts/inverse
++ export
PYTHONPATH=:/home/martin/gsd2xyz:/usr/local/share/votca/scripts/inverse
++ PYTHONPATH=:/home/martin/gsd2xyz:/usr/local/share/votca/scripts/inverse
++ IFS='
'
++ check_path_variable CSGSHARE PERL5LIB PYTHONPATH
++ local old_IFS dir
++ [[ -z CSGSHARE ]]
++ for var in '"$@"'
++ [[ -z CSGSHARE ]]
++ old_IFS='
'
++ IFS=:
++ for dir in '${!var}'
++ [[ -z /usr/local/share/votca/scripts/inverse ]]
++ [[ /usr/local/share/votca/scripts/inverse = *votca* ]]
++ [[ -d /usr/local/share/votca/scripts/inverse ]]
++ IFS='
'
++ for var in '"$@"'
++ [[ -z PERL5LIB ]]
++ old_IFS='
'
++ IFS=:
++ for dir in '${!var}'
++ [[ -z /usr/local/share/votca/scripts/inverse ]]
++ [[ /usr/local/share/votca/scripts/inverse = *votca* ]]
++ [[ -d /usr/local/share/votca/scripts/inverse ]]
++ IFS='
'
++ for var in '"$@"'
++ [[ -z PYTHONPATH ]]
++ old_IFS='
'
++ IFS=:
++ for dir in '${!var}'
++ [[ -z '' ]]
++ continue
++ for dir in '${!var}'
++ [[ -z /home/martin/gsd2xyz ]]
++ [[ /home/martin/gsd2xyz = *votca* ]]
++ continue
++ for dir in '${!var}'
++ [[ -z /usr/local/share/votca/scripts/inverse ]]
++ [[ /usr/local/share/votca/scripts/inverse = *votca* ]]
++ [[ -d /usr/local/share/votca/scripts/inverse ]]
++ IFS='
'
+ do_iterations=
+ waittime=10
+ unset CSGXMLFILE CSGENDING CSGDEBUG
+ shopt -s extglob
+ [[ -debug != --debug ]]
+ [[ debug = --debug ]]
+ case $1 in
+ export CSGDEBUG=yes
+ CSGDEBUG=yes
+ shift
+ [[ -options != --options ]]
+ [[ options = --options ]]
+ case $1 in
+ CSGXMLFILE=settings.xml
+ [[ -f settings.xml ]]
++ globalize_file settings.xml
++ [[ -z settings.xml ]]
++ [[ -f settings.xml ]]
++ local dir
++ [[ settings.xml = settings.xml ]]
++ dir=.
+++ globalize_dir .
+++ [[ -z . ]]
+++ [[ -d . ]]
+++ cd .
+++ pwd
++ echo /home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml
+ export
CSGXMLFILE=/home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml
+ CSGXMLFILE=/home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml
+ shift 2
+ [[ '' != '' ]]
+ [[ -z /home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml ]]
+ [[ '' = \c\l\e\a\n ]]
+ enable_logging
+ local log
+ [[ -z '' ]]
++ csg_get_property cg.inverse.log_file
Terminated
Am Mittwoch, 22. August 2018 14:32:26 UTC+2 schrieb Christoph Junghans:
>
> On Wed, Aug 22, 2018 at 5:54 AM <[email protected] <javascript:>> wrote:
> >
> > No it did not create an inverse.log
> Ok, try running:
> $ csg_inverse --debug --options settings.xml
> and post the output of that.
>
> Christoph
> >
> > Am Mittwoch, 22. August 2018 13:52:54 UTC+2 schrieb Christoph Junghans:
> >>
> >>
> >>
> >> On Wed, Aug 22, 2018 at 05:49 <[email protected]> wrote:
> >>>
> >>> Yes I tried that as well but then it just says: Terminated
> >>
> >> Does it have any output before that?
> >>
> >> Did it create an inverse.log? And if so what are the last couple of
> lines in there?
> >>
> >> Christoph
> >>>
> >>>
> >>>
> >>> Am Mittwoch, 22. August 2018 13:15:41 UTC+2 schrieb Christoph
> Junghans:
> >>>>
> >>>> On Wed, Aug 22, 2018 at 4:59 AM <[email protected]> wrote:
> >>>> >
> >>>> > Hello,
> >>>> > I do not know why votca will not run this tutorial. I changed the
> settings.xml to point to the lammps executable but when I run the run.sh
> script:
> >>>> > running csg_inverse --options "settings.xml"
> >>>> > ./run.sh: line 4: 6983 Terminated csg_inverse
> --options settings.xml
> >>>> It there any output before that? Can you try to run "csg_inverse
> >>>> --options settings.xml" directly?
> >>>>
> >>>> >
> >>>> > this is what I get. I compiled the latest master version of votca
> with the following options sucessfully .cmake -DBUILD_CSGAPPS=ON
> -DBUILD_CTP=OFF -DBUILD_XTP=OFF -DWITH_SQLITE3=OFF -DWITH_GMX=OFF
> >>>> >
> >>>> > I noticed that in the settings.xml the file CG_CG.pot is mentioned
> but it is not in folder.
> >>>> That is correct, CG_CG.pot gets generated every iteration for IBI by
> VOTCA.
> >>>>
> >>>> Christoph
> >>>> >
> >>>> > Here is also the settings.xml
> >>>> > <cg>
> >>>> > <!-- example for a non-bonded interaction entry -->
> >>>> > <non-bonded>
> >>>> > <!-- name of the interaction -->
> >>>> > <name>CG-CG</name>
> >>>> > <!-- types involved in this interaction -->
> >>>> > <type1>1</type1>
> >>>> > <type2>1</type2>
> >>>> > <!-- dimension + grid spacing of tables for calculations -->
> >>>> > <min>0.0</min>
> >>>> > <max>0.9</max>
> >>>> > <step>0.01</step>
> >>>> > <inverse>
> >>>> > <!-- target distribution (rdf) -->
> >>>> > <target>CG-CG.dist.tgt</target>
> >>>> > <lammps>
> >>>> > <!-- name of the table for lammps run -->
> >>>> > <table>CG_CG.pot</table>
> >>>> > <table_begin>0.20</table_begin>
> >>>> > <table_bins>0.002</table_bins>
> >>>> > </lammps>
> >>>> > </inverse>
> >>>> > </non-bonded>
> >>>> >
> >>>> > <!-- general options for inverse script -->
> >>>> > <inverse>
> >>>> > <!-- 300*0.00831451 lammps units -->
> >>>> > <kBT>2.49435</kBT>
> >>>> > <!-- use lammps as simulation program -->
> >>>> > <program>lammps</program>
> >>>> > <!-- lammps specific options -->
> >>>> > <lammps>
> >>>> > <command>/usr/bin/lammps-daily</command>
> >>>> > <!-- lammps script to run !-->
> >>>> > <script>spce.in</script>
> >>>> > <!-- topology to be used by csg_stat !-->
> >>>> > <topol>spce.data</topol>
> >>>> > <!-- traj file created by lammps !-->
> >>>> > <traj>traj.dump</traj>
> >>>> > </lammps>
> >>>> > <initial_configuration>maindir</initial_configuration>
> >>>> > <!-- these files are copied for each new run -->
> >>>> > <filelist>spce.data spce.in</filelist>
> >>>> > <!-- do so many iterations -->
> >>>> > <iterations_max>300</iterations_max>
> >>>> > <!-- ibi: inverse biltzmann imc: inverse monte carlo -->
> >>>> > <method>ibi</method>
> >>>> > </inverse>
> >>>> > </cg>
> >>>> >
> >>>> > Any help would be great.
> >>>> > Thank you
> >>>> >
> >>>> > --
> >>>> > You received this message because you are subscribed to the Google
> Groups "votca" group.
> >>>>
> >>>> > To unsubscribe from this group and stop receiving emails from it,
> send an email to [email protected].
> >>>> > To post to this group, send email to [email protected].
> >>>>
> >>>> > Visit this group at https://groups.google.com/group/votca.
> >>>> > For more options, visit https://groups.google.com/d/optout.
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Christoph Junghans
> >>>> Web: http://www.compphys.de
> >>>
> >>> --
> >>> You received this message because you are subscribed to the Google
> Groups "votca" group.
> >>> To unsubscribe from this group and stop receiving emails from it, send
> an email to [email protected].
> >>> To post to this group, send email to [email protected].
> >>> Visit this group at https://groups.google.com/group/votca.
> >>> For more options, visit https://groups.google.com/d/optout.
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "votca" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to [email protected] <javascript:>.
> > To post to this group, send email to [email protected]
> <javascript:>.
> > Visit this group at https://groups.google.com/group/votca.
> > For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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