Hi, I would like to ask one additional question. So the csg_stat during IBI is calculated by the following scripts: 1)calc_rdf_generic.sh 2)calc_target_rdf_generic.sh
I guess the second one is not used during inversion. Are there any additional scripts used. Christianna > On 8 May 2019, at 5:37 PM, Christoph Junghans <[email protected]> wrote: > > On Wed, May 8, 2019 at 8:22 AM CHRISTINA-ANNA GATSIOU > <[email protected] <mailto:[email protected]>> wrote: >> >> Yes I understand this but I what I do not understand why or where it fails >> to generate this. > It should be generated by csg_stat. Just look for the last csg_stat > execution in the log file before the error occurs. > > Christoph >> >> -- >> 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] >> <mailto:[email protected]>. >> To post to this group, send email to [email protected] >> <mailto:[email protected]>. >> Visit this group at https://groups.google.com/group/votca >> <https://groups.google.com/group/votca>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com >> >> <https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com>. >> For more options, visit https://groups.google.com/d/optout >> <https://groups.google.com/d/optout>. >> >> >> On 8 May 2019, at 4:00 PM, Christoph Junghans <[email protected]> wrote: >> >> >> >> On Wed, May 8, 2019, 01:43 CHRISTINA-ANNA GATSIOU >> <[email protected]> wrote: >>> >>> Hi, >>> >>> Thanks for the help! The error message I get now looks like this: >>> Running subscript 'update_ibi_pot.pl P4_P4.dist.tgt P4_P4.dist.new >>> P4_P4.pot.cur P4_P4.dpot.pure_ibi' (from tags update ibi_pot) dir /usr/s >>> hare/votca/scripts/inverse >>> readin_table: could not open file P4_P4.dist.new >>> >>> Callstack: >>> D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/inverse.sh - linenumber >>> 301 >>> do_external - linenumber 240 in >>> D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/functions_common.sh >>> /usr/share/votca/scripts/inverse/update_ibi.sh - linenumber 32 >>> for_all - linenumber 22 (see 'csg_call --cat function for_all') >>> do_external - linenumber 19 (see 'csg_call --cat >>> function do_external') >>> >>> /usr/share/votca/scripts/inverse/update_ibi_single.sh - linenumber 39 >>> do_external - linenumber 22 (see 'csg_call --cat >>> function do_external') >>> die - linenumber 2 (see 'csg_call --cat >>> function die') >>> ###################################################################################################################### >>> # >>> # >>> # ERROR: >>> # >>> # do_external: subscript >>> # >>> # /usr/share/votca/scripts/inverse/update_ibi_pot.pl P4_P4.dist.tgt >>> P4_P4.dist.new P4_P4.pot.cur P4_P4.dpot.pure_ibi # >>> # (from tags update ibi_pot) failed >>> # >>> # For details see the logfile /d/MAPS/DEMO2/CG_urea_water_2/inverse.log >>> # >>> # >>> # >>> ###################################################################################################################### >>> die: (called from 5888) CSG_MASTER_PID is 12388 >>> die: pids to kill: 0 >>> >>> Do you have ideas on what might be the problem. >> >> The error message says it all: could not open file P4_P4.dist.new >> >> This file is missing. >> >> Christoph >> >>> >>> Best regards, >>> Christianna >>> >>> On 28 Apr 2019, at 9:31 PM, Christoph Junghans <[email protected]> wrote: >>> >>> I found it, it was actually a bug in the code, when using multiple >>> mapping files, which I fixed here: >>> https://github.com/votca/csg/pull/371 >>> >>> As a workaround apply the patch or revert the order of the mapping >>> files in your settings.xml for now: >>> --- settings.xml.orig 2019-04-27 19:42:45.434237893 -0600 >>> +++ settings.xml 2019-04-27 19:43:08.314463798 -0600 >>> @@ -122,7 +122,7 @@ >>> <pot_max>1000000</pot_max> >>> <table_end>2.4</table_end> >>> </gromacs> >>> - <map>p4_topol.xml p2p1_topol.xml</map> >>> + <map>p2p1_topol.xml p4_topol.xml</map> >>> <filelist>grompp.mdp topol.top conf.gro index.ndx table.xvg</filelist> >>> <iterations_max>30</iterations_max> >>> <convergence_check> >>> >>> Christoph >>> >>> On Sat, Apr 27, 2019 at 6:48 PM CHRISTINA-ANNA GATSIOU >>> <[email protected]> wrote: >>> >>> >>> The error message looks like this >>> for_all: run 'do_external prepare_single ibi' for interaction named 'P2-P1' >>> Running subscript 'prepare_generic_single.sh' (from tags prepare_single >>> ibi) dir /scratch/cgatsiou/votca/share/votca/scripts/inverse >>> >>> Callstack: >>> /scratch/cgatsiou/votca/share/votca/scripts/inverse/inverse.sh - linenumber >>> 156 >>> do_external - linenumber 176 in >>> /scratch/cgatsiou/votca/share/votca/scripts/inverse/functions_common.sh >>> >>> /scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic.sh - >>> linenumber 31 >>> for_all - linenumber 22 (see 'csg_call --cat function for_all') >>> do_external - linenumber 19 (see 'csg_call --cat function >>> do_external') >>> >>> /scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic_single.sh >>> - linenumber 34 >>> csg_get_interaction_property - linenumber 44 (see >>> 'csg_call --cat function csg_get_interaction_property') >>> has_duplicate - linenumber 1 (see 'csg_call >>> --cat function has_duplicate') >>> die - linenumber 2 (see 'csg_call --cat >>> function die') >>> ######################################################################## >>> # # >>> # ERROR: # >>> # has_duplicate: Missing argument # >>> # For details see the logfile /home/cgatsiou/CG_urea_water/inverse.log # >>> # # >>> ######################################################################## >>> die: (called from 14553) CSG_MASTER_PID is 13536 >>> die: pids to kill: 13536 14455 14538 14553 >>> Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p' >>> Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p’ >>> >>> The has_duplicate signifies the existence of a duplicate interaction, or >>> option somewhere in the input but I cannot find an error in the inputs. >>> >>> Best regards, >>> >>> Christianna >>> >>> On 27 Apr 2019, at 7:11 PM, Christoph Junghans <[email protected]> wrote: >>> >>> >>> >>> On Fri, Apr 26, 2019, 07:52 <[email protected]> wrote: >>> >>> >>> Hi, >>> >>> >>> I have attached the neccessary files. IBI seems to be failing before the >>> inversion of the initial distributions! Some help would be very much >>> appreciated. >>> >>> >>> What is the error message? >>> >>> Christoph >>> >>> >>> >>> >>> Best regards, >>> Christianna >>> >>> -- >>> 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. >>> >>> >>> >>> -- >>> 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. >>> >>> >>> -- >>> 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. >>> >>> >>> >>> -- >>> 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. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/5A96003C-4D45-48E5-9DA5-6A9D03023606%40gmail.com. >>> For more options, visit https://groups.google.com/d/optout. >> >> >> -- >> 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. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e5_MeTvn%2BwU7B6q_D6To7ER7J2V%3DhY0uZdQJ4bE42Gh%3Dw%40mail.gmail.com. >> For more options, visit https://groups.google.com/d/optout. >> >> >> -- >> 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] >> <mailto:[email protected]>. >> To post to this group, send email to [email protected] >> <mailto:[email protected]>. >> Visit this group at https://groups.google.com/group/votca >> <https://groups.google.com/group/votca>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com >> >> <https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com>. >> For more options, visit https://groups.google.com/d/optout >> <https://groups.google.com/d/optout>. > > > > -- > Christoph Junghans > Web: http://www.compphys.de <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] > <mailto:[email protected]>. > To post to this group, send email to [email protected] > <mailto:[email protected]>. > Visit this group at https://groups.google.com/group/votca > <https://groups.google.com/group/votca>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e6-O%3DSDGFZS-RP8CAfvUNurigDM0NpsFnYE6ySQpxUw0w%40mail.gmail.com > > <https://groups.google.com/d/msgid/votca/CAHG27e6-O%3DSDGFZS-RP8CAfvUNurigDM0NpsFnYE6ySQpxUw0w%40mail.gmail.com>. > For more options, visit https://groups.google.com/d/optout > <https://groups.google.com/d/optout>. -- 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. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/F7860F64-884D-4A9A-AB18-281A6C279AAC%40gmail.com. For more options, visit https://groups.google.com/d/optout.
