Ok I will do this tomorrow as I leave early today from work. thank you so far for the quick replies :)
Martin Am Mittwoch, 22. August 2018 15:01:28 UTC+2 schrieb Christoph Junghans: > > 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] <javascript:>> 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] <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 > -- 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.
