You should "make install" before attempting to use Open Babel. You can do this locally if you configure CMake with "-DCMAKE_INSTALL_PREFIX=/home/user/whatever", and then set LD_LIBRARY_PATH appropriately.
- Noel On 24 May 2011 11:02, Jaap Kroes <jaap.kr...@epfl.ch> wrote: > Dear prof. Hutchison, > > Thank you for your response. > I have tried to add a new format following > http://openbabel.org/docs/2.3.0/WritePlugins/AddFileFormat.html > But I am stuck with perhaps a stupid question, the format is compiled but > somehow not recognized. > build$ make | grep qweformat > Scanning dependencies of target qweformat > Building CXX object src/formats/CMakeFiles/qweformat.dir/qweformat.o > Linking CXX shared module ../../lib/qweformat.so > [100%] Built target qweformat > build$ touch test.qwe > build$ bin/babel test.qwe test.xyz > ============================== > *** Open Babel Error in OpenAndSetFormat > Cannot read input format ".qwe" for file "test.qwe" > 0 molecules converted > 1 errors > Even though I have registered the format I think (in > src/formats/qweformat.cpp) > OBConversion::RegisterFormat("qwe",this); > And added a line with "qweformat" for cmake to src/formats/CMakeLists.txt. > The point where it goes wrong is "src/obconversion.cpp, line 1450" > pInFormat = FormatFromExt(InFilename.c_str()); > Which returns NULL because the extension ".qwe" is apparently still not > recognized. > > Is there another place where I have to 'register' the format? > > Many thanks, > Jaap > > On 23 May 2011 16:03, Geoffrey Hutchison <geo...@pitt.edu> wrote: >> >> > However, I would like to be able to plot forces from an external >> > calculation (e.g. some other geometry optimisation or perhaps some >> > molecular >> > dynamics run). >> >> Several file formats already support this. The code lives in Open Babel, >> which is responsible for reading/writing files for Avogadro. >> >> > Ideally I would take some file with atoms and forces, perhaps like the >> > xyz-format, for example for benzene (CPMD output in a.u.) >> >> I'm currently adding support for more solid-state computational codes to >> Open Babel (e.g., Abinit). Several others (VASP, DMol3) already exist. If >> you can send me some CPMD or other formats, I'll see what I can do -- >> supporting coordinates and forces is easy. >> >> > Then after opening the file with Avogadro I would select forces and the >> > forces arrows would appear! >> > I would like to be able to choose a color and scale for the arrows. >> >> Color should already be an option, but scale is a good idea. Right now, >> it's part of the vibration code, but it would be easy to add to the force >> display too. >> >> > + Could someone point me in the right direction for adding this >> > feature? >> > Perhaps commenting on the best (/easiest) way to implement this. >> >> Well, if you want to add it yourself, all you need to do is write a new >> format for Open Babel and add OBConformerData, which stores forces and other >> things for each coordinate "frame." >> >> Hope that helps, >> -Geoff >> >> --- >> Prof. Geoffrey Hutchison >> Assistant Professor, Department of Chemistry >> University of Pittsburgh >> http://hutchison.chem.pitt.edu/ >> Office: (412) 648-0492 >> > > > ------------------------------------------------------------------------------ > vRanger cuts backup time in half-while increasing security. > With the market-leading solution for virtual backup and recovery, > you get blazing-fast, flexible, and affordable data protection. > Download your free trial now. > http://p.sf.net/sfu/quest-d2dcopy1 > _______________________________________________ > Avogadro-Discuss mailing list > Avogadro-Discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > ------------------------------------------------------------------------------ vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
