Hmm, one step closer. What Linux Distribution and what version of it are you using?
Can you check that your xml file is valid, with $ xmlwf settings.xml (a good xml file should have no output) If that is the case, check what the output of: $ csg_call --options settings.xml function csg_get_property cg.inverse.log_file and $ csg_call --debug --options settings.xml function csg_get_property cg.inverse.log_file and post it. Christoph On Wed, Aug 22, 2018 at 6:42 AM <[email protected]> wrote: > > 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]> 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]. >> > 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. 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