Re: [votca] Running the spce water lammps_ibi tutorial
Ok thank very much than I will change to it as that seems the easiest way. Greetings Martin -- 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Running the spce water lammps_ibi tutorial
On Thu, Aug 23, 2018 at 5:15 PM wrote: > > > I got it to work on the linux mint 18.2 but I am not sure how. > > I tried to install it from a binary from this repository deb > http://archive.ubuntu.com/ubuntu/ bionic main > after I had already compiled the master version > During installation it said : > apt-cache search votca > libvotca-csg2 - VOTCA's coarse-graining library > libvotca-csg2-dev - VOTCA's coarse-graining library, development kit > libvotca-tools-dev - VOTCA's tools library, development kit > libvotca-tools2 - VOTCA's tools library > votca-csg - VOTCA's coarse-graining engine > votca-csg-scripts - VOTCA's coarse-graining scripts > votca-csg-tutorials - VOTCA's coarse-graining tutorials > martin@martin-linux ~ $ sudo apt-get install votca-csg > Reading package lists... Done > Building dependency tree > Reading state information... Done > The following packages were automatically installed and are no longer > required: > cabextract gstreamer0.10-ffmpeg libavcodec-extra libhal1-flash libmspack0 > libunshield0 oxideqt-codecs-extra unshield > Use 'sudo apt autoremove' to remove them. > The following additional packages will be installed: > libvotca-csg2 libvotca-tools2 votca-csg-scripts > Suggested packages: > votca-csg-tutorials > The following NEW packages will be installed: > libvotca-csg2 libvotca-tools2 votca-csg votca-csg-scripts > 0 upgraded, 4 newly installed, 0 to remove and 1524 not upgraded. > Need to get 584 kB of archives. > After this operation, 2.491 kB of additional disk space will be used. > Do you want to continue? [Y/n] y > Get:1 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libvotca-tools2 > amd64 1.2.4-1.1 [120 kB] > Get:2 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libvotca-csg2 > amd64 1.2.4-2.1 [155 kB] > Get:3 http://archive.ubuntu.com/ubuntu xenial/universe amd64 > votca-csg-scripts all 1.2.4-2.1 [45,7 kB] > Get:4 http://archive.ubuntu.com/ubuntu xenial/universe amd64 votca-csg amd64 > 1.2.4-2.1 [263 kB] > Fetched 584 kB in 0s (1.223 kB/s) > Selecting previously unselected package libvotca-tools2. > (Reading database ... 235011 files and directories currently installed.) > Preparing to unpack .../libvotca-tools2_1.2.4-1.1_amd64.deb ... > Unpacking libvotca-tools2 (1.2.4-1.1) ... > Selecting previously unselected package libvotca-csg2. > Preparing to unpack .../libvotca-csg2_1.2.4-2.1_amd64.deb ... > Unpacking libvotca-csg2 (1.2.4-2.1) ... > Selecting previously unselected package votca-csg-scripts. > Preparing to unpack .../votca-csg-scripts_1.2.4-2.1_all.deb ... > Unpacking votca-csg-scripts (1.2.4-2.1) ... > Selecting previously unselected package votca-csg. > Preparing to unpack .../votca-csg_1.2.4-2.1_amd64.deb ... > Unpacking votca-csg (1.2.4-2.1) ... > Processing triggers for libc-bin (2.23-0ubuntu10) ... > Processing triggers for man-db (2.7.5-1) ... > Setting up libvotca-tools2 (1.2.4-1.1) ... > Setting up libvotca-csg2 (1.2.4-2.1) ... > Setting up votca-csg-scripts (1.2.4-2.1) ... > Setting up votca-csg (1.2.4-2.1) ... > > I had tried this before on the ubuntu as the very first try but the 1.2.4 > version did not support lammps thats why I tried to build it from source. > My guess is that during compilation something went wrong or was missing and > was fixed by "installing" the older version over it. > Anyway it is running now as I am writing this post. > I was wondering if you could make a newer ubuntu binary available or if you > already have point me to it. Well, Ubuntu 18.04 comes with votca-1.4.1! > Also how can I check which votca_csg version I am running now? Run "csg_call --version" or "csg_stat --help" > > Thank you very much again for the quick replies and the help. I may need it > in the future again ;) Can you try this patch https://github.com/votca/votca/commit/1630c6b293849a0b2028d21a8d9c89a4d77a4b25 And rebuild everything with -DENABLE_RPATH_INJECT=ON ? Christoph > > Am Donnerstag, 23. August 2018 22:39:51 UTC+2 schrieb ifh...@gmail.com: >> >> I did but no change. >> I was however able to get more from the error message loop. It refers to >> line 348 in the common_functions.sh all the time. >> I also tried to compile it on another machine that runs Linux mint 18.04 but >> it shows the same behavior as the Ubuntu 16.04. >> >> Martin >> >> Am Donnerstag, 23. August 2018 14:49:53 UTC+2 schrieb Christoph Junghans: >>> >>> >>> >>> On Thu, Aug 23, 2018, 00:50 wrote: I am running Ubuntu 16.04.4 LTS The xml file is ok (no output from command) When I do either of the two csg_call commands the termiinal is stuck in a loop and tries to terminate a process that is not there I can only stop it with killall csg_call but I do get an error message: for the first one: ## #
Re: [votca] Running the spce water lammps_ibi tutorial
On Thu, Aug 23, 2018 at 2:39 PM wrote: > > I did but no change. > I was however able to get more from the error message loop. It refers to line > 348 in the common_functions.sh all the time. > I also tried to compile it on another machine that runs Linux mint 18.04 but > it shows the same behavior as the Ubuntu 16.04. Well the error was: csg_property: error while loading shared libraries: libvotca_csg.so.5: cannot open shared object file: No such file or directory which means the directory which contains libvotca_csg.so.5 isn't in your LD_LIBRARY_PATH and sourcing VOTCARC.bash should actually do that! Can you check your VOTCARC.bash and the value of LD_LIBRARY_PATH before and after sourcing it? Christoph > > Martin > > Am Donnerstag, 23. August 2018 14:49:53 UTC+2 schrieb Christoph Junghans: >> >> >> >> On Thu, Aug 23, 2018, 00:50 wrote: >>> >>> I am running Ubuntu 16.04.4 LTS >>> >>> The xml file is ok (no output from command) >>> >>> When I do either of the two csg_call commands the termiinal is stuck in a >>> loop and tries to terminate a process that is not there I can only stop it >>> with killall csg_call >>> but I do get an error message: >>> >>> for the first one: >>> >>> ## >>> # >>> # >>> # ERROR: >>> # >>> # critical: 'csg_property --file >>> /usr/local/share/votca/xml/csg_defaults.xml --path cg.inverse.program >>> --short --print .' failed # >>> # Details can be found above >>> # >>> # >>> # >>> ## >>> /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: kill: >>> (11334) - No such process >>> csg_property: error while loading shared libraries: libvotca_csg.so.5: >>> cannot open shared object file: No such file or directory >>> >>> for the second one: >>> >>> ### >>> # >>> # >>> # ERROR: >>> # >>> # critical: 'csg_property --file settings.xml --path cg.inverse.program >>> --short --print .' failed # >>> # Details can be found above >>> # >>> # >>> # >>> ### >>> /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: kill: >>> (14732) - No such process >>> csg_get_property: No value for 'cg.inverse.program' found in settings.xml, >>> trying /usr/local/share/votca/xml/csg_defaults.xml >>> csg_property: error while loading shared libraries: libvotca_csg.so.5: >>> cannot open shared object file: No such file or directory >>> >>> Maybe this can shed some light on the problem. >> >> Try to "source VOTCARC.bash" first and rerun! >> >> Christoph >>> >>> >>> Greetings Martin >>> >>> >>> >>> Am Mittwoch, 22. August 2018 15:42:05 UTC+2 schrieb ifh...@gmail.com: 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 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
Re: [votca] Running the spce water lammps_ibi tutorial
I got it to work on the linux mint 18.2 but I am not sure how. I tried to install it from a binary from this repository deb http://archive.ubuntu.com/ubuntu/ bionic main after I had already compiled the master version During installation it said : apt-cache search votca libvotca-csg2 - VOTCA's coarse-graining library libvotca-csg2-dev - VOTCA's coarse-graining library, development kit libvotca-tools-dev - VOTCA's tools library, development kit libvotca-tools2 - VOTCA's tools library votca-csg - VOTCA's coarse-graining engine votca-csg-scripts - VOTCA's coarse-graining scripts votca-csg-tutorials - VOTCA's coarse-graining tutorials martin@martin-linux ~ $ sudo apt-get install votca-csg Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: cabextract gstreamer0.10-ffmpeg libavcodec-extra libhal1-flash libmspack0 libunshield0 oxideqt-codecs-extra unshield Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: libvotca-csg2 libvotca-tools2 votca-csg-scripts Suggested packages: votca-csg-tutorials The following NEW packages will be installed: libvotca-csg2 libvotca-tools2 votca-csg votca-csg-scripts 0 upgraded, 4 newly installed, 0 to remove and 1524 not upgraded. Need to get 584 kB of archives. After this operation, 2.491 kB of additional disk space will be used. Do you want to continue? [Y/n] y Get:1 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libvotca-tools2 amd64 1.2.4-1.1 [120 kB] Get:2 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libvotca-csg2 amd64 1.2.4-2.1 [155 kB] Get:3 http://archive.ubuntu.com/ubuntu xenial/universe amd64 votca-csg-scripts all 1.2.4-2.1 [45,7 kB] Get:4 http://archive.ubuntu.com/ubuntu xenial/universe amd64 votca-csg amd64 1.2.4-2.1 [263 kB] Fetched 584 kB in 0s (1.223 kB/s) Selecting previously unselected package libvotca-tools2. (Reading database ... 235011 files and directories currently installed.) Preparing to unpack .../libvotca-tools2_1.2.4-1.1_amd64.deb ... Unpacking libvotca-tools2 (1.2.4-1.1) ... Selecting previously unselected package libvotca-csg2. Preparing to unpack .../libvotca-csg2_1.2.4-2.1_amd64.deb ... Unpacking libvotca-csg2 (1.2.4-2.1) ... Selecting previously unselected package votca-csg-scripts. Preparing to unpack .../votca-csg-scripts_1.2.4-2.1_all.deb ... Unpacking votca-csg-scripts (1.2.4-2.1) ... Selecting previously unselected package votca-csg. Preparing to unpack .../votca-csg_1.2.4-2.1_amd64.deb ... Unpacking votca-csg (1.2.4-2.1) ... Processing triggers for libc-bin (2.23-0ubuntu10) ... Processing triggers for man-db (2.7.5-1) ... Setting up libvotca-tools2 (1.2.4-1.1) ... Setting up libvotca-csg2 (1.2.4-2.1) ... Setting up votca-csg-scripts (1.2.4-2.1) ... Setting up votca-csg (1.2.4-2.1) ... I had tried this before on the ubuntu as the very first try but the 1.2.4 version did not support lammps thats why I tried to build it from source. My guess is that during compilation something went wrong or was missing and was fixed by "installing" the older version over it. Anyway it is running now as I am writing this post. I was wondering if you could make a newer ubuntu binary available or if you already have point me to it. Also how can I check which votca_csg version I am running now? Thank you very much again for the quick replies and the help. I may need it in the future again ;) Am Donnerstag, 23. August 2018 22:39:51 UTC+2 schrieb ifh...@gmail.com: > > I did but no change. > I was however able to get more from the error message loop. It refers to > line 348 in the common_functions.sh all the time. > I also tried to compile it on another machine that runs Linux mint 18.04 > but it shows the same behavior as the Ubuntu 16.04. > > Martin > > Am Donnerstag, 23. August 2018 14:49:53 UTC+2 schrieb Christoph Junghans: >> >> >> >> On Thu, Aug 23, 2018, 00:50 wrote: >> >>> I am running Ubuntu 16.04.4 LTS >>> >>> The xml file is ok (no output from command) >>> >>> When I do either of the two csg_call commands the termiinal is stuck in >>> a loop and tries to terminate a process that is not there I can only stop >>> it with killall csg_call >>> but I do get an error message: >>> >>> for the first one: >>> >>> >>> ## >>> # >>> # >>> # ERROR: >>> # >>> # critical: 'csg_property --file >>> /usr/local/share/votca/xml/csg_defaults.xml --path cg.inverse.program >>> --short --print .' failed # >>> # Details can be found above >>>
Re: [votca] Running the spce water lammps_ibi tutorial
I did but no change. I was however able to get more from the error message loop. It refers to line 348 in the common_functions.sh all the time. I also tried to compile it on another machine that runs Linux mint 18.04 but it shows the same behavior as the Ubuntu 16.04. Martin Am Donnerstag, 23. August 2018 14:49:53 UTC+2 schrieb Christoph Junghans: > > > > On Thu, Aug 23, 2018, 00:50 > wrote: > >> I am running Ubuntu 16.04.4 LTS >> >> The xml file is ok (no output from command) >> >> When I do either of the two csg_call commands the termiinal is stuck in a >> loop and tries to terminate a process that is not there I can only stop it >> with killall csg_call >> but I do get an error message: >> >> for the first one: >> >> >> ## >> # >> # >> # ERROR: >># >> # critical: 'csg_property --file >> /usr/local/share/votca/xml/csg_defaults.xml --path cg.inverse.program >> --short --print .' failed # >> # Details can be found above >># >> # >> # >> >> ## >> /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: >> kill: (11334) - No such process >> csg_property: error while loading shared libraries: libvotca_csg.so.5: >> cannot open shared object file: No such file or directory >> >> for the second one: >> >> >> ### >> # >> # >> # ERROR: >> # >> # critical: 'csg_property --file settings.xml --path cg.inverse.program >> --short --print .' failed # >> # Details can be found above >> # >> # >> # >> >> ### >> /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: >> kill: (14732) - No such process >> csg_get_property: No value for 'cg.inverse.program' found in >> settings.xml, trying /usr/local/share/votca/xml/csg_defaults.xml >> csg_property: error while loading shared libraries: libvotca_csg.so.5: >> cannot open shared object file: No such file or directory >> >> Maybe this can shed some light on the problem. >> > Try to "source VOTCARC.bash" first and rerun! > > Christoph > >> >> Greetings Martin >> >> >> >> Am Mittwoch, 22. August 2018 15:42:05 UTC+2 schrieb ifh...@gmail.com: >>> >>> 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 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
Re: [votca] Running the spce water lammps_ibi tutorial
On Thu, Aug 23, 2018, 00:50 wrote: > I am running Ubuntu 16.04.4 LTS > > The xml file is ok (no output from command) > > When I do either of the two csg_call commands the termiinal is stuck in a > loop and tries to terminate a process that is not there I can only stop it > with killall csg_call > but I do get an error message: > > for the first one: > > > ## > # > # > # ERROR: ># > # critical: 'csg_property --file > /usr/local/share/votca/xml/csg_defaults.xml --path cg.inverse.program > --short --print .' failed # > # Details can be found above ># > # > # > > ## > /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: > kill: (11334) - No such process > csg_property: error while loading shared libraries: libvotca_csg.so.5: > cannot open shared object file: No such file or directory > > for the second one: > > > ### > # ># > # ERROR: > # > # critical: 'csg_property --file settings.xml --path cg.inverse.program > --short --print .' failed # > # Details can be found above > # > # ># > > ### > /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: > kill: (14732) - No such process > csg_get_property: No value for 'cg.inverse.program' found in settings.xml, > trying /usr/local/share/votca/xml/csg_defaults.xml > csg_property: error while loading shared libraries: libvotca_csg.so.5: > cannot open shared object file: No such file or directory > > Maybe this can shed some light on the problem. > Try to "source VOTCARC.bash" first and rerun! Christoph > > Greetings Martin > > > > Am Mittwoch, 22. August 2018 15:42:05 UTC+2 schrieb ifh...@gmail.com: >> >> 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 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
Re: [votca] Running the spce water lammps_ibi tutorial
I am running Ubuntu 16.04.4 LTS The xml file is ok (no output from command) When I do either of the two csg_call commands the termiinal is stuck in a loop and tries to terminate a process that is not there I can only stop it with killall csg_call but I do get an error message: for the first one: ## # # # ERROR: # # critical: 'csg_property --file /usr/local/share/votca/xml/csg_defaults.xml --path cg.inverse.program --short --print .' failed # # Details can be found above # # # ## /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: kill: (11334) - No such process csg_property: error while loading shared libraries: libvotca_csg.so.5: cannot open shared object file: No such file or directory for the second one: ### # # # ERROR: # # critical: 'csg_property --file settings.xml --path cg.inverse.program --short --print .' failed # # Details can be found above # # # ### /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: kill: (14732) - No such process csg_get_property: No value for 'cg.inverse.program' found in settings.xml, trying /usr/local/share/votca/xml/csg_defaults.xml csg_property: error while loading shared libraries: libvotca_csg.so.5: cannot open shared object file: No such file or directory Maybe this can shed some light on the problem. Greetings Martin Am Mittwoch, 22. August 2018 15:42:05 UTC+2 schrieb ifh...@gmail.com: > > 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 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 >>
Re: [votca] Running the spce water lammps_ibi tutorial
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 > 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 ]]
> >
Re: [votca] Running the spce water lammps_ibi tutorial
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 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 ]]
>
Re: [votca] Running the spce water lammps_ibi tutorial
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 =
Re: [votca] Running the spce water lammps_ibi tutorial
On Wed, Aug 22, 2018 at 5:54 AM 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 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 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-CG > > 1 > 1 > > 0.0 > 0.9 > 0.01 > > > CG-CG.dist.tgt > > > CG_CG.pot > 0.20 > 0.002 > > > > > > > > 2.49435 > > lammps > > > /usr/bin/lammps-daily > > spce.in > > spce.data > > traj.dump > > maindir > > spce.data spce.in > > 300 > > ibi > > > > 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 votca+un...@googlegroups.com. > To post to this group, send email to vo...@googlegroups.com. > 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 votca+un...@googlegroups.com. >>> To post to this group, send email to vo...@googlegroups.com. >>> 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Running the spce water lammps_ibi tutorial
No it did not create an inverse.log Am Mittwoch, 22. August 2018 13:52:54 UTC+2 schrieb Christoph Junghans: > > > > On Wed, Aug 22, 2018 at 05:49 > 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 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-CG >>> > >>> > 1 >>> > 1 >>> > >>> > 0.0 >>> > 0.9 >>> > 0.01 >>> > >>> > >>> > CG-CG.dist.tgt >>> > >>> > >>> > CG_CG.pot >>> > 0.20 >>> > 0.002 >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > 2.49435 >>> > >>> > lammps >>> > >>> > >>> > /usr/bin/lammps-daily >>> > >>> > spce.in >>> > >>> > spce.data >>> > >>> > traj.dump >>> > >>> > maindir >>> > >>> > spce.data spce.in >>> > >>> > 300 >>> > >>> > ibi >>> > >>> > >>> > >>> > 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 votca+un...@googlegroups.com. >>> > To post to this group, send email to vo...@googlegroups.com. >>> >> > 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 votca+un...@googlegroups.com . >> To post to this group, send email to vo...@googlegroups.com >> . >> 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Running the spce water lammps_ibi tutorial
On Wed, Aug 22, 2018 at 05:49 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 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-CG >> > >> > 1 >> > 1 >> > >> > 0.0 >> > 0.9 >> > 0.01 >> > >> > >> > CG-CG.dist.tgt >> > >> > >> > CG_CG.pot >> > 0.20 >> > 0.002 >> > >> > >> > >> > >> > >> > >> > >> > 2.49435 >> > >> > lammps >> > >> > >> > /usr/bin/lammps-daily >> > >> > spce.in >> > >> > spce.data >> > >> > traj.dump >> > >> > maindir >> > >> > spce.data spce.in >> > >> > 300 >> > >> > ibi >> > >> > >> > >> > 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 votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Running the spce water lammps_ibi tutorial
Yes I tried that as well but then it just says: Terminated Am Mittwoch, 22. August 2018 13:15:41 UTC+2 schrieb Christoph Junghans: > > On Wed, Aug 22, 2018 at 4:59 AM > 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-CG > > > > 1 > > 1 > > > > 0.0 > > 0.9 > > 0.01 > > > > > > CG-CG.dist.tgt > > > > > > CG_CG.pot > > 0.20 > > 0.002 > > > > > > > > > > > > > > > > 2.49435 > > > > lammps > > > > > > /usr/bin/lammps-daily > > > > spce.in > > > > spce.data > > > > traj.dump > > > > maindir > > > > spce.data spce.in > > > > 300 > > > > ibi > > > > > > > > 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 votca+un...@googlegroups.com . > > To post to this group, send email to vo...@googlegroups.com > . > > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Running the spce water lammps_ibi tutorial
On Wed, Aug 22, 2018 at 4:59 AM 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-CG > > 1 > 1 > > 0.0 > 0.9 > 0.01 > > > CG-CG.dist.tgt > > > CG_CG.pot > 0.20 > 0.002 > > > > > > > > 2.49435 > > lammps > > > /usr/bin/lammps-daily > > spce.in > > spce.data > > traj.dump > > maindir > > spce.data spce.in > > 300 > > ibi > > > > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
