echempp-devel Mailing List for EChem++ (Page 19)
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From: Kai L. <kai...@un...> - 2006-05-15 08:59:39
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Hello Bernd, I've done a check out and compiled everything with --disable-optimization --disable-static without problems (today, I will check the optimization option - that may take a while). > (1) we have again the linker warnings about some links into the > `discarded section', like > /usr/lib/gcc-lib/i586-suse-linux/3.3.5/../../../../i586-suse-linux/bin/= ld: > `.gnu.linkonce.t._ZN11BSUtilities4xmlw9XmlStreamlsERKNS1_10ControllerE' > referenced in section `.rodata' of ModSim-mechanismDialog.o: defined in > discarded section > `.gnu.linkonce.t._ZN11BSUtilities4xmlw9XmlStreamlsERKNS1_10ControllerE' > of ModSim-mechanismDialog.o the warnings are related to a linker-bug of g++ (half a year ago, I found something in a mailing list). Hopefully, they are gone with the next g++ version. > (2)and more severe, there is some liker error when using Quantities in > modelParametersDialog.cpp and other similar errors. Unfortunately, as > usual, the error message is difficult to read. So, first question: has > something been changed in modelParametersDialog.cpp recently? Can't remember a change in the modelParametersDialog.cpp. But I will check the optimized code this day. Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: Kai L. <kai...@un...> - 2006-05-15 08:34:15
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Hello Bernd, > the cvs problem (compilation of most recent version) I just reported > does only seem to be present if I use the default flag for optimization. > If I use --disable-optimize only the warnings from the linker are still > there. Maybe this help locating the problem? Do you mean '--disable-optimization'? The old option '--disable-optimize' was renamed. Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: Kai L. <kai...@un...> - 2006-05-15 08:29:40
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Hello Bernd, I have not tried to translate the test programs (with 'make check') since a couple of weeks. So there seems to be some problems due to changes in the libs - but not related to the new cvs-stuff. I will check this today. Regards, Kai > HI all, > > it seems that I have been able to correct at least one of the errors > encountered while compiling the present cvs version of EChem++. > I added `-lloki' to the Makefile.am in Adapters/test. > Still, another error occurs, see the attached output. > Regards > Bernd > > -- > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > Bernd Speiser > Institut f"ur Organische Chemie > Auf der Morgenstelle 18 > D-72076 T"ubingen > Germany > phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) > fax: +49-7071-295518 > e-mail: ber...@un... > Internet: http://www.uni-tuebingen.de/speiser > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: <ber...@t-...> - 2006-05-14 15:48:42
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HI all, it seems that I have been able to correct at least one of the errors encountered while compiling the present cvs version of EChem++. I added `-lloki' to the Makefile.am in Adapters/test. Still, another error occurs, see the attached output. Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: Bernd S. <ber...@us...> - 2006-05-14 15:44:45
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Update of /cvsroot/echempp/Model/Adapters/test In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv5965/test Modified Files: Makefile.am Log Message: Makefile Index: Makefile.am =================================================================== RCS file: /cvsroot/echempp/Model/Adapters/test/Makefile.am,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** Makefile.am 6 Jan 2006 21:51:37 -0000 1.10 --- Makefile.am 14 May 2006 15:44:41 -0000 1.11 *************** *** 8,12 **** -L$(QUANTITIESLIB) -lQuantity \ -L$(BSUTILITIESLIB) -lBSUtilities \ ! -lginac adaptersTest_CXXFLAGS = -Wall -Werror -pedantic-errors -Wno-deprecated \ -DTIXML_USE_STL --- 8,12 ---- -L$(QUANTITIESLIB) -lQuantity \ -L$(BSUTILITIESLIB) -lBSUtilities \ ! -lginac -lloki adaptersTest_CXXFLAGS = -Wall -Werror -pedantic-errors -Wno-deprecated \ -DTIXML_USE_STL |
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From: <ber...@t-...> - 2006-05-14 08:33:35
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Hi there, when trying to compile the test programs from the cvs version, I get another error, see attachment, this time in the adapter library. I thought I had a recent version of Loki ... Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: <ber...@t-...> - 2006-05-13 19:57:22
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HI all, the cvs problem (compilation of most recent version) I just reported does only seem to be present if I use the default flag for optimization. If I use --disable-optimize only the warnings from the linker are still there. Maybe this help locating the problem? Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: <ber...@t-...> - 2006-05-13 19:45:51
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Hi all, I had changed my link to the cvs server for EChem++ and checked out a new working copy. When trying to compile, I get the error message attached. There are two problems: (1) we have again the linker warnings about some links into the `discarded section', like /usr/lib/gcc-lib/i586-suse-linux/3.3.5/../../../../i586-suse-linux/bin/ld: `.gnu.linkonce.t._ZN11BSUtilities4xmlw9XmlStreamlsERKNS1_10ControllerE' referenced in section `.rodata' of ModSim-mechanismDialog.o: defined in discarded section `.gnu.linkonce.t._ZN11BSUtilities4xmlw9XmlStreamlsERKNS1_10ControllerE' of ModSim-mechanismDialog.o (2)and more severe, there is some liker error when using Quantities in modelParametersDialog.cpp and other similar errors. Unfortunately, as usual, the error message is difficult to read. So, first question: has something been changed in modelParametersDialog.cpp recently? Second question: does anyone else also observe this? Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: <ber...@t-...> - 2006-05-13 12:22:30
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Hi all, since sourceforge has now done some changes to the cvs system, there's some stuff to discuss: (1) please change the name of the cvs server according to the information sent around by sourceforge yesterday: echempp.cvs.sourceforge.net the old name will no longer work. (2) According to the sourceforge instructions, get a new copy of the cvs version of EChem++ software and do the necessary steps to get it compiled (see README_FIRST and README). Check that everything compiles correctly. (3) I have added some monitoring function to the new cvs server, that will send an e-mail message to echempp-devel if some commit has been made. Please test this feature by doing a commit. (4) Sourceforge does no longer make nightly tarballs of the cvs tree of projects. Thus, it seems that we are responsible on our own for getting backup copies. They suggest to use rsync, which I have never employed. What do you think - are there any other suggestions? How often would be want to get such backups. I guess that a call to rsync could be automated from echem9 and the copies could be stored on echem9 (with further backup in the ZDV). Best regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: <ber...@t-...> - 2006-05-12 06:45:09
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Hi all, please take into account this message from sourceforge. This will affect our CVS use. We should also check how it does influence our documentation. As regards backups, I will check these new services in time. Best regards Bernd -------- Original Message -------- Subject: SUBJECT: SourceForge.net: CVS service offering changes Date: Thu, 11 May 2006 17:32:39 -0700 (PDT) From: SourceForge.net Team <no...@so...> To: ber...@un... Greetings, You are receiving this mail because you are a project admin for a SourceForge.net-hosted project. One of our primary services, CVS, suffered a series of interrelated, critical hardware failures in recent weeks. We understand how frustrating this CVS outage must be to you and your users; however, our top priority remains preservation of the integrity of your data. The series of CVS hardware failures prompted us to expedite the deployment of planed improvements to our CVS infrastructure, drawing upon much of the knowledge that we gained from our Subversion deployment. Our improved CVS service architecture, which we plan to deploy tomorrow afternoon (2006-05-12), will offer greater performance and stability and will eliminate several single points of failure. The Site Status page (https://www.sf.net/docs/A04) will be updated as soon as the new infrastructure is rolled out. In the interim, please read the important information provided below to learn about how these changes will affect your project. Summary of changes, effective 2006-05-12: 1. Hostname for CVS service Old: cvs.sourceforge.net New: PROJECT_UNIX_NAME.cvs.sourceforge.net This change will require new working copies to be checked out of all repositories (so control files in the working copy will point to the right place). We will be updating the instructions we supply, but instructions that your team has written within documentation, etc. will need to be updated. cvs -d:pserver:ano...@cv...:/cvsroot/gaim co gaim would be changed to cvs -d:pserver:ano...@ga...:/cvsroot/gaim co gaim 2. ViewCVS We are moving from ViewCVS to its successor, ViewVC. ViewVC is currently in use for our Subversion service. 3. Sync delay Old: CVS pserver, tarballs and ViewCVS provided against a separate server which is a minimum of three hours behind developer CVS. New: ViewVC will be provided against developer CVS (it will be current). CVS pserver will be provided against a secondary server (not developer server) with a maximum expected delay of two hours. Follow-up work is planned (this infrastructure takes us 80% of the way) to essentially eliminate the sync delay. 4. Read-only rsync service As a new service offering, we are now providing read-only rsync access against developer CVS. This allows projects to efficiently make on-demand backups of their entire CVS repository. All projects should be making regular backups of their CVS repository contents using this service. 5. Nightly tarball service Nightly tarball service is being dropped in lieu of read-only rsync service. Projects which currently depend on nightly tarballs for repository backups will need to begin using rsync to make a backup copy of their repository contents. We see this as a major functional improvement. For a number of reasons, tarballs have fallen out of sync with the data in the repository at times in the past few years. Tarballs required a substantial amount of additional disk, and I/O to generate. The move to read-only rsync allows backups to be produced on-demand, with an update frequency chosen by the project. 6. Points of failure In the past, developer CVS service for all projects was provided from a single host. CVS pserver service was provided from individual backend heads based on a split of the data. Under our new design, developer CVS and most of our CVS-related services are provided from one of ten CVS hosts (count subject to increase with growth). Each host is independent, and makes a backup copy of the repository data of another host (which is used to provide the pserver CVS service). Failure of a single host will impact only the availability of data on that host. Since the data is split among a larger number of hosts, the size of data impacted by an individual host outage is substantially smaller, and the time required for us to restore service will be substantially shorter. This rapid architecture change has been made possible specifically using the research we performed for our recent launch of Subversion service. We've applied our best practices, produced a substantial amount of internal documentation, and kept an eye toward maintainability. This effort has allowed us to deploy this new architecture quickly once hardware was received, and will permit us to quickly scale this service horizontally as growth and demand requires. Many other minor improvements have also been made to improve the service offering and make it less trouble-prone. The most important of which are listed above. For a full description of the new service offering, and for information on how to use the services described above, please refer to the site documentation for the CVS service after the service has been launched: https://www.sf.net/docs/E04 Thank you, The SourceForge.net Team . -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: Kai L. <kai...@un...> - 2006-05-05 14:57:35
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Hello Bernd > Did you use excitation function's XML load and save functions? These > should be available (as far as I remember, see also the test programs). yes sure, for the implementation, I could reuse many functions (of the GUI dialogs) for the export of our XML project files. In particular, the XML-load/save-functions of the excitation function are used within the ExperimentDialog class. It was therefore very simple to write XML-structured information prior to simulated data. Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: Bernd S. <ber...@un...> - 2006-05-05 13:59:20
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Kai Ludwig wrote: > Hi Elana, > > as promised yesterday, I've implemented a more > advanced data-export function. It is now > on CVS. > When exporting the data (GUI), you should > use the XML file format (it is the default). > Then, the header of the XML-file includes all > information about the excitation function > and model parameters. The data colomns > are included in XML-style (as in the old > txt-files). Kai, thanks, Did you use excitation function's XML load and save functions? These should be available (as far as I remember, see also the test programs). Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: Kai L. <kai...@un...> - 2006-05-05 13:54:42
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Hi Elana, as promised yesterday, I've implemented a more advanced data-export function. It is now on CVS. When exporting the data (GUI), you should use the XML file format (it is the default). Then, the header of the XML-file includes all information about the excitation function and model parameters. The data colomns are included in XML-style (as in the old txt-files). Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: <ber...@t-...> - 2006-04-08 12:03:22
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Hi all, I have just uploaded to the cvs server improved and revised Experiment classes within the EChem++ hierarchy. Note that (1) you need the latest cvs version of Quantity to compile this code and (2) these classes are far from complete at present. However, if you test them and tell me what interface component you would need, this would help me to find out what's important! Have fun Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: <ber...@t-...> - 2006-02-23 17:03:10
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Hi, I have just downloaded and installed on echem9 the most rcent version of the loki library (cvs version). It has been installed in parallel to the previous (stable) version 0.1.3. Th enew headers and the library are available through the same paths as the previous ones, which have been moved to /usr/lib/libloki-0.1.3 and /usr/include/loki-0.1.3. I needed the new version due to a bug which has been fixed upon my request. The cvs version of EChem++ should not be influenced by this. Once I upload the Experiment hierarchy you might need to use the new loki lib also on your local machines. Best regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: Kai L. <kai...@un...> - 2006-02-08 09:23:59
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Hi All, I've started to introduce a recommended concept for the versioning of libtool libraries, see e.g. http://sourceware.org/autobook/autobook/autobook_91.html Therefore, I've added the line libepp<'NAME_OF_LIB'>_la_LDFLAGS =3D -version-info c:r:a to all the Makefile.am. The combination c:r:a depends on the interface, implementation and compatibility of the library and should be used also within the Doxyfile of each library. Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: Kai L. <kai...@un...> - 2006-01-30 16:50:21
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> OK: > > CV excitation function 0. --> +0.7 --> 0.0 V > > A + e- <=3D> B; b<0>; > > parameters: > c(A)(t=3D0) =3D 0.0 > c(b)(t=3D0) =3D 0.0001 mol/l > > D(A) =3D D(B) =3D 1e-6 cm^2/s > > E0 =3D0.4 V > alpha =3D 0.5 > kh =3D 0.1 cm/s > > that's about it. Ok - the drawing routines were still incorrect. The bug should be fixed now on CVS. Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: Bernd S. <ber...@un...> - 2006-01-30 11:36:13
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Kai Ludwig wrote: > Hello Bernd, > > could you post me the mechanism > and model parameters - I observed > a similar problem last week and > probably fixed it already. > The error occured in the central > drawing routine of the > ModelPlotWidget class - a stable > version should be on CVS. OK: CV excitation function 0. --> +0.7 --> 0.0 V A + e- <=> B; b<0>; parameters: c(A)(t=0) = 0.0 c(b)(t=0) = 0.0001 mol/l D(A) = D(B) = 1e-6 cm^2/s E0 =0.4 V alpha = 0.5 kh = 0.1 cm/s that's about it. Let me know ... Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: Kai L. <kai...@un...> - 2006-01-30 10:47:41
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> Hi, > sorry - still another problem with ModSim-0.1. > I have installed ModSim-0.1 in > /usr/local/src/ModSim/ModSim-0.1 > and > EPP_ICONS to /usr/local/src/ModSim/ModSim-0.1/icons > as well as > EPP_MANUAL to /usr/local/src/ModSim/ModSim-0.1/manual/manual.html > > also > PATH is /usr/local/src/ModSim/ModSim-0.1:/ etc > > Now, if I go to /usr/local/src/ModSim/ModSim-0.1 > and type > > ModSim > > evrything is ok. However, if I want to start the program from some othe= r > location in my directory hierarchy, I get > > % ModSim > couldn't open fontconfigs chosen font with Xft!!! > couldn't open fontconfigs chosen font with Xft!!! > couldn't open fontconfigs chosen font with Xft!!! > couldn't open fontconfigs chosen font with Xft!!! > couldn't open fontconfigs chosen font with Xft!!! > couldn't open fontconfigs chosen font with Xft!!! > couldn't open fontconfigs chosen font with Xft!!! > couldn't open fontconfigs chosen font with Xft!!! > cd ~/echempp ...... ok > ~/echempp/.internals ... ok > ~/echempp/data ... ok > Abort maybe the read/write settings of the EPP_ICONS (/usr/local/src/ModSim/ModSim-0.1/icons) EPP_MANUAL (/usr/local/src/ModSim/ModSim-0.1/manual/manual.html) paths? Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: Kai L. <kai...@un...> - 2006-01-30 10:44:25
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Hello Bernd, could you post me the mechanism and model parameters - I observed a similar problem last week and probably fixed it already. The error occured in the central drawing routine of the ModelPlotWidget class - a stable version should be on CVS. Regards, Kai > Hi, > I encountered another problem with ModSim-0.1: > > If I try to do a simulation and have switched on the dynamic > visualization ofconcentration profiles, I get an error message: > > Tick steo is zero in VtkAxis::setTick() > > and after that: > Curve size mismatch in ModelPlotWidget:plot() > again and again, so that I can only kill the program from the command > line! > > Maybe I should say that I have a case, where at t =3D 0 the concentrati= on > of species A is 0.0. > Maybe that's a problem? > > Regards > Bernd > > -- > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > Bernd Speiser > Institut f"ur Organische Chemie > Auf der Morgenstelle 18 > D-72076 T"ubingen > Germany > phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) > fax: +49-7071-295518 > e-mail: ber...@un... > Internet: http://www.uni-tuebingen.de/speiser > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat= =3D121642 > _______________________________________________ > Echempp-devel mailing list > Ech...@li... > https://lists.sourceforge.net/lists/listinfo/echempp-devel > --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: Bernd S. <ber...@un...> - 2006-01-30 10:27:05
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Hi, sorry - still another problem with ModSim-0.1. I have installed ModSim-0.1 in /usr/local/src/ModSim/ModSim-0.1 and EPP_ICONS to /usr/local/src/ModSim/ModSim-0.1/icons as well as EPP_MANUAL to /usr/local/src/ModSim/ModSim-0.1/manual/manual.html also PATH is /usr/local/src/ModSim/ModSim-0.1:/ etc Now, if I go to /usr/local/src/ModSim/ModSim-0.1 and type > ModSim evrything is ok. However, if I want to start the program from some other location in my directory hierarchy, I get % ModSim couldn't open fontconfigs chosen font with Xft!!! couldn't open fontconfigs chosen font with Xft!!! couldn't open fontconfigs chosen font with Xft!!! couldn't open fontconfigs chosen font with Xft!!! couldn't open fontconfigs chosen font with Xft!!! couldn't open fontconfigs chosen font with Xft!!! couldn't open fontconfigs chosen font with Xft!!! couldn't open fontconfigs chosen font with Xft!!! cd ~/echempp ...... ok ~/echempp/.internals ... ok ~/echempp/data ... ok Abort which is bad ... Some idea? Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: Bernd S. <ber...@un...> - 2006-01-30 10:17:56
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Hi, I encountered another problem with ModSim-0.1: If I try to do a simulation and have switched on the dynamic visualization ofconcentration profiles, I get an error message: Tick steo is zero in VtkAxis::setTick() and after that: Curve size mismatch in ModelPlotWidget:plot() again and again, so that I can only kill the program from the command line! Maybe I should say that I have a case, where at t = 0 the concentration of species A is 0.0. Maybe that's a problem? Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: <ber...@t-...> - 2006-01-28 11:29:55
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Dear all, when presenting ModSim to a guest, I encountered some problems within ModSim, which might be interesting to change. (1) In Ecco, the electron can apparently still only have a positive stoichiometry coefficient. So, I can not write A - e- <=> B. Should weadd some more flexibility? Of course, the determination whether a reaction is oxidation or reduction might become more complex. (2) When defining the model parameters of dissolved species, it is an error to first enter the value 0. for a compound with zero concentration. Later concentrations can be 0.0 without problem. This might be technically necessary, but for the user it is somehow disturbing that the first entry is treated differently. Could one defer the determination of the reference concentration until a non-zero concentration is typed, regardless of which species is this? At the end in any case it must be tested that at least one concentration is non-zero anyway, I guess. (3) not reproducible, so I need more test, but: I could not get dynamic concentration profiles to display on echem3. I'll do another test about this on Monday. Regards Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
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From: Kai L. <kai...@un...> - 2006-01-25 13:55:24
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Hi All, I've just uploaded some changes that enable portable XML-project files for the next ModSim release. Moreover, the error scaling has changed (and is still under construction). Therefore, you'll need an cvs update of at least the GUI and Model modules. Note that after that your old XML-project files won't work any more. Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Mail: kai...@un... |
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From: <ber...@t-...> - 2006-01-22 16:34:37
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Hi all, maybe someone has seen the following problem, which might have to do with the timing problems at start-up that I observed earlier: I'm compiling test programs for the Experiment classes. If link a new executable and call it for the first time, start-up time is much longer than for subsequent calls. Any suggestion? Bernd -- ======================================================================= Bernd Speiser Institut f"ur Organische Chemie Auf der Morgenstelle 18 D-72076 T"ubingen Germany phone: +49-7071-2976205 (office) +49-7071-2976242 (laboratory) fax: +49-7071-295518 e-mail: ber...@un... Internet: http://www.uni-tuebingen.de/speiser ======================================================================= |
