US3 SOMO notes

• checkout: svn co ​svn+ssh://username@bcf2.uthscsa.edu/us3_somo/trunk us3_somo
• to compile

  $ cd us3_somo/develop
  $ qmake libus_somo.pro
  $ make
  $ qmake us_somo.pro
  $ make
  

• REVISION is in us3_somo/develop/include/us_revision.h and is NOT the same as the subversion reported revision
• on windows
  • assuming installed in /cygdrive/c/Users/Admin/Documents/us3_somo/
    • extra/windev/copytodist.sh contains the appropriate install bits after compiling
• on OSX
  • needs us3_somo app link to desktop (?) or app bar (?)
  • icons are in etc/us3_somo.icns

• this is "alpha" until all testers approve

• compiler warnings
  • you may get some
  • expect these:

    src/us_hydrodyn_pdb_tool.cpp: In member function 'double US_Hydrodyn_Pdb_Tool::minimum_pair_distance(Q3ListView*, QString, QString, QString&, QString&)':
    src/us_hydrodyn_pdb_tool.cpp:6186:30: warning: 'min_lvp.lvipair::lvi1' may be used uninitialized in this function [-Wuninitialized]
    src/us_hydrodyn_pdb_tool.cpp:6187:30: warning: 'min_lvp.lvipair::lvi2' may be used uninitialized in this function [-Wuninitialized]
    ^^^ this is not true, the compiler is wrong, it can not logically be used uninitialized ^^^
    

    src/us_pm_objects.cpp:903:11: warning: variable 'theta' set but not used [-Wunused-but-set-variable]
        double theta;
    ^^^ this is a work in progress and it will stay until I finish the code ^^^
    

src/../include/us_pfortran.h:4095:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       return *(LONG*)&af == *(LONG*)&bf;
                       ^
src/../include/us_pfortran.h:4095:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       return *(LONG*)&af == *(LONG*)&bf;
                                      ^
src/../include/us_pfortran.h: In function 'int zeno::fifnef(float, float)':
src/../include/us_pfortran.h:4852:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       return *(LONG*)&af != *(LONG*)&bf;
                       ^
src/../include/us_pfortran.h:4852:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       return *(LONG*)&af != *(LONG*)&bf;
^^^ don't know what to do about this as it is part of the fortran to c support code ^^^

maybe a bunch like this...
src/us_hydrodyn_other.cpp:6267: warning: format not a string literal and no format arguments
^^^
a lot of these are format strings that are strings (i.e. can change based upon settings) not prespecified "%.4f" strings etc.
would have to be rewritten