Changes in / [a91710:4c9101]


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  • LinearAlgebra/src/LinearAlgebra/Makefile.am

    ra91710 r4c9101  
    22# Also indentation by a single tab
    33
     4INCLUDES = -I$(top_srcdir)/src
     5
    46AM_LDFLAGS = -ldl
    5 AM_CPPFLAGS = -I$(top_srcdir)/src $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
     7AM_CPPFLAGS = $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
    68
    79LINALGSOURCE = \

  • LinearAlgebra/src/unittests/Makefile.am

    ra91710 r4c9101  
    22# Also indentation by a single tab
    33
     4INCLUDES = -I$(top_srcdir)/src/LinearAlgebra
     5
    46AM_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl
    5 AM_CPPFLAGS = -I$(top_srcdir)/src/LinearAlgebra $(CPPUNIT_CFLAGS) $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
     7AM_CPPFLAGS = $(CPPUNIT_CFLAGS) $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
    68
    79if CONDCPPUNIT
    … …  
    9395        VectorUnitTest.cpp \
    9496        VectorUnitTest.hpp
    95 VectorUnitTest_LDADD = ${GSLLIBS} \
    96         $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS)
     97VectorUnitTest_LDADD = ${GSLLIBS}
    9798
    9899VectorSetUnitTest_SOURCES = UnitTestMain.cpp \

  • configure.ac

    ra91710 r4c9101  
    1313# color-tests: us coloring to indicate success/failure when available
    1414# tar-pax: use newer tar implementation with longer filename (>99 chars)
    15 AM_INIT_AUTOMAKE([dist-bzip2 1.5 parallel-tests color-tests tar-pax subdir-objects])
     15AM_INIT_AUTOMAKE([dist-bzip2 1.5 parallel-tests color-tests tar-pax])
    1616
    1717# Checks for programs.

  • m4/boost.m4

    ra91710 r4c9101  
    11# boost.m4: Locate Boost headers and libraries for autoconf-based projects.
    2 # Copyright (C) 2007-2011, 2014  Benoit Sigoure <tsuna@lrde.epita.fr>
     2# Copyright (C) 2007, 2008, 2009, 2010, 2011  Benoit Sigoure <tsuna@lrde.epita.fr>
    33#
    44# This program is free software: you can redistribute it and/or modify
    … …  
    2323
    2424m4_define([_BOOST_SERIAL], [m4_translit([
    25 # serial 22
     25# serial 16
    2626], [#
    2727], [])])
    … …  
    6060# value of any macro.
    6161m4_define([_BOOST_SED_CPP],
    62 [AC_LANG_PUSH([C++])dnl
    63 AC_LANG_PREPROC_REQUIRE()dnl
     62[AC_LANG_PREPROC_REQUIRE()dnl
    6463AC_REQUIRE([AC_PROG_SED])dnl
    6564AC_LANG_CONFTEST([AC_LANG_SOURCE([[$2]])])
    … …  
    7978  [$4])
    8079rm -rf conftest*
    81 AC_LANG_POP([C++])dnl
    82 ])# _BOOST_SED_CPP
     80])# AC_EGREP_CPP
    8381
    8482
    … …  
    137135    # If the user provided a value to --with-boost, use it and only it.
    138136    case $with_boost in #(
    139       ''|yes) set x '' /opt/local/include /usr/local/include /opt/include \
    140                  /usr/include C:/Boost/include;; #(
     137      ''|yes) set x '' /usr/local/include /usr/include \
     138              /opt/local/include /opt/include \
     139              C:/Boost/include;; #(
    141140      *)      set x "$with_boost/include" "$with_boost";;
    142141    esac
    … …  
    224223])# BOOST_REQUIRE
    225224
    226 
    227225# BOOST_STATIC()
    228226# --------------
    … …  
    231229AC_DEFUN([BOOST_STATIC],
    232230  [AC_ARG_ENABLE([static-boost],
    233      [AS_HELP_STRING([--enable-static-boost],
     231     [AC_HELP_STRING([--enable-static-boost],
    234232               [Prefer the static boost libraries over the shared ones [no]])],
    235233     [enable_static_boost=yes],
    236234     [enable_static_boost=no])])# BOOST_STATIC
    237 
    238235
    239236# BOOST_FIND_HEADER([HEADER-NAME], [ACTION-IF-NOT-FOUND], [ACTION-IF-FOUND])
    … …  
    269266
    270267
    271 # BOOST_FIND_LIBS([COMPONENT-NAME], [CANDIDATE-LIB-NAMES],
    272 #                 [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
    273 #                 [CXX-PROLOGUE])
    274 # --------------------------------------------------------------
    275 # Look for the Boost library COMPONENT-NAME (e.g., `thread', for
    276 # libboost_thread) under the possible CANDIDATE-LIB-NAMES (e.g.,
    277 # "thread_win32 thread").  Check that HEADER-NAME works and check that
    278 # libboost_LIB-NAME can link with the code CXX-TEST.  The optional
    279 # argument CXX-PROLOGUE can be used to include some C++ code before
    280 # the `main' function.
     268# BOOST_FIND_LIB([LIB-NAME], [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
     269#                [CXX-PROLOGUE])
     270# -------------------------------------------------------------------------
     271# Look for the Boost library LIB-NAME (e.g., LIB-NAME = `thread', for
     272# libboost_thread).  Check that HEADER-NAME works and check that
     273# libboost_LIB-NAME can link with the code CXX-TEST.  The optional argument
     274# CXX-PROLOGUE can be used to include some C++ code before the `main'
     275# function.
    281276#
    282277# Invokes BOOST_FIND_HEADER([HEADER-NAME]) (see above).
    … …  
    292287# ...  If you want to make sure you have a specific version of Boost
    293288# (eg, >= 1.33) you *must* invoke BOOST_REQUIRE before this macro.
    294 AC_DEFUN([BOOST_FIND_LIBS],
     289AC_DEFUN([BOOST_FIND_LIB],
    295290[AC_REQUIRE([BOOST_REQUIRE])dnl
    296291AC_REQUIRE([_BOOST_FIND_COMPILER_TAG])dnl
    … …  
    306301AS_VAR_PUSHDEF([Boost_lib_LDPATH], [boost_cv_lib_$1_LDPATH])dnl
    307302AS_VAR_PUSHDEF([Boost_lib_LIBS], [boost_cv_lib_$1_LIBS])dnl
    308 BOOST_FIND_HEADER([$4])
     303BOOST_FIND_HEADER([$3])
    309304boost_save_CPPFLAGS=$CPPFLAGS
    310305CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
     306# Now let's try to find the library.  The algorithm is as follows: first look
     307# for a given library name according to the user's PREFERRED-RT-OPT.  For each
     308# library name, we prefer to use the ones that carry the tag (toolset name).
     309# Each library is searched through the various standard paths were Boost is
     310# usually installed.  If we can't find the standard variants, we try to
     311# enforce -mt (for instance on MacOSX, libboost_threads.dylib doesn't exist
     312# but there's -obviously- libboost_threads-mt.dylib).
    311313AC_CACHE_CHECK([for the Boost $1 library], [Boost_lib],
    312                [_BOOST_FIND_LIBS($@)])
    313 case $Boost_lib in #(
    314   (no) _AC_MSG_LOG_CONFTEST
    315     AC_MSG_ERROR([cannot find the flags to link with Boost $1])
    316     ;;
    317 esac
    318 AC_SUBST(AS_TR_CPP([BOOST_$1_LDFLAGS]), [$Boost_lib_LDFLAGS])dnl
    319 AC_SUBST(AS_TR_CPP([BOOST_$1_LDPATH]), [$Boost_lib_LDPATH])dnl
    320 AC_SUBST([BOOST_LDPATH], [$Boost_lib_LDPATH])dnl
    321 AC_SUBST(AS_TR_CPP([BOOST_$1_LIBS]), [$Boost_lib_LIBS])dnl
    322 CPPFLAGS=$boost_save_CPPFLAGS
    323 AS_VAR_POPDEF([Boost_lib])dnl
    324 AS_VAR_POPDEF([Boost_lib_LDFLAGS])dnl
    325 AS_VAR_POPDEF([Boost_lib_LDPATH])dnl
    326 AS_VAR_POPDEF([Boost_lib_LIBS])dnl
    327 AC_LANG_POP([C++])dnl
    328 fi
    329 ])
    330 
    331 
    332 # BOOST_FIND_LIB([LIB-NAME],
    333 #                [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
    334 #                [CXX-PROLOGUE])
    335 # --------------------------------------------------------------
    336 # Backward compatibility wrapper for BOOST_FIND_LIBS.
    337 AC_DEFUN([BOOST_FIND_LIB],
    338 [BOOST_FIND_LIBS([$1], $@)])
    339 
    340 
    341 # _BOOST_FIND_LIBS([LIB-NAME], [CANDIDATE-LIB-NAMES],
    342 #                 [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
    343 #                 [CXX-PROLOGUE])
    344 # --------------------------------------------------------------
    345 # Real implementation of BOOST_FIND_LIBS: rely on these local macros:
    346 # Boost_lib, Boost_lib_LDFLAGS, Boost_lib_LDPATH, Boost_lib_LIBS
    347 #
    348 # The algorithm is as follows: first look for a given library name
    349 # according to the user's PREFERRED-RT-OPT.  For each library name, we
    350 # prefer to use the ones that carry the tag (toolset name).  Each
    351 # library is searched through the various standard paths were Boost is
    352 # usually installed.  If we can't find the standard variants, we try
    353 # to enforce -mt (for instance on MacOSX, libboost_thread.dylib
    354 # doesn't exist but there's -obviously- libboost_thread-mt.dylib).
    355 AC_DEFUN([_BOOST_FIND_LIBS],
    356 [Boost_lib=no
    357   case "$3" in #(
    358     (mt | mt-) boost_mt=-mt; boost_rtopt=;; #(
    359     (mt* | mt-*) boost_mt=-mt; boost_rtopt=`expr "X$3" : 'Xmt-*\(.*\)'`;; #(
    360     (*) boost_mt=; boost_rtopt=$3;;
     314  [Boost_lib=no
     315  case "$2" in #(
     316    mt | mt-) boost_mt=-mt; boost_rtopt=;; #(
     317    mt* | mt-*) boost_mt=-mt; boost_rtopt=`expr "X$2" : 'Xmt-*\(.*\)'`;; #(
     318    *) boost_mt=; boost_rtopt=$2;;
    361319  esac
    362320  if test $enable_static_boost = yes; then
    … …  
    365323  # Find the proper debug variant depending on what we've been asked to find.
    366324  case $boost_rtopt in #(
    367     (*d*) boost_rt_d=$boost_rtopt;; #(
    368     (*[[sgpn]]*) # Insert the `d' at the right place (in between `sg' and `pn')
     325    *d*) boost_rt_d=$boost_rtopt;; #(
     326    *[[sgpn]]*) # Insert the `d' at the right place (in between `sg' and `pn')
    369327      boost_rt_d=`echo "$boost_rtopt" | sed 's/\(s*g*\)\(p*n*\)/\1\2/'`;; #(
    370     (*) boost_rt_d='-d';;
     328    *) boost_rt_d='-d';;
    371329  esac
    372330  # If the PREFERRED-RT-OPT are not empty, prepend a `-'.
    … …  
    379337  boost_save_ac_objext=$ac_objext
    380338  # Generate the test file.
    381   AC_LANG_CONFTEST([AC_LANG_PROGRAM([#include <$4>
    382 $6], [$5])])
     339  AC_LANG_CONFTEST([AC_LANG_PROGRAM([#include <$3>
     340$5], [$4])])
    383341dnl Optimization hacks: compiling C++ is slow, especially with Boost.  What
    384342dnl we're trying to do here is guess the right combination of link flags
    … …  
    402360  ac_objext=$boost_save_ac_objext
    403361  boost_failed_libs=
    404 # Don't bother to ident the following nested for loops, only the 2
    405 # innermost ones matter.
    406 for boost_lib_ in $2; do
     362# Don't bother to ident the 6 nested for loops, only the 2 innermost ones
     363# matter.
    407364for boost_tag_ in -$boost_cv_lib_tag ''; do
    408365for boost_ver_ in -$boost_cv_lib_version ''; do
    409 for boost_mt_ in $boost_mt -mt ''; do
     366for boost_mt_ in $boost_mt '' -mt; do
    410367for boost_rtopt_ in $boost_rtopt '' -d; do
    411368  for boost_lib in \
    412     boost_$boost_lib_$boost_tag_$boost_mt_$boost_rtopt_$boost_ver_ \
    413     boost_$boost_lib_$boost_tag_$boost_rtopt_$boost_ver_ \
    414     boost_$boost_lib_$boost_tag_$boost_mt_$boost_ver_ \
    415     boost_$boost_lib_$boost_tag_$boost_ver_
     369    boost_$1$boost_tag_$boost_mt_$boost_rtopt_$boost_ver_ \
     370    boost_$1$boost_tag_$boost_rtopt_$boost_ver_ \
     371    boost_$1$boost_tag_$boost_mt_$boost_ver_ \
     372    boost_$1$boost_tag_$boost_ver_
    416373  do
    417374    # Avoid testing twice the same lib
    418375    case $boost_failed_libs in #(
    419       (*@$boost_lib@*) continue;;
     376      *@$boost_lib@*) continue;;
    420377    esac
    421378    # If with_boost is empty, we'll search in /lib first, which is not quite
    … …  
    424381    test x"$with_boost" = x && boost_tmp_lib=${boost_cv_inc_path%/include}
    425382    for boost_ldpath in "$boost_tmp_lib/lib" '' \
    426              /opt/local/lib* /usr/local/lib* /opt/lib* /usr/lib* \
    427              "$with_boost" C:/Boost/lib /lib*
     383             /usr/local/lib* /usr/lib* \
     384             "$with_boost" C:/Boost/lib /lib* \
     385             /opt/local/lib* /opt/lib*
    428386    do
    429       # Don't waste time with directories that don't exist.
    430       if test x"$boost_ldpath" != x && test ! -e "$boost_ldpath"; then
    431         continue
    432       fi
     387      test -e "$boost_ldpath" || continue
    433388      boost_save_LDFLAGS=$LDFLAGS
    434389      # Are we looking for a static library?
    435390      case $boost_ldpath:$boost_rtopt_ in #(
    436         (*?*:*s*) # Yes (Non empty boost_ldpath + s in rt opt)
     391        *?*:*s*) # Yes (Non empty boost_ldpath + s in rt opt)
    437392          Boost_lib_LIBS="$boost_ldpath/lib$boost_lib.$libext"
    438393          test -e "$Boost_lib_LIBS" || continue;; #(
    439         (*) # No: use -lboost_foo to find the shared library.
     394        *) # No: use -lboost_foo to find the shared library.
    440395          Boost_lib_LIBS="-l$boost_lib";;
    441396      esac
    … …  
    451406      LIBS=$boost_save_LIBS
    452407      if test x"$Boost_lib" = xyes; then
    453         # Check or used cached result of whether or not using -R or
    454         # -rpath makes sense.  Some implementations of ld, such as for
    455         # Mac OSX, require -rpath but -R is the flag known to work on
    456         # other systems.  https://github.com/tsuna/boost.m4/issues/19
    457         AC_CACHE_VAL([boost_cv_rpath_link_ldflag],
    458           [case $boost_ldpath in
    459            '') # Nothing to do.
    460              boost_cv_rpath_link_ldflag=
    461              boost_rpath_link_ldflag_found=yes;;
    462            *)
    463             for boost_cv_rpath_link_ldflag in -Wl,-R, -Wl,-rpath,; do
    464               LDFLAGS="$boost_save_LDFLAGS -L$boost_ldpath $boost_cv_rpath_link_ldflag$boost_ldpath"
    465               LIBS="$boost_save_LIBS $Boost_lib_LIBS"
    466               _BOOST_AC_LINK_IFELSE([],
    467                 [boost_rpath_link_ldflag_found=yes
    468                 break],
    469                 [boost_rpath_link_ldflag_found=no])
    470             done
    471             ;;
    472           esac
    473           AS_IF([test "x$boost_rpath_link_ldflag_found" != "xyes"],
    474             [AC_MSG_ERROR([Unable to determine whether to use -R or -rpath])])
    475           LDFLAGS=$boost_save_LDFLAGS
    476           LIBS=$boost_save_LIBS
    477           ])
    478         test x"$boost_ldpath" != x &&
    479           Boost_lib_LDFLAGS="-L$boost_ldpath $boost_cv_rpath_link_ldflag$boost_ldpath"
     408        Boost_lib_LDFLAGS="-L$boost_ldpath -Wl,-R$boost_ldpath"
    480409        Boost_lib_LDPATH="$boost_ldpath"
    481         break 7
     410        break 6
    482411      else
    483412        boost_failed_libs="$boost_failed_libs@$boost_lib@"
    … …  
    489418done
    490419done
    491 done # boost_lib_
    492420rm -f conftest.$ac_objext
    493421])
    494 
     422case $Boost_lib in #(
     423  no) _AC_MSG_LOG_CONFTEST
     424    AC_MSG_ERROR([cannot find the flags to link with Boost $1])
     425    ;;
     426esac
     427AC_SUBST(AS_TR_CPP([BOOST_$1_LDFLAGS]), [$Boost_lib_LDFLAGS])dnl
     428AC_SUBST(AS_TR_CPP([BOOST_$1_LDPATH]), [$Boost_lib_LDPATH])dnl
     429AC_SUBST([BOOST_LDPATH], [$Boost_lib_LDPATH])dnl
     430AC_SUBST(AS_TR_CPP([BOOST_$1_LIBS]), [$Boost_lib_LIBS])dnl
     431CPPFLAGS=$boost_save_CPPFLAGS
     432AS_VAR_POPDEF([Boost_lib])dnl
     433AS_VAR_POPDEF([Boost_lib_LDFLAGS])dnl
     434AS_VAR_POPDEF([Boost_lib_LDPATH])dnl
     435AS_VAR_POPDEF([Boost_lib_LIBS])dnl
     436AC_LANG_POP([C++])dnl
     437fi
     438])# BOOST_FIND_LIB
    495439
    496440
    … …  
    539483BOOST_FIND_HEADER([boost/asio.hpp])])
    540484
    541 
    542485# BOOST_BIMAP()
    543486# ------------
    … …  
    546489[BOOST_FIND_HEADER([boost/bimap.hpp])])
    547490
    548 
    549491# BOOST_BIND()
    550492# ------------
    551 # Look for Boost.Bind.
     493# Look for Boost.Bind
    552494BOOST_DEFUN([Bind],
    553495[BOOST_FIND_HEADER([boost/bind.hpp])])
    554 
    555496
    556497# BOOST_CAST()
    … …  
    559500BOOST_DEFUN([Cast],
    560501[BOOST_FIND_HEADER([boost/cast.hpp])])
    561 
    562 
    563 # BOOST_CHRONO()
    564 # --------------
    565 # Look for Boost.Chrono.
    566 BOOST_DEFUN([Chrono],
    567 [# Do we have to check for Boost.System?  This link-time dependency was
    568 # added as of 1.35.0.  If we have a version <1.35, we must not attempt to
    569 # find Boost.System as it didn't exist by then.
    570 if test $boost_major_version -ge 135; then
    571   BOOST_SYSTEM([$1])
    572 fi # end of the Boost.System check.
    573 boost_filesystem_save_LIBS=$LIBS
    574 boost_filesystem_save_LDFLAGS=$LDFLAGS
    575 m4_pattern_allow([^BOOST_SYSTEM_(LIBS|LDFLAGS)$])dnl
    576 LIBS="$LIBS $BOOST_SYSTEM_LIBS"
    577 LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS"
    578 BOOST_FIND_LIB([chrono], [$1],
    579                 [boost/chrono.hpp],
    580                 [boost::chrono::thread_clock d;])
    581 if test $enable_static_boost = yes && test $boost_major_version -ge 135; then
    582   BOOST_FILESYSTEM_LIBS="$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS"
    583 fi
    584 LIBS=$boost_filesystem_save_LIBS
    585 LDFLAGS=$boost_filesystem_save_LDFLAGS
    586 ])# BOOST_CHRONO
    587 
    588502
    589503# BOOST_CONVERSION()
    … …  
    594508BOOST_FIND_HEADER([boost/lexical_cast.hpp])
    595509])# BOOST_CONVERSION
    596 
    597 
    598 # BOOST_CRC()
    599 # -----------
    600 # Look for Boost.CRC
    601 BOOST_DEFUN([CRC],
    602 [BOOST_FIND_HEADER([boost/crc.hpp])
    603 ])# BOOST_CRC
    604510
    605511
    … …  
    633539# find Boost.System as it didn't exist by then.
    634540if test $boost_major_version -ge 135; then
    635   BOOST_SYSTEM([$1])
     541BOOST_SYSTEM([$1])
    636542fi # end of the Boost.System check.
    637543boost_filesystem_save_LIBS=$LIBS
    … …  
    643549                [boost/filesystem/path.hpp], [boost::filesystem::path p;])
    644550if test $enable_static_boost = yes && test $boost_major_version -ge 135; then
    645   BOOST_FILESYSTEM_LIBS="$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS"
     551    AC_SUBST([BOOST_FILESYSTEM_LIBS], ["$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS"])
    646552fi
    647553LIBS=$boost_filesystem_save_LIBS
    … …  
    650556
    651557
    652 # BOOST_FUSION()
    653 # -----------------
    654 # Look for Boost.Fusion
    655 BOOST_DEFUN([Fusion],
    656 [BOOST_FIND_HEADER([boost/fusion/sequence.hpp])])
    657 
    658 
    659 # BOOST_FLYWEIGHT()
    660 # -----------------
    661 # Look for Boost.Flyweight.
    662 BOOST_DEFUN([Flyweight],
    663 [dnl There's a hidden dependency on pthreads.
    664 AC_REQUIRE([_BOOST_PTHREAD_FLAG])dnl
    665 BOOST_FIND_HEADER([boost/flyweight.hpp])
    666 AC_SUBST([BOOST_FLYWEIGHT_LIBS], [$boost_cv_pthread_flag])
    667 ])
    668 
    669 
    670558# BOOST_FOREACH()
    671559# ---------------
    672 # Look for Boost.Foreach.
     560# Look for Boost.Foreach
    673561BOOST_DEFUN([Foreach],
    674562[BOOST_FIND_HEADER([boost/foreach.hpp])])
    … …  
    677565# BOOST_FORMAT()
    678566# --------------
    679 # Look for Boost.Format.
     567# Look for Boost.Format
    680568# Note: we can't check for boost/format/format_fwd.hpp because the header isn't
    681569# standalone.  It can't be compiled because it triggers the following error:
    … …  
    693581
    694582
    695 # BOOST_GEOMETRY()
     583# BOOST_FUSION()
    696584# ----------------
    697 # Look for Boost.Geometry (new since 1.47.0).
    698 BOOST_DEFUN([Geometry],
    699 [BOOST_FIND_HEADER([boost/geometry.hpp])
    700 ])# BOOST_GEOMETRY
     585# Look for Boost.Fusion
     586BOOST_DEFUN([Fusion],
     587[BOOST_FIND_HEADER([boost/fusion/sequence.hpp])])
    701588
    702589
    … …  
    745632# BOOST_LOG([PREFERRED-RT-OPT])
    746633# -----------------------------
    747 # Look for Boost.Log. For the documentation of PREFERRED-RT-OPT, see the
     634# Look for Boost.Log For the documentation of PREFERRED-RT-OPT, see the
    748635# documentation of BOOST_FIND_LIB above.
    749636BOOST_DEFUN([Log],
    … …  
    756643# BOOST_LOG_SETUP([PREFERRED-RT-OPT])
    757644# -----------------------------------
    758 # Look for Boost.Log. For the documentation of PREFERRED-RT-OPT, see the
     645# Look for Boost.Log For the documentation of PREFERRED-RT-OPT, see the
    759646# documentation of BOOST_FIND_LIB above.
    760647BOOST_DEFUN([Log_Setup],
    761648[AC_REQUIRE([BOOST_LOG])dnl
    762649BOOST_FIND_LIB([log_setup], [$1],
    763     [boost/log/utility/setup/from_settings.hpp],
     650    [boost/log/utility/init/from_settings.hpp],
    764651    [boost::log::basic_settings<char> bs; bs.empty();])
    765652])# BOOST_LOG_SETUP
    … …  
    778665
    779666
    780 # BOOST_MPI([PREFERRED-RT-OPT])
    781 # -------------------------------
    782 # Look for Boost MPI.  For the documentation of PREFERRED-RT-OPT, see the
    783 # documentation of BOOST_FIND_LIB above.  Uses MPICXX variable if it is
    784 # set, otherwise tries CXX
    785 #
    786 BOOST_DEFUN([MPI],
    787 [boost_save_CXX=${CXX}
    788 boost_save_CXXCPP=${CXXCPP}
    789 if test x"${MPICXX}" != x; then
    790   CXX=${MPICXX}
    791   CXXCPP="${MPICXX} -E"
    792 fi
    793 BOOST_FIND_LIB([mpi], [$1],
    794                [boost/mpi.hpp],
    795                [int argc = 0;
    796                 char **argv = 0;
    797                 boost::mpi::environment env(argc,argv);])
    798 CXX=${boost_save_CXX}
    799 CXXCPP=${boost_save_CXXCPP}
    800 ])# BOOST_MPI
    801 
    802 
    803 # BOOST_MPL()
     667# BOOST_MULTIARRAY()
     668# ------------------
     669# Look for Boost.MultiArray
     670BOOST_DEFUN([MultiArray],
     671[BOOST_FIND_HEADER([boost/mpl/list.hpp])])
     672
     673
     674# BOOST_MMPL()
    804675# ------------------
    805676# Look for Boost.MPL
    806677BOOST_DEFUN([MPL],
    807678[BOOST_FIND_HEADER([boost/mpl/for_each.hpp])])
    808 
    809 
    810 # BOOST_MULTIARRAY()
    811 # ------------------
    812 # Look for Boost.MultiArray
    813 BOOST_DEFUN([MultiArray],
    814 [BOOST_FIND_HEADER([boost/multi_array.hpp])])
    815 
    816 
    817 # BOOST_NUMERIC_UBLAS()
    818 # --------------------------
    819 # Look for Boost.NumericUblas (Basic Linear Algebra)
    820 BOOST_DEFUN([Numeric_Ublas],
    821 [BOOST_FIND_HEADER([boost/numeric/ublas/vector.hpp])
    822 ])# BOOST_NUMERIC_UBLAS
    823 
    824679
    825680# BOOST_NUMERIC_CONVERSION()
    … …  
    909764_BOOST_PYTHON_CONFIG([LIBS],      [libs])
    910765m4_pattern_allow([^BOOST_PYTHON_MODULE$])dnl
    911 BOOST_FIND_LIBS([python], [python python3], [$1],
    912                 [boost/python.hpp],
    913                 [], [BOOST_PYTHON_MODULE(empty) {}])
     766BOOST_FIND_LIB([python], [$1],
     767               [boost/python.hpp],
     768               [], [BOOST_PYTHON_MODULE(empty) {}])
    914769CPPFLAGS=$boost_python_save_CPPFLAGS
    915770LDFLAGS=$boost_python_save_LDFLAGS
    … …  
    957812                [boost::signal<void ()> s;])
    958813])# BOOST_SIGNALS
    959 
    960 
    961 # BOOST_SIGNALS2()
    962 # ----------------
    963 # Look for Boost.Signals2 (new since 1.39.0).
    964 BOOST_DEFUN([Signals2],
    965 [BOOST_FIND_HEADER([boost/signals2.hpp])
    966 ])# BOOST_SIGNALS2
    967814
    968815
    … …  
    1017864
    1018865
    1019 # BOOST_THREAD([PREFERRED-RT-OPT])
     866# BOOST_THREADS([PREFERRED-RT-OPT])
    1020867# ---------------------------------
    1021868# Look for Boost.Thread.  For the documentation of PREFERRED-RT-OPT, see the
    1022869# documentation of BOOST_FIND_LIB above.
    1023 BOOST_DEFUN([Thread],
     870# FIXME: Provide an alias "BOOST_THREAD".
     871BOOST_DEFUN([Threads],
    1024872[dnl Having the pthread flag is required at least on GCC3 where
    1025873dnl boost/thread.hpp would complain if we try to compile without
    1026874dnl -pthread on GNU/Linux.
    1027875AC_REQUIRE([_BOOST_PTHREAD_FLAG])dnl
    1028 boost_thread_save_LIBS=$LIBS
    1029 boost_thread_save_LDFLAGS=$LDFLAGS
    1030 boost_thread_save_CPPFLAGS=$CPPFLAGS
    1031 # Link-time dependency from thread to system was added as of 1.49.0.
    1032 if test $boost_major_version -ge 149; then
    1033 BOOST_SYSTEM([$1])
    1034 fi # end of the Boost.System check.
    1035 m4_pattern_allow([^BOOST_SYSTEM_(LIBS|LDFLAGS)$])dnl
    1036 LIBS="$LIBS $BOOST_SYSTEM_LIBS $boost_cv_pthread_flag"
    1037 LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS"
     876boost_threads_save_LIBS=$LIBS
     877boost_threads_save_CPPFLAGS=$CPPFLAGS
     878LIBS="$LIBS $boost_cv_pthread_flag"
     879# Yes, we *need* to put the -pthread thing in CPPFLAGS because with GCC3,
     880# boost/thread.hpp will trigger a #error if -pthread isn't used:
     881#   boost/config/requires_threads.hpp:47:5: #error "Compiler threading support
     882#   is not turned on. Please set the correct command line options for
     883#   threading: -pthread (Linux), -pthreads (Solaris) or -mthreads (Mingw32)"
    1038884CPPFLAGS="$CPPFLAGS $boost_cv_pthread_flag"
    1039 
    1040 # When compiling for the Windows platform, the threads library is named
    1041 # differently.
    1042 case $host_os in
    1043   (*mingw*) boost_thread_lib_ext=_win32;;
    1044 esac
    1045 BOOST_FIND_LIBS([thread], [thread$boost_thread_lib_ext],
    1046                 [$1],
    1047                 [boost/thread.hpp], [boost::thread t; boost::mutex m;])
    1048 
    1049 BOOST_THREAD_LIBS="$BOOST_THREAD_LIBS $BOOST_SYSTEM_LIBS $boost_cv_pthread_flag"
    1050 BOOST_THREAD_LDFLAGS="$BOOST_SYSTEM_LDFLAGS"
     885BOOST_FIND_LIB([thread], [$1],
     886               [boost/thread.hpp], [boost::thread t; boost::mutex m;])
     887BOOST_THREAD_LIBS="$BOOST_THREAD_LIBS $boost_cv_pthread_flag"
    1051888BOOST_CPPFLAGS="$BOOST_CPPFLAGS $boost_cv_pthread_flag"
    1052 LIBS=$boost_thread_save_LIBS
    1053 LDFLAGS=$boost_thread_save_LDFLAGS
    1054 CPPFLAGS=$boost_thread_save_CPPFLAGS
    1055 ])# BOOST_THREAD
    1056 
    1057 AU_ALIAS([BOOST_THREADS], [BOOST_THREAD])
     889LIBS=$boost_threads_save_LIBS
     890CPPFLAGS=$boost_threads_save_CPPFLAGS
     891])# BOOST_THREADS
    1058892
    1059893
    … …  
    1104938
    1105939
    1106 # BOOST_POINTER_CONTAINER()
    1107 # ------------------------
    1108 # Look for Boost.PointerContainer
    1109 BOOST_DEFUN([Pointer_Container],
    1110 [BOOST_FIND_HEADER([boost/ptr_container/ptr_deque.hpp])
    1111 BOOST_FIND_HEADER([boost/ptr_container/ptr_list.hpp])
    1112 BOOST_FIND_HEADER([boost/ptr_container/ptr_vector.hpp])
    1113 BOOST_FIND_HEADER([boost/ptr_container/ptr_array.hpp])
    1114 BOOST_FIND_HEADER([boost/ptr_container/ptr_set.hpp])
    1115 BOOST_FIND_HEADER([boost/ptr_container/ptr_map.hpp])
    1116 ])# BOOST_POINTER_CONTAINER
    1117 
    1118 
    1119940# BOOST_WAVE([PREFERRED-RT-OPT])
    1120941# ------------------------------
    1121942# NOTE: If you intend to use Wave/Spirit with thread support, make sure you
    1122 # call BOOST_THREAD first.
     943# call BOOST_THREADS first.
    1123944# Look for Boost.Wave.  For the documentation of PREFERRED-RT-OPT, see the
    1124945# documentation of BOOST_FIND_LIB above.
    … …  
    1129950boost_wave_save_LDFLAGS=$LDFLAGS
    1130951m4_pattern_allow([^BOOST_((FILE)?SYSTEM|DATE_TIME|THREAD)_(LIBS|LDFLAGS)$])dnl
    1131 LIBS="$LIBS $BOOST_SYSTEM_LIBS $BOOST_FILESYSTEM_LIBS $BOOST_DATE_TIME_LIBS \
     952LIBS="$LIBS $BOOST_SYSTEM_LIBS $BOOST_FILESYSTEM_LIBS $BOOST_DATE_TIME_LIBS\
    1132953$BOOST_THREAD_LIBS"
    1133 LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS $BOOST_FILESYSTEM_LDFLAGS \
     954LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS $BOOST_FILESYSTEM_LDFLAGS\
    1134955$BOOST_DATE_TIME_LDFLAGS $BOOST_THREAD_LDFLAGS"
    1135956BOOST_FIND_LIB([wave], [$1],
    … …  
    1155976# _BOOST_PTHREAD_FLAG()
    1156977# ---------------------
    1157 # Internal helper for BOOST_THREAD.  Computes boost_cv_pthread_flag
    1158 # which must be used in CPPFLAGS and LIBS.
    1159 #
    1160 # Yes, we *need* to put the -pthread thing in CPPFLAGS because with GCC3,
    1161 # boost/thread.hpp will trigger a #error if -pthread isn't used:
    1162 #   boost/config/requires_threads.hpp:47:5: #error "Compiler threading support
    1163 #   is not turned on. Please set the correct command line options for
    1164 #   threading: -pthread (Linux), -pthreads (Solaris) or -mthreads (Mingw32)"
    1165 #
    1166 # Based on ACX_PTHREAD: http://autoconf-archive.cryp.to/acx_pthread.html
     978# Internal helper for BOOST_THREADS.  Based on ACX_PTHREAD:
     979# http://autoconf-archive.cryp.to/acx_pthread.html
    1167980AC_DEFUN([_BOOST_PTHREAD_FLAG],
    1168981[AC_REQUIRE([AC_PROG_CXX])dnl
    … …  
    12321045["defined __GNUC__ && __GNUC__ == $1 && __GNUC_MINOR__ == $2 && !defined __ICC @ gcc$1$2"])dnl
    12331046
    1234 # _BOOST_mingw_test(MAJOR, MINOR)
    1235 # -----------------------------
    1236 # Internal helper for _BOOST_FIND_COMPILER_TAG.
    1237 m4_define([_BOOST_mingw_test],
    1238 ["defined __GNUC__ && __GNUC__ == $1 && __GNUC_MINOR__ == $2 && !defined __ICC && \
    1239   (defined WIN32 || defined WINNT || defined _WIN32 || defined __WIN32 \
    1240          || defined __WIN32__ || defined __WINNT || defined __WINNT__) @ mgw$1$2"])dnl
    1241 
    12421047
    12431048# _BOOST_FIND_COMPILER_TAG()
    … …  
    12671072  # the same defines as GCC's).
    12681073  for i in \
    1269     _BOOST_mingw_test(4,8) \
    1270     _BOOST_gcc_test(4, 8) \
    1271     _BOOST_mingw_test(4,7) \
    1272     _BOOST_gcc_test(4, 7) \
    1273     _BOOST_mingw_test(4,6) \
    12741074    _BOOST_gcc_test(4, 6) \
    1275     _BOOST_mingw_test(4,5) \
    12761075    _BOOST_gcc_test(4, 5) \
    1277     _BOOST_mingw_test(4,4) \
    12781076    _BOOST_gcc_test(4, 4) \
    1279     _BOOST_mingw_test(4,3) \
    12801077    _BOOST_gcc_test(4, 3) \
    1281     _BOOST_mingw_test(4,2) \
    12821078    _BOOST_gcc_test(4, 2) \
    1283     _BOOST_mingw_test(4,1) \
    12841079    _BOOST_gcc_test(4, 1) \
    1285     _BOOST_mingw_test(4,0) \
    12861080    _BOOST_gcc_test(4, 0) \
    12871081    "defined __GNUC__ && __GNUC__ == 3 && !defined __ICC \
    … …  
    13491143AC_DEFUN([_BOOST_GUESS_WHETHER_TO_USE_MT],
    13501144[# Check whether we do better use `mt' even though we weren't ask to.
    1351 AC_LANG_PUSH([C++])dnl
    13521145AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
    13531146#if defined _REENTRANT || defined _MT || defined __MT__
    … …  
    13571150#endif
    13581151]])], [boost_guess_use_mt=:], [boost_guess_use_mt=false])
    1359 AC_LANG_POP([C++])dnl
    13601152])
    13611153
    … …  
    13811173  _AS_ECHO_LOG([re-using the existing conftest.$ac_objext])
    13821174AS_IF([_AC_DO_STDERR($ac_link) && {
    1383         test -z "$ac_[]_AC_LANG_ABBREV[]_werror_flag" ||
    1384         test ! -s conftest.err
     1175        test -z "$ac_[]_AC_LANG_ABBREV[]_werror_flag" ||
     1176        test ! -s conftest.err
    13851177       } && test -s conftest$ac_exeext && {
    1386         test "$cross_compiling" = yes ||
    1387         $as_executable_p conftest$ac_exeext
     1178        test "$cross_compiling" = yes ||
     1179        $as_executable_p conftest$ac_exeext
    13881180dnl FIXME: use AS_TEST_X instead when 2.61 is widespread enough.
    13891181       }],

  • m4/qwt.m4

    ra91710 r4c9101  
    8080  AC_TRY_LINK(
    8181    [#include <qwt_plot.h>],
    82     [QwtPlot * plot = new QwtPlot();],
     82    [QwtPlot * plot = new QwtPlot(QString("Two Curves"));],
    8383    [mol_ac_have_qwt=true])
    8484  AC_LANG_RESTORE

  • src/Actions/ActionQueue.cpp

    ra91710 r4c9101  
    145145      run_thread.sleep(boost::get_system_time() + boost::posix_time::milliseconds(100));
    146146#else
    147       boost::this_thread::sleep_for(boost::chrono::milliseconds(100));
     147      run_thread.sleep_for(100);
    148148#endif
    149149    } catch(boost::thread_interrupted &e) {

  • src/Actions/Action_impl_python.hpp

    ra91710 r4c9101  
    2121#include <boost/preprocessor/punctuation/comma_if.hpp>
    2222#include <boost/preprocessor/punctuation/paren.hpp>
    23 #include <boost/preprocessor/seq/elem.hpp>
    24 #include <boost/preprocessor/seq/size.hpp>
    25 #include <boost/preprocessor/seq/transform.hpp>
    2623
    2724// some derived names: if CATEGORY is not given, we don't prefix with it
    … …  
    5148BOOST_PP_ASSERT_MSG(BOOST_PP_EQUAL(MAXPARAMTYPES, BOOST_PP_SEQ_SIZE(paramdescriptions)),\
    5249  ERROR: There are not the same number of "paramtokens" and "paramdescriptions" in: __FILE__ \
    53 )
    54 #endif
    55 #ifdef paramreferences
    56 BOOST_PP_ASSERT_MSG(BOOST_PP_EQUAL(MAXPARAMTYPES, BOOST_PP_SEQ_SIZE(paramreferences)),\
    57   ERROR: There are not the same number of "paramtokens" and "paramreferences" in: __FILE__ \
    58 )
    59 #endif
    60 
    61 #ifdef paramtypes
    62 BOOST_PP_ASSERT_MSG(BOOST_PP_EQUAL(MAXPARAMTYPES, BOOST_PP_SEQ_SIZE(paramtypes)),\
    63   ERROR: There are not the same number of "paramtokens" and "paramtypes" in: __FILE__ \
    6450)
    6551#endif
    … …  
    9783// print a list of type ref followed, i.e. "int i, double position"
    9884#define type_list(z,n,TYPELIST, VARLIST) \
    99   BOOST_PP_COMMA_IF(n) \
     85  BOOST_PP_COMMA_IF(n)\
    10086  BOOST_PP_SEQ_ELEM(n, TYPELIST) \
    10187  BOOST_PP_SEQ_ELEM(n, VARLIST)
    … …  
    10490#define value_print(z, n, container, prefix) \
    10591  prefix \
    106   BOOST_PP_SEQ_ELEM(n, container) \
    107   .set( \
    108   BOOST_PP_SEQ_ELEM(n, container) \
     92  BOOST_PP_SEQ_ELEM(n, container)\
     93  .set(\
     94  BOOST_PP_SEQ_ELEM(n, container)\
    10995  );
    11096
    … …  
    124110BOOST_PP_CAT( COMMAND, _stringargs)(
    125111#if defined paramtypes
    126 #define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, BOOST_PP_SEQ_TRANSFORM( type2string, ~, paramtypes), paramreferences)
     112#define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, BOOST_PP_SEQ_TRANSFORM( type2string, , paramtypes), paramreferences)
    127113#define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    128114#include BOOST_PP_LOCAL_ITERATE()

  • src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

    ra91710 r4c9101  
    175175        params.executable.get().string()
    176176        );
    177     if (NoJobs != NumberJobs) {
    178       ELOG(1, "Not all jobs were added succesfully.");
    179       return Action::failure;
    180     }
    181177    LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");
    182178

  • src/Actions/unittests/Makefile.am

    ra91710 r4c9101  
    2525
    2626ACTIONLIBS = \
    27         libUnitTest.la \
    28         ../libMolecuilder.la \
    2927        ../libMolecuilderUI.la
    3028if CONDJOBMARKET
    … …  
    3533# note that DummyUI inherits Dialog which depends on boost/file_system ...
    3634
    37 ActionRegistryUnitTest_SOURCES = \
     35ActionRegistryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3836        ../Actions/unittests/ActionRegistryUnitTest.cpp \
    3937        ../Actions/unittests/ActionRegistryUnitTest.hpp \
    … …  
    4240        ../Parameters/unittests/stubs/BoxVectorValidatorStub.cpp \
    4341        ../Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp
    44 ActionRegistryUnitTest_LDADD = ${ACTIONLIBS} \
    45         $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS)
     42ActionRegistryUnitTest_LDADD = ${ACTIONLIBS}
    4643
    47 ActionSequenceUnitTest_SOURCES = \
     44ActionSequenceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4845        ../Actions/unittests/ActionSequenceUnitTest.cpp \
    4946        ../Actions/unittests/ActionSequenceUnitTest.hpp \
    … …  
    5855        $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS)
    5956
    60 AtomsCalculationUnitTest_SOURCES = \
     57AtomsCalculationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6158        ../Actions/unittests/AtomsCalculationUnitTest.cpp \
    6259        ../Actions/unittests/AtomsCalculationUnitTest.hpp
    6360AtomsCalculationUnitTest_LDADD = ${ACTIONLIBS}
    6461
    65 ManipulateAtomsUnitTest_SOURCES = \
     62ManipulateAtomsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6663        ../Actions/unittests/ManipulateAtomsUnitTest.cpp \
    6764        ../Actions/unittests/ManipulateAtomsUnitTest.hpp \

  • src/Analysis/unittests/Makefile.am

    ra91710 r4c9101  
    2828
    2929ANALYSISLIBS = \
    30         libUnitTest.la \
    3130        ../libMolecuilderAnalysis.la \
    3231        ../libMolecuilderUI.la \
    … …  
    4140        $(BOOST_LIB)
    4241
    43 AnalysisBondsUnitTest_SOURCES = \
     42AnalysisBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4443        ../Analysis/unittests/AnalysisBondsUnitTest.cpp \
    4544        ../Analysis/unittests/AnalysisBondsUnitTest.hpp
    4645AnalysisBondsUnitTest_LDADD = ${ANALYSISLIBS}
    4746
    48 AnalysisCorrelationToPointUnitTest_SOURCES = \
     47AnalysisCorrelationToPointUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4948        ../Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp \
    5049        ../Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp
    5150AnalysisCorrelationToPointUnitTest_LDADD = ${ANALYSISLIBS}
    5251
    53 AnalysisCorrelationToSurfaceUnitTest_SOURCES = \
     52AnalysisCorrelationToSurfaceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5453        ../Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp \
    5554        ../Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp
    5655AnalysisCorrelationToSurfaceUnitTest_LDADD = ${ANALYSISLIBS}
    5756
    58 AnalysisPairCorrelationUnitTest_SOURCES = \
     57AnalysisPairCorrelationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5958        ../Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp \
    6059        ../Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp
    6160AnalysisPairCorrelationUnitTest_LDADD = ${ANALYSISLIBS}
    6261
    63 CountBondsUnitTest_SOURCES = \
     62CountBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6463        ../Analysis/unittests/CountBondsUnitTest.cpp \
    6564        ../Analysis/unittests/CountBondsUnitTest.hpp

  • src/Atom/unittests/Makefile.am

    ra91710 r4c9101  
    2121
    2222ATOMTESTLIBS = \
    23         libUnitTest.la \
    24         ../libMolecuilder.la \
    2523        ../libMolecuilderUI.la
    2624ATOMTESTLIBS += \
    … …  
    2927        $(BOOST_LIB)
    3028
    31 AtomObserverUnitTest_SOURCES = \
     29AtomObserverUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3230        ../Atom/unittests/AtomObserverUnitTest.cpp \
    3331        ../Atom/unittests/AtomObserverUnitTest.hpp \
    … …  
    3634AtomObserverUnitTest_LDADD = ${ATOMTESTLIBS}
    3735
    38 CopyAtomsInterfaceUnitTest_SOURCES = \
     36CopyAtomsInterfaceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3937        ../Atom/unittests/CopyAtomsInterfaceUnitTest.cpp \
    4038        ../Atom/unittests/CopyAtomsInterfaceUnitTest.hpp

  • src/Descriptors/unittests/Makefile.am

    ra91710 r4c9101  
    1919
    2020DESCRIPTORLIBS = \
    21         libUnitTest.la \
    22         ../libMolecuilder.la \
    2321        ../libMolecuilderUI.la
    2422if CONDJOBMARKET
    … …  
    3230
    3331
    34 AtomDescriptorUnitTest_SOURCES = \
     32AtomDescriptorUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3533        ../Descriptors/unittests/AtomDescriptorUnitTest.cpp \
    3634        ../Descriptors/unittests/AtomDescriptorUnitTest.hpp
    3735AtomDescriptorUnitTest_LDADD = ${DESCRIPTORLIBS}
    3836
    39 MoleculeDescriptorTest_SOURCES = \
     37MoleculeDescriptorTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4038        ../Descriptors/unittests/MoleculeDescriptorUnitTest.cpp \
    4139        ../Descriptors/unittests/MoleculeDescriptorUnitTest.hpp

  • src/Element/unittests/Makefile.am

    ra91710 r4c9101  
    2222
    2323ELEMENTLIBS = \
    24         libUnitTest.la \
    25         ../libMolecuilder.la \
    2624        ../libMolecuilderElement.la \
    2725        ../libMolecuilderHelpers.la \
    28         $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS) \
    2926        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
    3027        ${CodePatterns_LIBS}
    3128
    32 ElementUnitTest_SOURCES = \
     29ElementUnitTest_SOURCES =   $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3330  ../Element/unittests/ElementUnitTest.cpp \
    3431  ../Element/unittests/ElementUnitTest.hpp
    3532ElementUnitTest_LDADD = $(ELEMENTLIBS)
    3633
    37 IonUnitTest_SOURCES = \
     34IonUnitTest_SOURCES =   $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3835  ../Element/unittests/IonUnitTest.cpp \
    3936  ../Element/unittests/IonUnitTest.hpp
    4037IonUnitTest_LDADD = $(ELEMENTLIBS)
    4138
    42 PeriodentafelUnitTest_SOURCES = \
     39PeriodentafelUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4340        ../Element/unittests/PeriodentafelUnitTest.cpp \
    4441        ../Element/unittests/PeriodentafelUnitTest.hpp

  • src/Filling/unittests/Makefile.am

    ra91710 r4c9101  
    3434
    3535FILLINGLIBS = \
    36         libUnitTest.la \
    37         ../libMolecuilder.la \
    3836        ../libMolecuilderFilling.la \
    39         ../libMolecuilderShapes.la \
    40         ../libMolecuilderUI.la
     37        ../libMolecuilderUI.la \
     38        ../libMolecuilder.la
    4139if CONDJOBMARKET
    4240FILLINGLIBS += \
    … …  
    4846        $(BOOST_LIB)
    4947
    50 ClusterUnitTest_SOURCES = \
     48ClusterUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5149        ../Filling/unittests/ClusterUnitTest.cpp \
    5250        ../Filling/unittests/ClusterUnitTest.hpp
    5351ClusterUnitTest_LDADD = $(FILLINGLIBS)
    5452
    55 FillerUnitTest_SOURCES = \
     53FillerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5654        ../Filling/unittests/FillerUnitTest.cpp \
    5755        ../Filling/unittests/FillerUnitTest.hpp
    5856FillerUnitTest_LDADD = $(FILLINGLIBS)
    5957
    60 IsInsideDomain_FillPredicateUnitTest_SOURCES = \
     58IsInsideDomain_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6159        ../Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp \
    6260        ../Filling/unittests/IsInsideDomain_FillPredicateUnitTest.hpp
    6361IsInsideDomain_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    6462
    65 IsInsideSurface_FillPredicateUnitTest_SOURCES = \
     63IsInsideSurface_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6664        ../Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp \
    6765        ../Filling/unittests/IsInsideSurface_FillPredicateUnitTest.hpp
    6866IsInsideSurface_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    6967
    70 IsValidInDomain_FillPredicateUnitTest_SOURCES = \
     68IsValidInDomain_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7169        ../Filling/unittests/IsValidInDomain_FillPredicateUnitTest.cpp \
    7270        ../Filling/unittests/IsValidInDomain_FillPredicateUnitTest.hpp
    7371IsValidInDomain_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    7472
    75 IsVoidNode_FillPredicateUnitTest_SOURCES = \
     73IsVoidNode_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7674        ../Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp \
    7775        ../Filling/unittests/IsVoidNode_FillPredicateUnitTest.hpp
    7876IsVoidNode_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    7977
    80 Ops_FillPredicateUnitTest_SOURCES = \
     78Ops_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    8179        ../Filling/unittests/Ops_FillPredicateUnitTest.cpp \
    8280        ../Filling/unittests/Ops_FillPredicateUnitTest.hpp

  • src/Fragmentation/Automation/MPQCCommandFragmentController.cpp

    ra91710 r4c9101  
    7474//    job->DoValenceOnly = _DoValenceOnly;
    7575#ifndef HAVE_JOBMARKET
    76     JobId_t id = getAvailableId();
    77     if (id == (JobId_t)JobId::IllegalJob) {
    78       queue.clear();
    79       break;
    80     }
    81     job->setId(id);
     76    job->setId(getAvailableId());
    8277    if (!_executable.empty())
    8378      job->setCommand(_executable);

  • src/Fragmentation/Automation/MPQCFragmentController.cpp

    ra91710 r4c9101  
    6767    job->DoValenceOnly = _DoValenceOnly;
    6868    JobId_t id = getAvailableId();
    69     if (id == (JobId_t)JobId::IllegalJob) {
     69    if (id == FragmentJob::IllegalJob) {
    7070      status = false;
    7171      break;
    … …  
    7474  }
    7575  // add the jobs
    76   if (status)
    77     addJobs(newjobs);
     76  addJobs(newjobs);
    7877  status &= (newjobs.size() != 0);
    7978

  • src/Fragmentation/Automation/Makefile.am

    ra91710 r4c9101  
    4040noinst_LTLIBRARIES += libMolecuilderFragmentationAutomation.la
    4141libMolecuilderFragmentationAutomation_la_includedir = $(includedir)/MoleCuilder/
    42 libMolecuilderFragmentationAutomation_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
     42libMolecuilderFragmentationAutomation_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
    4343libMolecuilderFragmentationAutomation_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    4444libMolecuilderFragmentationAutomation_la_LIBADD = \

  • src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp

    ra91710 r4c9101  
    3232  // convert
    3333  std::vector<T> fragmentData;
    34   SpecificFragmentController::ReceiveResultContainer<T>::ConvertFragmentResultTo(
    35     fragmentresults,
    36     fragmentData);
     34  ConvertFragmentResultTo(fragmentresults, fragmentData);
    3735
    3836  // insert into map
    39   SpecificFragmentController::ReceiveResultContainer<T>::insertResults(
    40     fragmentresults,
    41     fragmentData);
     37  insertResults(fragmentresults, fragmentData);
    4238
    4339  return fragmentData.size();

  • src/Fragmentation/Exporters/unittests/Makefile.am

    ra91710 r4c9101  
    2222
    2323FRAGMENTATIONEXPORTERSLIBS = \
    24         libUnitTest.la \
    25         ../libMolecuilder.la \
    2624        ../libMolecuilderFragmentation.la \
    2725        ${CodePatterns_LIBS} \
    2826        $(BOOST_LIB)
    2927
    30 HydrogenPoolUnitTest_SOURCES = \
     28HydrogenPoolUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3129        ../Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp \
    3230        ../Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.hpp
    … …  
    3533        ${FRAGMENTATIONEXPORTERSLIBS}
    3634       
    37 SaturatedFragmentUnitTest_SOURCES = \
     35SaturatedFragmentUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3836        ../Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp \
    3937        ../Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.hpp
    … …  
    4341        ${FRAGMENTATIONEXPORTERSLIBS}
    4442
    45 SaturationDistanceMaximizerUnitTest_SOURCES = \
     43SaturationDistanceMaximizerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4644        ../Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp \
    4745        ../Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.hpp \

  • src/Fragmentation/Homology/unittests/Makefile.am

    ra91710 r4c9101  
    2525
    2626FRAGMENTATIONHOMOLOGYLIBS = \
    27         libUnitTest.la \
    28         ../libMolecuilder.la \
    2927        ../libMolecuilderFragmentationSetValues.la \
    3028        ../libMolecuilderFragmentation.la \
    … …  
    3533        $(BOOST_LIB)
    3634
    37 FragmentEdgeUnitTest_SOURCES = \
     35FragmentEdgeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3836        ../Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp \
    3937        ../Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp
    4038FragmentEdgeUnitTest_LDADD = ${FRAGMENTATIONHOMOLOGYLIBS}
    4139
    42 FragmentNodeUnitTest_SOURCES = \
     40FragmentNodeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4341        ../Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp \
    4442        ../Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp
    4543FragmentNodeUnitTest_LDADD = ${FRAGMENTATIONHOMOLOGYLIBS}
    4644       
    47 HomologyContainerUnitTest_SOURCES = \
     45HomologyContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4846        ../Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp \
    4947        ../Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp \
    … …  
    5654        $(BOOST_LIB)
    5755
    58 HomologyGraphUnitTest_SOURCES = \
     56HomologyGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5957        ../Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp \
    6058        ../Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp

  • src/Fragmentation/Interfragmenter.cpp

    ra91710 r4c9101  
    136136    // create a lookup specific to this fragment
    137137    atomkeyset_t fragmentmap;
    138     for (candidates_t::const_iterator candidateiter = candidates.begin();
    139         candidateiter != candidates.end(); ++candidateiter) {
    140       const atom * _atom = *candidateiter;
     138    for (candidates_t::const_iterator iter = candidates.begin();
     139        iter != candidates.end(); ++iter) {
     140      const atom * _atom = *iter;
    141141      atomkeyset_t::const_iterator iter = atomkeyset.find(_atom);
    142142      ASSERT( iter != atomkeyset.end(),
    … …  
    153153      const atom *_atom = *candidateiter;
    154154      LOG(3, "DEBUG: Current candidate is " << *_atom << ".");
    155       atomkeyset_t::iterator finditer = fragmentmap.find(_atom);
    156       ASSERT( finditer != fragmentmap.end(),
     155      atomkeyset_t::iterator iter = fragmentmap.find(_atom);
     156      ASSERT( iter != fragmentmap.end(),
    157157          "Interfragmenter::operator() - could not find atom "
    158158          +toString(_atom->getId())+" in fragment specific lookup.");
    159       keysets_t &othersets = finditer->second;
     159      keysets_t &othersets = iter->second;
    160160      keysets_t::iterator otheriter = othersets.begin();
    161161      while (otheriter != othersets.end()) {

  • src/Fragmentation/Summation/Containers/Makefile.am

    ra91710 r4c9101  
    4141noinst_LTLIBRARIES += libMolecuilderFragmentationContainers.la
    4242libMolecuilderFragmentationContainers_la_includedir = $(includedir)/MoleCuilder/
    43 libMolecuilderFragmentationContainers_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
     43libMolecuilderFragmentationContainers_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
    4444libMolecuilderFragmentationContainers_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    4545libMolecuilderFragmentationContainers_la_LIBADD = \

  • src/Fragmentation/Summation/Containers/unittests/Makefile.am

    ra91710 r4c9101  
    1717
    1818FRAGMENTATIONCONTAINERLIBS = \
    19   libUnitTest.la \
    20   ../libMolecuilder.la \
    2119  ../libMolecuilderFragmentationSummation.la \
    2220  $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
    … …  
    2624
    2725MPQCDataUnitTest_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl
    28 MPQCDataUnitTest_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
    29 MPQCDataUnitTest_SOURCES = \
     26MPQCDataUnitTest_CPPFLAGS = ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
     27MPQCDataUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3028  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp \
    3129  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp

  • src/Fragmentation/Summation/Converter/Makefile.am

    ra91710 r4c9101  
    1010noinst_LTLIBRARIES += libMolecuilderFragmentationConverter.la
    1111libMolecuilderFragmentationConverter_la_includedir = $(includedir)/MoleCuilder/
    12 libMolecuilderFragmentationConverter_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     12libMolecuilderFragmentationConverter_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    1313libMolecuilderFragmentationConverter_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    1414libMolecuilderFragmentationConverter_la_LIBADD = \

  • src/Fragmentation/Summation/Makefile.am

    ra91710 r4c9101  
    3434lib_LTLIBRARIES += libMolecuilderFragmentationSummation.la
    3535libMolecuilderFragmentationSummation_la_includedir = $(includedir)/MoleCuilder/
    36 libMolecuilderFragmentationSummation_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     36libMolecuilderFragmentationSummation_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    3737libMolecuilderFragmentationSummation_la_LDFLAGS = -ldl \
    3838        $(BOOST_SERIALIZATION_LDFLAGS) \

  • src/Fragmentation/Summation/SetValues/Makefile.am

    ra91710 r4c9101  
    2222noinst_LTLIBRARIES += libMolecuilderFragmentationSetValues.la
    2323libMolecuilderFragmentationSetValues_la_includedir = $(includedir)/MoleCuilder/
    24 libMolecuilderFragmentationSetValues_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     24libMolecuilderFragmentationSetValues_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    2525libMolecuilderFragmentationSetValues_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    2626libMolecuilderFragmentationSetValues_la_LIBADD = \

  • src/Fragmentation/Summation/SetValues/unittests/Makefile.am

    ra91710 r4c9101  
    3131
    3232FRAGMENTATIONSETVALUESLIBS = \
    33         libUnitTest.la \
    34         ../libMolecuilder.la \
    3533        ../libMolecuilderFragmentationSetValues.la \
    3634        ${CodePatterns_LIBS} \
    3735        $(BOOST_LIB)
    3836
    39 EigenvaluesUnitTest_SOURCES = \
     37EigenvaluesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4038        ../Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp \
    4139        ../Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.hpp
    … …  
    4442        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
    4543
    46 FragmentUnitTest_SOURCES = \
     44FragmentUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4745        ../Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp \
    4846        ../Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.hpp
    … …  
    5149        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
    5250
    53 HistogramUnitTest_SOURCES = \
     51HistogramUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5452        ../Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp \
    5553        ../Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp
    5654HistogramUnitTest_LDADD = ${FRAGMENTATIONSETVALUESLIBS}
    5755
    58 IndexedVectorsUnitTest_SOURCES = \
     56IndexedVectorsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5957        ../Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp \
    6058        ../Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp
    6159IndexedVectorsUnitTest_LDADD = ${FRAGMENTATIONSETVALUESLIBS}
    6260
    63 SamplingGridPropertiesUnitTest_SOURCES = \
     61SamplingGridPropertiesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6462        ../Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp \
    6563        ../Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp
    6664SamplingGridPropertiesUnitTest_LDADD = ${FRAGMENTATIONSETVALUESLIBS}
    6765
    68 SamplingGridUnitTest_SOURCES = \
     66SamplingGridUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6967        ../Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp \
    7068        ../Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp

  • src/Fragmentation/Summation/unittests/Makefile.am

    ra91710 r4c9101  
    3434
    3535FRAGMENTATIONSUMMATIONLIBS = \
    36         libUnitTest.la \
    37         ../libMolecuilder.la \
    3836        ../libMolecuilderFragmentationSummation.la \
    3937        ${CodePatterns_LIBS} \
    … …  
    4139
    4240
    43 IndexSetUnitTest_SOURCES = \
     41IndexSetUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4442        ../Fragmentation/Summation/unittests/IndexSetUnitTest.cpp \
    4543        ../Fragmentation/Summation/unittests/IndexSetUnitTest.hpp
    4644IndexSetUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    4745
    48 IndexSetContainerUnitTest_SOURCES = \
     46IndexSetContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4947        ../Fragmentation/Summation/unittests/IndexSetContainerUnitTest.cpp \
    5048        ../Fragmentation/Summation/unittests/IndexSetContainerUnitTest.hpp
    … …  
    5553        ${FRAGMENTATIONSUMMATIONLIBS}
    5654
    57 OrthogonalSummationUnitTest_SOURCES = \
     55OrthogonalSummationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5856        ../Fragmentation/Summation/unittests/OrthogonalSummationUnitTest.cpp \
    5957        ../Fragmentation/Summation/unittests/OrthogonalSummationUnitTest.hpp \
    … …  
    6260OrthogonalSummationUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    6361
    64 SetValueUnitTest_SOURCES = \
     62SetValueUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6563        ../Fragmentation/Summation/unittests/SetValueUnitTest.cpp \
    6664        ../Fragmentation/Summation/unittests/SetValueUnitTest.hpp \
    … …  
    6967SetValueUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    7068
    71 SetValueMapUnitTest_SOURCES = \
     69SetValueMapUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7270        ../Fragmentation/Summation/unittests/SetValueMapUnitTest.cpp \
    7371        ../Fragmentation/Summation/unittests/SetValueMapUnitTest.hpp
    7472SetValueMapUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    7573
    76 SubsetMapUnitTest_SOURCES = \
     74SubsetMapUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7775        ../Fragmentation/Summation/unittests/SubsetMapUnitTest.cpp \
    7876        ../Fragmentation/Summation/unittests/SubsetMapUnitTest.hpp
    7977SubsetMapUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    8078
    81 SummationUnitTest_SOURCES = \
     79SummationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    8280        ../Fragmentation/Summation/unittests/SummationUnitTest.cpp \
    8381        ../Fragmentation/Summation/unittests/SummationUnitTest.hpp \

  • src/Fragmentation/unittests/Makefile.am

    ra91710 r4c9101  
    1919
    2020FRAGMENTATIONLIBS = \
    21         libUnitTest.la \
    22         ../libMolecuilder.la \
    2321        ../libMolecuilderFragmentation.la \
    2422        ../libMolecuilderFragmentation_KeysetsContainer.la \
    … …  
    2826
    2927
    30 KeySetsContainerUnitTest_SOURCES = \
     28KeySetsContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3129        ../Fragmentation/unittests/KeySetsContainerUnitTest.cpp \
    3230        ../Fragmentation/unittests/KeySetsContainerUnitTest.hpp
    3331KeySetsContainerUnitTest_LDADD = ${FRAGMENTATIONLIBS}
    3432
    35 MatrixContainerUnitTest_SOURCES = \
     33MatrixContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3634        ../Fragmentation/unittests/MatrixContainerUnitTest.cpp \
    3735        ../Fragmentation/unittests/MatrixContainerUnitTest.hpp

  • src/FunctionApproximation/unittests/Makefile.am

    ra91710 r4c9101  
    1919
    2020FUNCTIONAPPROXIMATIONLIBS = \
    21         libUnitTest.la \
    22         ../libMolecuilder.la \
    2321        ../libMolecuilderFunctionApproximation.la \
    2422        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    … …  
    2725        $(BOOST_LIB)
    2826
    29 ExtractorsUnitTest_SOURCES = \
     27ExtractorsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3028        ../FunctionApproximation/unittests/ExtractorsUnitTest.cpp \
    3129        ../FunctionApproximation/unittests/ExtractorsUnitTest.hpp
    … …  
    3432        ${FUNCTIONAPPROXIMATIONLIBS}
    3533
    36 FunctionArgumentUnitTest_SOURCES = \
     34FunctionArgumentUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3735        ../FunctionApproximation/unittests/FunctionArgumentUnitTest.cpp \
    3836        ../FunctionApproximation/unittests/FunctionArgumentUnitTest.hpp

  • src/Graph/unittests/Makefile.am

    ra91710 r4c9101  
    2020
    2121GRAPHLIBS = \
    22         libUnitTest.la \
    23         ../libMolecuilder.la \
    2422        ../libMolecuilderUI.la \
    2523        ../libMolecuilderGraph.la
    … …  
    3432
    3533
    36 AdjacencyListUnitTest_SOURCES = \
     34AdjacencyListUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3735        ../Graph/unittests/AdjacencyListUnitTest.cpp \
    3836        ../Graph/unittests/AdjacencyListUnitTest.hpp
    3937AdjacencyListUnitTest_LDADD = ${ALLLIBS}
    4038
    41 BondGraphUnitTest_SOURCES = \
     39BondGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4240        ../Graph/unittests/BondGraphUnitTest.cpp \
    4341        ../Graph/unittests/BondGraphUnitTest.hpp

  • src/Jobs/Makefile.am

    ra91710 r4c9101  
    5656libMolecuilderJobs_la_includedir = $(includedir)/MoleCuilder/
    5757nobase_libMolecuilderJobs_la_include_HEADERS = $(JOBSHEADER)
    58 libMolecuilderJobs_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
     58libMolecuilderJobs_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
    5959libMolecuilderJobs_la_LDFLAGS = $(AM_LDFLAGS) \
    6060  $(BOOST_IOSTREAMS_LDFLAGS) \

  • src/Jobs/unittests/Makefile.am

    ra91710 r4c9101  
    1717
    1818JOBSLIBS = \
    19         libUnitTest.la \
    20         ../libMolecuilder.la \
    2119        ../libMolecuilderJobs.la \
    2220        ../libMolecuilderFragmentationContainers.la \
    … …  
    2927
    3028MPQCCommandJobUnitTest_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl
    31 MPQCCommandJobUnitTest_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS}
    32 MPQCCommandJobUnitTest_SOURCES = \
     29MPQCCommandJobUnitTest_CPPFLAGS = ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS}
     30MPQCCommandJobUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3331  ../Jobs/unittests/MPQCCommandJobUnitTest.cpp \
    3432  ../Jobs/unittests/MPQCCommandJobUnitTest.hpp

  • src/LinkedCell/unittests/Makefile.am

    ra91710 r4c9101  
    2929
    3030LINKEDCELLLIBS = \
    31         libUnitTest.la \
    32         ../libMolecuilder.la \
    3331        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    3432        ${CodePatterns_LIBS} \
    3533        $(BOOST_LIB)
    3634
    37 linkedcellUnitTest_SOURCES = \
     35linkedcellUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3836        ../LinkedCell/unittests/linkedcellUnitTest.cpp \
    3937        ../LinkedCell/unittests/linkedcellUnitTest.hpp
    … …  
    4846        $(LINKEDCELLLIBS)
    4947
    50 LinkedCellUnitTest_SOURCES = \
     48LinkedCellUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5149        ../LinkedCell/unittests/LinkedCellUnitTest.cpp \
    5250        ../LinkedCell/unittests/LinkedCellUnitTest.hpp \
    … …  
    5654        $(LINKEDCELLLIBS)
    5755
    58 LinkedCell_ControllerUnitTest_SOURCES = \
     56LinkedCell_ControllerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5957        ../LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp \
    6058        ../LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp \
    … …  
    6664        ../LinkedCell/unittests/stubs/WorldTimeStub.cpp \
    6765        stubs/WorldStub.cpp \
    68         ../LinkedCell/PointCloudAdaptor.hpp
     66        ../LinkedCell/PointCloudAdaptor.hpp \
     67        ../Box_BoundaryConditions.cpp \
     68        ../Box_BoundaryConditions.hpp
    6969LinkedCell_ControllerUnitTest_LDADD = \
    70         ../libMolecuilderUI.la \
    71         ../libMolecuilder.la
    72 if CONDJOBMARKET
    73 LinkedCell_ControllerUnitTest_LDADD += \
    74         ../libMolecuilderJobs.la
    75 endif
    76 LinkedCell_ControllerUnitTest_LDADD += \
     70        ../libMolecuilderLinkedCell.la \
    7771        $(LINKEDCELLLIBS)
    7872
    79 LinkedCell_ModelUnitTest_SOURCES = \
     73LinkedCell_ModelUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    8074        ../LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp \
    8175        ../LinkedCell/unittests/LinkedCell_ModelUnitTest.hpp \
    … …  
    9185        $(LINKEDCELLLIBS)
    9286
    93 LinkedCell_ViewUnitTest_SOURCES = \
     87LinkedCell_ViewUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    9488        ../LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp \
    9589        ../LinkedCell/unittests/LinkedCell_ViewUnitTest.hpp \

  • src/Makefile.am

    ra91710 r4c9101  
    1010EXTRA_DIST =
    1111
    12 # libMolecuilder.la requires the libraries listed below
    13 
     12include Actions/Makefile.am
     13include Analysis/Makefile.am
     14include Atom/Makefile.am
     15include Element/Makefile.am
     16include Filling/Makefile.am
     17include Fragmentation/Makefile.am
     18include Fragmentation/Automation/Makefile.am
     19include Fragmentation/Summation/Containers/Makefile.am
     20include Fragmentation/Summation/Converter/Makefile.am
     21include Fragmentation/Summation/Makefile.am
     22include Fragmentation/Summation/SetValues/Makefile.am
     23include FunctionApproximation/Makefile.am
     24include Graph/Makefile.am
    1425include Helpers/Makefile.am
     26include Jobs/Makefile.am
     27
     28if CONDPYTHON
     29include Python/Makefile.am
     30endif
     31
     32include LinkedCell/Makefile.am
     33include Parameters/Makefile.am
     34include Parser/Makefile.am
     35include Potentials/Makefile.am
     36include RandomNumbers/Makefile.am
    1537include Shapes/Makefile.am
    1638include Tesselation/Makefile.am
    17 
    18 # then comes the library itself
     39include UIElements/Makefile.am
    1940
    2041AM_LDFLAGS = -ldl ${BOOST_LDFLAGS} ${CodePatterns_LDFLAGS}
    21 AM_CPPFLAGS = \
    22         -I$(top_srcdir)/src/unittests \
    23         -I$(top_srcdir)/src/Actions \
    24         -I$(top_srcdir)/src/UIElements \
    25         -I$(top_srcdir)/LinearAlgebra/src \
    26         ${BOOST_CPPFLAGS} \
    27         ${CodePatterns_CFLAGS}
    28 
     42AM_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    2943
    3044BONDSOURCE = \
    … …  
    181195  WorldTime.hpp
    182196
    183 lib_LTLIBRARIES += libMolecuilder.la
     197noinst_LTLIBRARIES += libMolecuilder.la
    184198libMolecuilder_la_includedir = $(includedir)/MoleCuilder/
    185199libMolecuilder_la_LDFLAGS = \
    … …  
    191205        libMolecuilderTesselation.la \
    192206        libMolecuilderShapes.la \
    193         libMolecuilderHelpers.la \
    194207        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    195208        ${CodePatterns_LIBS} \
    … …  
    215228## library file (.so).  The library ABI version is defined in configure.ac, so
    216229## that all version information is kept in one place.
    217 libMolecuilder_la_LDFLAGS += -version-info $(MOLECUILDER_SO_VERSION)
     230#libMolecuilder_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
    218231
    219232## The generated configuration header is installed in its own subdirectory of
    … …  
    238251pkgconfig_DATA = $(top_builddir)/MoleCuilder.pc
    239252
    240 # then we compile the remainder of all other libraries, especially
    241 # libMolecuilderUI.la, which requires libMolecuilder.la on install
    242 
    243 include Actions/Makefile.am
    244 include Analysis/Makefile.am
    245 include Atom/Makefile.am
    246 include Element/Makefile.am
    247 include Filling/Makefile.am
    248 include Fragmentation/Makefile.am
    249 include Fragmentation/Automation/Makefile.am
    250 include Fragmentation/Summation/Containers/Makefile.am
    251 include Fragmentation/Summation/Converter/Makefile.am
    252 include Fragmentation/Summation/Makefile.am
    253 include Fragmentation/Summation/SetValues/Makefile.am
    254 include FunctionApproximation/Makefile.am
    255 include Graph/Makefile.am
    256 include Jobs/Makefile.am
    257 
    258 if CONDPYTHON
    259 include Python/Makefile.am
    260 endif
    261 
    262 include LinkedCell/Makefile.am
    263 include Parameters/Makefile.am
    264 include Parser/Makefile.am
    265 include Potentials/Makefile.am
    266 include RandomNumbers/Makefile.am
    267 include UIElements/Makefile.am
     253
     254INCLUDES = \
     255        -I$(top_srcdir)/src/unittests \
     256        -I$(top_srcdir)/src/Actions \
     257        -I$(top_srcdir)/src/UIElements \
     258        -I$(top_srcdir)/LinearAlgebra/src
    268259
    269260bin_PROGRAMS += molecuilder
    … …  
    292283        Actions/GlobalListOfActions.hpp \
    293284        Actions/ActionHistory.hpp
    294 pyMoleCuilder_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS) -I$(PYTHON_INCLUDE_DIR)
     285pyMoleCuilder_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS) -I$(PYTHON_INCLUDE_DIR)
    295286pyMoleCuilder_la_LDFLAGS = -module -avoid-version -shared $(BOOST_PYTHON_LDFLAGS)
    296287pyMoleCuilder_la_LIBADD = \
    … …  
    308299molecuilder_LDFLAGS = \
    309300        $(AM_LDFLAGS) \
    310         $(CodePatterns_LDFLAGS) \
    311301        $(BOOST_FILESYSTEM_LDFLAGS) \
    312302        $(BOOST_PROGRAM_OPTIONS_LDFLAGS) \
    … …  
    317307        builder.cpp \
    318308        builder_init.cpp \
    319         builder_init.hpp \
    320         Python/PythonScripting.hpp
     309        builder_init.hpp
    321310molecuilder_LDADD = \
    322         libMolecuilder.la \
    323311        libMolecuilderUI.la
    324312molecuilder_LDADD += \
     313        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    325314        ${CodePatterns_LIBS} \
    326315        $(BOOST_THREAD_LIBS) \
    … …  
    358347        $(BOOST_THREAD_LDFLAGS)
    359348molecuildergui_LDADD = \
    360         libMolecuilder.la \
    361349        libMolecuilderQtUI.la \
    362350        libMolecuilderUI.la
    363351molecuildergui_LDADD += \
     352        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    364353        ${CodePatterns_LIBS} \
    365354        $(BOOST_THREAD_LIBS) \

  • src/Parameters/Makefile.am

    ra91710 r4c9101  
    3333        Parameters/Parameter_impl.hpp \
    3434        Parameters/ParameterInterface.hpp \
    35         Parameters/StreamOperators.hpp \
    3635        Parameters/Validators/DiscreteValidator.hpp \
    3736        Parameters/Validators/DiscreteValidator_impl.hpp \

  • src/Parameters/unittests/Makefile.am

    ra91710 r4c9101  
    2929
    3030PARAMETERSLIBS = \
    31         libUnitTest.la \
    32         ../libMolecuilder.la \
    3331        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    3432        ${CodePatterns_LIBS} \
    … …  
    3634
    3735
    38 ContinuousValueTest_SOURCES = \
     36ContinuousValueTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3937        ../Parameters/unittests/ContinuousValueTest.cpp \
    4038        ../Parameters/unittests/ContinuousValueTest.hpp \
    … …  
    4947        $(PARAMETERSLIBS)
    5048 
    51 ContinuousParameterTest_SOURCES = \
     49ContinuousParameterTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5250        ../Parameters/unittests/ContinuousParameterTest.cpp \
    5351        ../Parameters/unittests/ContinuousParameterTest.hpp \
    … …  
    6260        $(PARAMETERSLIBS)
    6361 
    64 DiscreteValueTest_SOURCES = \
     62DiscreteValueTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6563        ../Parameters/unittests/DiscreteValueTest.cpp \
    6664        ../Parameters/unittests/DiscreteValueTest.hpp \
    … …  
    7674        $(PARAMETERSLIBS)
    7775
    78 DiscreteParameterTest_SOURCES = \
     76DiscreteParameterTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7977        ../Parameters/unittests/DiscreteParameterTest.cpp \
    8078        ../Parameters/unittests/DiscreteParameterTest.hpp \
    … …  
    9290        $(PARAMETERSLIBS)
    9391
    94 Ops_ValidatorTest_SOURCES = \
     92Ops_ValidatorTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    9593        ../Parameters/unittests/Ops_ValidatorTest.cpp \
    9694        ../Parameters/unittests/Ops_ValidatorTest.hpp \

  • src/Parser/Parameters/unittests/Makefile.am

    ra91710 r4c9101  
    2020
    2121PARSERPARAMETERSLIBS = \
    22         libUnitTest.la \
    23         ../libMolecuilder.la \
    2422        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    2523        ${CodePatterns_LIBS} \
    … …  
    2725
    2826
    29 ParameterStorageUnitTest_SOURCES = \
     27ParameterStorageUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3028        ../Parser/Parameters/unittests/ParameterStorageUnitTest.cpp \
    31         ../Parser/Parameters/unittests/ParameterStorageUnitTest.hpp
     29        ../Parser/Parameters/unittests/ParameterStorageUnitTest.hpp \
     30        ../Parser/Parameters/ParameterStorage.cpp \
     31        ../Parser/Parameters/ParameterStorage.hpp \
     32        ../Parameters/Parameter.hpp \
     33        ../Parameters/Validators/DummyValidator.hpp \
     34        ../Parameters/Validators/RangeValidator.hpp \
     35        ../Parameters/Validators/RangeValidator_impl.hpp \
     36        ../Parameters/Validators/Validator.hpp \
     37        ../Parameters/Value.hpp \
     38        ../Parameters/Value_impl.hpp \
     39        ../Parameters/ValueInterface.hpp
    3240ParameterStorageUnitTest_LDADD = \
    33         ../libMolecuilderParser.la \
    34         $(PARSERPARAMETERSLIBS)
     41        $(PARSERPARAMETERSLIBS)
    3542
    36 StringParameterUnitTest_SOURCES = \
     43StringParameterUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3744        ../Parser/Parameters/unittests/StringParameterUnitTest.cpp \
    38         ../Parser/Parameters/unittests/StringParameterUnitTest.hpp
     45        ../Parser/Parameters/unittests/StringParameterUnitTest.hpp \
     46        ../Parameters/StreamOperators.hpp \
     47        ../Parameters/Validators/DiscreteValidator.hpp \
     48        ../Parameters/Validators/DiscreteValidator_impl.hpp \
     49        ../Parameters/Validators/DummyValidator.hpp \
     50        ../Parameters/Validators/RangeValidator.hpp \
     51        ../Parameters/Validators/RangeValidator_impl.hpp \
     52        ../Parameters/Validators/Validator.hpp \
     53        ../Parameters/Value.hpp \
     54        ../Parameters/Value_impl.hpp \
     55        ../Parameters/Value_string.hpp \
     56        ../Parameters/ValueInterface.hpp
    3957StringParameterUnitTest_LDADD = \
    4058        ../libMolecuilderParameters.la \

  • src/Parser/unittests/Makefile.am

    ra91710 r4c9101  
    3939
    4040PARSERLIBS = \
    41         libUnitTest.la \
    42         ../libMolecuilder.la \
    4341        ../libMolecuilderUI.la
    4442if CONDJOBMARKET
    … …  
    5250
    5351
    54 ParserMpqcUnitTest_SOURCES = \
     52ParserMpqcUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5553        ../Parser/unittests/ParserMpqcUnitTest.cpp \
    5654        ../Parser/unittests/ParserMpqcUnitTest.hpp
    5755ParserMpqcUnitTest_LDADD = ${PARSERLIBS}
    5856
    59 ParserPcpUnitTest_SOURCES = \
     57ParserPcpUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6058        ../Parser/unittests/ParserPcpUnitTest.cpp \
    6159        ../Parser/unittests/ParserPcpUnitTest.hpp
    6260ParserPcpUnitTest_LDADD = ${PARSERLIBS}
    6361
    64 ParserPdbUnitTest_SOURCES = \
     62ParserPdbUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6563        ../Parser/unittests/ParserPdbUnitTest.cpp \
    6664        ../Parser/unittests/ParserPdbUnitTest.hpp
    6765ParserPdbUnitTest_LDADD = ${PARSERLIBS}
    6866
    69 ParserPsi3UnitTest_SOURCES = \
     67ParserPsi3UnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7068        ../Parser/unittests/ParserPsi3UnitTest.cpp \
    7169        ../Parser/unittests/ParserPsi3UnitTest.hpp
    7270ParserPsi3UnitTest_LDADD = ${PARSERLIBS}
    7371
    74 ParserTremoloUnitTest_SOURCES = \
     72ParserTremoloUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7573        ../Parser/unittests/ParserTremoloUnitTest.cpp \
    7674        ../Parser/unittests/ParserTremoloUnitTest.hpp
    7775ParserTremoloUnitTest_LDADD = ${PARSERLIBS}
    7876
    79 ParserTremolo_ElementKeysUnitTest_SOURCES = \
     77ParserTremolo_ElementKeysUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    8078        ../Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp \
    8179        ../Parser/unittests/ParserTremolo_ElementKeysUnitTest.hpp
    8280ParserTremolo_ElementKeysUnitTest_LDADD = ${PARSERLIBS}
    8381
    84 ParserXmlUnitTest_SOURCES = \
     82ParserXmlUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    8583        ../Parser/unittests/ParserXmlUnitTest.cpp \
    8684        ../Parser/unittests/ParserXmlUnitTest.hpp
    8785ParserXmlUnitTest_LDADD = ${PARSERLIBS}
    8886
    89 ParserXyzUnitTest_SOURCES = \
     87ParserXyzUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    9088        ../Parser/unittests/ParserXyzUnitTest.cpp \
    9189        ../Parser/unittests/ParserXyzUnitTest.hpp

  • src/Potentials/Specifics/unittests/Makefile.am

    ra91710 r4c9101  
    3737
    3838POTENTIALSSPECIFICSLIBS = \
    39         libUnitTest.la \
    40         ../libMolecuilder.la \
    4139        ../libMolecuilderPotentials.la \
    4240        ../libMolecuilderFragmentation.la \
    … …  
    5048        $(BOOST_LIB)
    5149
    52 ConstantPotentialUnitTest_SOURCES = \
     50ConstantPotentialUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5351        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp \
    5452        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp
    5553ConstantPotentialUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    5654
    57 FourBodyPotential_ImproperUnitTest_SOURCES = \
     55FourBodyPotential_ImproperUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5856        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp \
    5957        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp
    6058FourBodyPotential_ImproperUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    6159
    62 FourBodyPotential_TorsionUnitTest_SOURCES = \
     60FourBodyPotential_TorsionUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6361        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp \
    6462        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp
    6563FourBodyPotential_TorsionUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    6664
    67 ManyBodyPotential_TersoffUnitTest_SOURCES = \
     65ManyBodyPotential_TersoffUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6866        ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp \
    6967        ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp
    7068ManyBodyPotential_TersoffUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    7169
    72 PairPotential_HarmonicUnitTest_SOURCES = \
     70PairPotential_HarmonicUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7371        ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp \
    7472        ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.hpp
    7573PairPotential_HarmonicUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    7674
    77 PairPotential_LennardJonesUnitTest_SOURCES = \
     75PairPotential_LennardJonesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7876        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp \
    7977        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp
    8078PairPotential_LennardJonesUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    8179
    82 PairPotential_MorseUnitTest_SOURCES = \
     80PairPotential_MorseUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    8381        ../Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp \
    8482        ../Potentials/Specifics/unittests/PairPotential_MorseUnitTest.hpp
    8583PairPotential_MorseUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    8684
    87 ThreeBodyPotential_AngleUnitTest_SOURCES = \
     85ThreeBodyPotential_AngleUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    8886        ../Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp \
    8987        ../Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.hpp

  • src/Potentials/unittests/Makefile.am

    ra91710 r4c9101  
    2222
    2323POTENTIALSLIBS = \
    24         libUnitTest.la \
    25         ../libMolecuilder.la \
    2624        ../libMolecuilderPotentials.la \
    2725        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    … …  
    3028        $(BOOST_LIB)
    3129
    32 CompoundPotentialUnitTest_SOURCES = \
     30CompoundPotentialUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3331        ../Potentials/unittests/CompoundPotentialUnitTest.cpp \
    3432        ../Potentials/unittests/CompoundPotentialUnitTest.hpp
    3533CompoundPotentialUnitTest_LDADD = \
    36         libUnitTest.la \
    3734        ../libMolecuilderPotentials.la \
    3835        ../libMolecuilderFragmentation.la \
    … …  
    4643        $(BOOST_LIB)
    4744
    48 PartialNucleiChargeFitterUnitTest_SOURCES = \
     45PartialNucleiChargeFitterUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4946        ../Potentials/unittests/PartialNucleiChargeFitterUnitTest.cpp \
    5047        ../Potentials/unittests/PartialNucleiChargeFitterUnitTest.hpp
    … …  
    5350        ${POTENTIALSLIBS}
    5451
    55 SerializablePotentialUnitTest_SOURCES = \
     52SerializablePotentialUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5653        ../Potentials/unittests/SerializablePotentialUnitTest.cpp \
    5754        ../Potentials/unittests/SerializablePotentialUnitTest.hpp \

  • src/RandomNumbers/Makefile.am

    ra91710 r4c9101  
    11# PLEASE adhere to the alphabetical ordering in this Makefile!
    22# Also indentation by a single tab
     3
     4#INCLUDES = -I$(top_srcdir)/src
    35
    46# Position-Independent Code necessary for shared library
    … …  
    4042
    4143lib_LTLIBRARIES += libMolecuilderRandomNumbers.la
    42 libMolecuilderRandomNumbers_la_includedir = $(includedir)/MoleCuilder/
    43 libMolecuilderRandomNumbers_la_LIBADD = \
    44         ${CodePatterns_LIBS}
    45 nobase_libMolecuilderRandomNumbers_la_include_HEADERS = ${RANDOMHEADER} ${RANDOMDEFS}
     44libMolecuilderRandomNumbers_includedir = $(includedir)/MoleCuilder/
     45nobase_libMolecuilderRandomNumbers_include_HEADERS = ${RANDOMHEADER} ${RANDOMDEFS}
    4646
    4747## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"

  • src/RandomNumbers/unittests/Makefile.am

    ra91710 r4c9101  
    11# PLEASE adhere to the alphabetical ordering in this Makefile!
    22# Also indentation by a single tab
     3
     4#INCLUDES = -I$(top_srcdir)/src
    35
    46#AM_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl ${BOOST_LDFLAGS}
    … …  
    2830
    2931RANDOMNUMBERLIBS = \
    30         libUnitTest.la \
    31         ../libMolecuilder.la \
    3232        ../libMolecuilderRandomNumbers.la \
    3333        ${CodePatterns_LIBS} \
    3434        $(BOOST_LIB)
    3535
    36 RandomNumberDistributionFactoryUnitTest_SOURCES = \
     36RandomNumberDistributionFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3737        ../RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp \
    3838        ../RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.hpp
    3939RandomNumberDistributionFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    4040
    41 RandomNumberEngineFactoryUnitTest_SOURCES = \
     41RandomNumberEngineFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4242        ../RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp \
    4343        ../RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.hpp
    4444RandomNumberEngineFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    4545
    46 RandomNumberGeneratorFactoryUnitTest_SOURCES = \
     46RandomNumberGeneratorFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4747        ../RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp \
    4848        ../RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp
    4949RandomNumberGeneratorFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    5050
    51 RandomNumberGeneratorUnitTest_SOURCES = \
     51RandomNumberGeneratorUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5252        ../RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp \
    5353        ../RandomNumbers/unittests/RandomNumberGeneratorUnitTest.hpp

  • src/Shapes/Makefile.am

    ra91710 r4c9101  
    2121lib_LTLIBRARIES += libMolecuilderShapes.la
    2222libMolecuilderShapes_la_includedir = $(includedir)/MoleCuilder/
    23 libMolecuilderShapes_la_LIBADD = \
    24         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    25         ${CodePatterns_LIBS}
    2623nobase_libMolecuilderShapes_la_include_HEADERS = ${SHAPEHEADER}
    2724

  • src/Shapes/unittests/Makefile.am

    ra91710 r4c9101  
    2929
    3030SHAPELIBS = \
    31         libUnitTest.la \
    32         ../libMolecuilder.la \
    33         ../libMolecuilderUI.la \
     31        ../libMolecuilderShapes.la \
    3432        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    3533        ${CodePatterns_LIBS}
    3634#       $(BOOST_LIB)
    3735
    38 BaseShapesUnitTest_SOURCES = \
     36BaseShapesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3937        ../Shapes/unittests/BaseShapesUnitTest.cpp \
    4038        ../Shapes/unittests/BaseShapesUnitTest.hpp \
    4139        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    4240        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    43 BaseShapesUnitTest_LDADD = \
    44         ../libMolecuilderShapes.la \
    45         $(SHAPELIBS)
     41nodist_BaseShapesUnitTest_SOURCES = \
     42        ../Helpers/defs.hpp \
     43        ../Helpers/defs.cpp
     44BaseShapesUnitTest_LDADD = $(SHAPELIBS)
    4645
    47 ShapeFactoryUnitTest_SOURCES = \
     46ShapeFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4847        ../Shapes/unittests/ShapeFactoryUnitTest.cpp \
    4948        ../Shapes/unittests/ShapeFactoryUnitTest.hpp \
    … …  
    5251        ../Shapes/unittests/stubs/moleculeStub.cpp \
    5352        ../Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp
     53nodist_ShapeFactoryUnitTest_SOURCES = \
     54        ../Helpers/defs.hpp \
     55        ../Helpers/defs.cpp \
     56        ../Shapes/ShapeFactory.cpp \
     57        ../Shapes/ShapeFactory.hpp
    5458ShapeFactoryUnitTest_LDADD = \
    55         ../libMolecuilderShapes.la \
     59        ../libMolecuilderElement.la \
    5660        $(SHAPELIBS)
    5761
    58 ShapeOpsUnitTest_SOURCES = \
     62ShapeOpsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5963        ../Shapes/unittests/ShapeOpsUnitTest.cpp \
    6064        ../Shapes/unittests/ShapeOpsUnitTest.hpp \
    6165        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    6266        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    63 ShapeOpsUnitTest_LDADD = \
    64         ../libMolecuilderShapes.la \
    65         $(SHAPELIBS)
     67nodist_ShapeOpsUnitTest_SOURCES = \
     68        ../Helpers/defs.hpp \
     69        ../Helpers/defs.cpp
     70ShapeOpsUnitTest_LDADD = $(SHAPELIBS)
    6671
    67 ShapeRegistryUnitTest_SOURCES = \
     72ShapeRegistryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6873        ../Shapes/unittests/ShapeRegistryUnitTest.cpp \
    6974        ../Shapes/unittests/ShapeRegistryUnitTest.hpp \
    7075        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    7176        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    72 ShapeRegistryUnitTest_LDADD = \
    73         ../libMolecuilderShapes.la \
    74         $(SHAPELIBS)
     77nodist_ShapeRegistryUnitTest_SOURCES = \
     78        ../Helpers/defs.hpp \
     79        ../Helpers/defs.cpp
     80ShapeRegistryUnitTest_LDADD = $(SHAPELIBS)
    7581
    76 Shape_HomogeneousPointsUnitTest_SOURCES = \
     82Shape_HomogeneousPointsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7783        ../Shapes/unittests/Shape_HomogeneousPointsUnitTest.cpp \
    7884        ../Shapes/unittests/Shape_HomogeneousPointsUnitTest.hpp \
    7985        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    8086        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    81 Shape_HomogeneousPointsUnitTest_LDADD = \
    82         ../libMolecuilderShapes.la \
    83         $(SHAPELIBS)
     87nodist_Shape_HomogeneousPointsUnitTest_SOURCES = \
     88        ../Helpers/defs.hpp \
     89        ../Helpers/defs.cpp
     90Shape_HomogeneousPointsUnitTest_LDADD = $(SHAPELIBS)
    8491
    8592

  • src/Tesselation/unittests/Makefile.am

    ra91710 r4c9101  
    2222
    2323TESSELATIONLIBS = \
    24         libUnitTest.la \
    25         ../libMolecuilder.la \
    2624        ../libMolecuilderUI.la \
    2725        ../libMolecuilder.la
    … …  
    3634
    3735
    38 TesselationUnitTest_SOURCES = \
     36TesselationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3937        ../Tesselation/unittests/TesselationUnitTest.cpp \
    4038        ../Tesselation/unittests/TesselationUnitTest.hpp
    4139TesselationUnitTest_LDADD = ${TESSELATIONLIBS}
    4240
    43 Tesselation_BoundaryTriangleUnitTest_SOURCES = \
     41Tesselation_BoundaryTriangleUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4442        ../Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp \
    4543        ../Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp
    4644Tesselation_BoundaryTriangleUnitTest_LDADD = ${TESSELATIONLIBS}
    4745
    48 Tesselation_InOutsideUnitTest_SOURCES = \
     46Tesselation_InOutsideUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4947        ../Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp \
    5048        ../Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp

  • src/UIElements/CommandLineUI/unittests/Makefile.am

    ra91710 r4c9101  
    1515noinst_PROGRAMS += $(UIELEMENTSCOMMANDLINEPARSERTESTS)
    1616
    17 CommandLineParser_ActionRegistry_ConsistencyUnitTest_SOURCES = \
     17CommandLineParser_ActionRegistry_ConsistencyUnitTest_SOURCES =  $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    1818  ../UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp \
    1919  ../UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.hpp
    2020CommandLineParser_ActionRegistry_ConsistencyUnitTest_LDADD = \
    21   libUnitTest.la \
    22   ../libMolecuilder.la \
    2321  ../libMolecuilderUI.la
    2422if CONDJOBMARKET

  • src/UIElements/Makefile.am

    ra91710 r4c9101  
    226226lib_LTLIBRARIES += libMolecuilderUI.la
    227227libMolecuilderUI_la_includedir = $(includedir)/MoleCuilder/
    228 libMolecuilderUI_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     228libMolecuilderUI_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    229229if CONDJOBMARKET
    230230libMolecuilderUI_la_CPPFLAGS += ${JobMarket_CFLAGS}
    … …  
    344344
    345345libMolecuilderQtUI_la_includedir = $(includedir)/MoleCuilder/
    346 libMolecuilderQtUI_la_CPPFLAGS = $(AM_CPPFLAGS) ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
     346libMolecuilderQtUI_la_CPPFLAGS = ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
    347347libMolecuilderQtUI_la_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS) $(mol_ac_qwt_ldflags)
    348348

  • src/UIElements/Menu/unittests/Makefile.am

    ra91710 r4c9101  
    1919
    2020MENULIBS = \
    21   libUnitTest.la \
    22   ../libMolecuilder.la \
    2321  ../libMolecuilderUI.la
    2422if CONDJOBMARKET
    … …  
    3129  $(BOOST_LIB)
    3230
    33 MenuDescriptionUnitTest_SOURCES = \
     31MenuDescriptionUnitTest_SOURCES =  $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3432  ../UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp \
    35   ../UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp
     33  ../UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp \
     34  ../UIElements/Menu/MenuDescription.cpp \
     35  ../UIElements/Menu/MenuDescription.hpp
    3636MenuDescriptionUnitTest_CXXFLAGS = -I$(top_srcdir)/src/UIElements
    3737MenuDescriptionUnitTest_LDADD = $(MENULIBS)
    3838
    39 MenuDescription_ActionRegistry_ConsistencyUnitTest_SOURCES = \
     39MenuDescription_ActionRegistry_ConsistencyUnitTest_SOURCES =  $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4040  ../UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp \
    4141  ../UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp

  • src/UIElements/Views/Qt4/Plotting/Makefile.am

    ra91710 r4c9101  
    3737
    3838libMolecuilderQwtUI_la_includedir = $(includedir)/MoleCuilder/
    39 libMolecuilderQwtUI_la_CPPFLAGS = $(AM_CPPFLAGS) ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
     39libMolecuilderQwtUI_la_CPPFLAGS = ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
    4040libMolecuilderQwtUI_la_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS) $(mol_ac_qwt_ldflags)
    4141

  • src/builder_init.cpp

    ra91710 r4c9101  
    5454#include "CodePatterns/Log.hpp"
    5555
    56 //#include "Graph/BondGraph.hpp"
     56#include "Graph/BondGraph.hpp"
     57
     58#include "Parser/ChangeTracker.hpp"
     59#include "Parser/FormatParserStorage.hpp"
    5760
    5861#include "UIElements/UIFactory.hpp"
    … …  
    6669
    6770#include "version.h"
     71
     72#include "World.hpp"
    6873
    6974#include <boost/filesystem.hpp>
    … …  
    111116void initUI(int argc, char **argv)
    112117{
    113   //std::string BondGraphFileName("\n");
     118  std::string BondGraphFileName("\n");
    114119  // Parse command line options and if present create respective UI
    115120  // construct bond graph
    116   //if (boost::filesystem::exists(BondGraphFileName)) {
    117   //  std::ifstream input(BondGraphFileName.c_str());
    118   //  if ((input.good()) && (World::getInstance().getBondGraph()->LoadBondLengthTable(input))) {
    119   //    LOG(0, "Bond length table loaded successfully.");
    120   //  } else {
    121   //    ELOG(1, "Bond length table loading failed.");
    122   //  }
    123   //  input.close();
    124   //}
     121  if (boost::filesystem::exists(BondGraphFileName)) {
     122    std::ifstream input(BondGraphFileName.c_str());
     123    if ((input.good()) && (World::getInstance().getBondGraph()->LoadBondLengthTable(input))) {
     124      LOG(0, "Bond length table loaded successfully.");
     125    } else {
     126      ELOG(1, "Bond length table loading failed.");
     127    }
     128    input.close();
     129  }
    125130
    126131  // if we have python, autoexecute a molecuilder script in current folder

  • src/documentation/install.dox

    ra91710 r4c9101  
    6464 *  -# autotools: autoconf automake autoheader autoconf libtool
    6565 *
    66  *      Under Ubuntu 14.04 the required packages remain the same but the following
    67  *  notes apply:
    68  *  -# boost must be at least 1.50 as there is some bug with recognizing
    69  *     pthreads with the new gcc version.
    70  *  -# no need to compile VTK on your own, just use the VTK-5.8 that comes with
    71  *     this Ubuntu version.
    72  *  -# note that prior to 1.4.7 Ubuntu 14.04 is not supported and requires some
    73  *     changes in the automake/autoconf parts.
    74  *
    7566 * \subsection install-prerequisites-other Other packages
    7667 *
    … …  
    342333 *  from a distributed archive. This is checked for each release version.
    343334 *
    344  * \date 2014-08-21
     335 * \date 2014-03-10
    345336 */

  • src/unittests/Makefile.am

    ra91710 r4c9101  
    77XFAIL_TESTS =
    88MOSTLYCLEANFILES =
    9 noinst_LTLIBRARIES =
    10 
    11 #AUTOMAKE_OPTIONS = no-dependencies
    129
    1310if CONDCPPUNIT
    … …  
    4340include ../../src/UIElements/Menu/unittests/Makefile.am
    4441
     42INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/LinearAlgebra/src
     43
    4544AM_LDFLAGS = \
    4645        ${CodePatterns_LIBS} \
    4746        $(CPPUNIT_LIBS) \
    4847        -ldl
    49 AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/LinearAlgebra/src ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
     48AM_CPPFLAGS = ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
    5049
    5150GENERALTESTS = \
    … …  
    6968endif
    7069
    71 noinst_LTLIBRARIES += libUnitTest.la
    72 libUnitTest_la_LDFLAGS = \
    73         $(AM_LDFLAGS)
    74 libUnitTest_la_LIBADD =
    75 
    76 #nobase_libUnitTest_la_include_HEADERS =
    77 
    78 ## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
    79 ## target.  Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
    80 ## will therefore be treated as if it were literally part of the target name,
    81 ## and the variable name derived from that.
    82 ## The file extension .cc is recognized by Automake, and makes it produce
    83 ## rules which invoke the C++ compiler to produce a libtool object file (.lo)
    84 ## from each source file.  Note that it is not necessary to list header files
    85 ## which are already listed elsewhere in a _HEADERS variable assignment.
    86 libUnitTest_la_SOURCES = UnitTestMain.cpp
    87 
    88 ## Instruct libtool to include ABI version information in the generated shared
    89 ## library file (.so).  The library ABI version is defined in configure.ac, so
    90 ## that all version information is kept in one place.
    91 #libUnitTest_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
    92 
    93 ## The generated configuration header is installed in its own subdirectory of
    94 ## $(libdir).  The reason for this is that the configuration information put
    95 ## into this header file describes the target platform the installed library
    96 ## has been built for.  Thus the file must not be installed into a location
    97 ## intended for architecture-independent files, as defined by the Filesystem
    98 ## Hierarchy Standard (FHS).
    99 ## The nodist_ prefix instructs Automake to not generate rules for including
    100 ## the listed files in the distribution on 'make dist'.  Files that are listed
    101 ## in _HEADERS variables are normally included in the distribution, but the
    102 ## configuration header file is generated at configure time and should not be
    103 ## shipped with the source tarball.
    104 #libUnitTest_la_libincludedir = $(libdir)/MoleCuilder/include
    105 #nodist_libUnitTest_la_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
    106 
    107 ## Install the generated pkg-config file (.pc) into the expected location for
    108 ## architecture-dependent package configuration information.  Occasionally,
    109 ## pkg-config files are also used for architecture-independent data packages,
    110 ## in which case the correct install location would be $(datadir)/pkgconfig.
    111 #pkgconfigdir = $(libdir)/pkgconfig
    112 #pkgconfig_DATA = $(top_builddir)/MoleCuilder.pc
    113 
    11470
    11571BOOST_LIB = \
    … …  
    12783
    12884ALLLIBS = \
    129         libUnitTest.la \
    130         ../libMolecuilder.la \
    13185        ../libMolecuilderUI.la
    13286if CONDJOBMARKET
    … …  
    192146 
    193147
    194 BoxUnitTest_SOURCES = \
     148BoxUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    195149        BoxUnitTest.cpp \
    196150        BoxUnitTest.hpp \
    … …  
    200154        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    201155BoxUnitTest_LDADD = \
    202         $(ALLLIBS) \
     156        ../libMolecuilder.la \
    203157        ../libMolecuilderShapes.la \
    204         ../libMolecuilderHelpers.la
    205 
    206 AtomIdSetUnitTest_SOURCES = \
     158        ../libMolecuilderHelpers.la \
     159        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
     160        ${CodePatterns_LIBS} \
     161        $(BOOST_LIB)
     162
     163AtomIdSetUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    207164        AtomIdSetUnitTest.cpp \
    208165        AtomIdSetUnitTest.hpp
    209166AtomIdSetUnitTest_LDADD =  $(ALLLIBS)
    210167
    211 Box_BoundaryConditionsTest_SOURCES = \
     168Box_BoundaryConditionsTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    212169        Box_BoundaryConditionsUnitTest.cpp \
    213         Box_BoundaryConditionsUnitTest.hpp
     170        Box_BoundaryConditionsUnitTest.hpp \
     171        ../Box_BoundaryConditions.cpp \
     172        ../Box_BoundaryConditions.hpp
    214173Box_BoundaryConditionsTest_LDADD = \
    215         $(ALLLIBS) \
    216         ../libMolecuilderShapes.la \
    217         ../libMolecuilderHelpers.la
    218 
    219 FormulaUnittest_SOURCES = \
     174        ${CodePatterns_LIBS} \
     175        $(BOOST_LIB)
     176
     177FormulaUnittest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    220178        FormulaUnitTest.cpp \
    221179        FormulaUnitTest.hpp
    222180FormulaUnittest_LDADD = $(ALLLIBS)
    223181
    224 ListOfBondsUnitTest_SOURCES = \
     182ListOfBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    225183        ListOfBondsUnitTest.cpp \
    226184        ListOfBondsUnitTest.hpp
    227185ListOfBondsUnitTest_LDADD = $(ALLLIBS)
    228186
    229 MoleculeUnitTest_SOURCES = \
     187MoleculeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    230188        MoleculeUnitTest.cpp \
    231189        MoleculeUnitTest.hpp
    … …  
    235193        ../libMolecuilderHelpers.la
    236194
    237 WorldTimeUnitTest_SOURCES = \
     195WorldTimeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    238196        WorldTimeUnitTest.cpp \
    239         WorldTimeUnitTest.hpp
    240 WorldTimeUnitTest_LDADD = \
    241         $(ALLLIBS) \
    242         ../libMolecuilderShapes.la \
    243         ../libMolecuilderHelpers.la
     197        WorldTimeUnitTest.hpp \
     198        ../WorldTime.cpp \
     199        ../WorldTime.hpp
     200WorldTimeUnitTest_LDADD = ${BOOST_LIB}
    244201
    245202

  • tests/JobMarket/Makefile.am

    ra91710 r4c9101  
    22
    33if CONDJOBMARKET
    4 mpqc_SOURCES = mpqc.cpp
    5 mpqc_CPPFLAGS = $(AM_CPPFLAGS) ${CodePatterns_CFLAGS} $(BOOST_CPPFLAGS)
     4mpqc_SOURCES = $(srcdir)/mpqc.cpp
     5mpqc_CPPFLAGS = ${CodePatterns_CFLAGS} $(BOOST_CPPFLAGS)
    66mpqc_LDADD = \
    77        ${CodePatterns_LIBS}
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