diff --git a/configure b/configure
index f6abe64159..128d64be35 100755
--- a/configure
+++ b/configure
@@ -2402,7 +2402,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
 # PLUMED_SEARCH_LIBS(function,search-libs[,action-if-found][,action-if-not-found][,other-libraries])
-# same as AC_SEARCH_LIBS, but does not try any library unless $libsearch==true
+# same as AC_SEARCH_LIBS, but does not try any library unless $libsearch=true
 # Should be used instead of AC_SEARCH_LIBS in order to make --disable-libsearch work correctly
 
 
@@ -2429,10 +2429,10 @@ rm -f src/*.on src/*.off
 if test "${enable_modules+set}" = set; then :
   enableval=$enable_modules;
    rm -f src/*.on src/*.off
-   if test "${enableval}" == yes ; then
+   if test "${enableval}" = yes ; then
      enableval=reset
    fi
-   if test "${enableval}" == no ; then
+   if test "${enableval}" = no ; then
      enableval=none
    fi
    for modules_mod in `echo "${enableval}" | sed 's/:/ /g' | sed 's/+/ +/g' | sed 's/-/ -/g'`
@@ -3303,7 +3303,7 @@ case `(uname)` in
 esac
 
 # if searching for MPI, try first mpi-like compilers
-if test $mpi == true ; then
+if test $mpi = true ; then
 compilers="mpic++ mpicxx mpiicpc openmpic++ openmpicxx $compilers"
 fi
 
@@ -4413,7 +4413,7 @@ $as_echo "$as_me: Initial LDSHARED:    $LDSHARED" >&6;}
 $as_echo "$as_me: Initial SOEXT:       $SOEXT" >&6;}
 
 # check C++ flags
-if test $shared == true
+if test $shared = true
 then
 
 
@@ -4523,7 +4523,7 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 fi
 
-if test $basic_warnings == true
+if test $basic_warnings = true
 then
 
   save_CXXFLAGS="$CXXFLAGS"
@@ -4665,7 +4665,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
 fi
 
-if test $debug == true
+if test $debug = true
 then
 
   save_CXXFLAGS="$CXXFLAGS"
@@ -4715,7 +4715,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
 fi
 
-if test $gcov == true
+if test $gcov = true
 then
   CXX="$CXX --coverage"
   LDSHARED="$LDSHARED --coverage"
@@ -4749,7 +4749,7 @@ rm -f core conftest.err conftest.$ac_objext \
   STATIC_LIBS="$STATIC_LIBS --coverage"
 fi
 
-if test $fussy == true
+if test $fussy = true
 then
 
   save_CXXFLAGS="$CXXFLAGS"
@@ -5771,7 +5771,7 @@ lapack_found=
 
 # external lapack can only work with external blas
 # thus, if external blas are disabled also external lapack should be disabled
-if test "$external_blas" == false && test "$external_lapack" == true ; then
+if test "$external_blas" = false && test "$external_lapack" = true ; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: Internal blas can only be used with internal lapack" >&5
 $as_echo "$as_me: Internal blas can only be used with internal lapack" >&6;}
   { $as_echo "$as_me:${as_lineno-$LINENO}: Will not search for external lapack" >&5
@@ -5780,7 +5780,7 @@ $as_echo "$as_me: Will not search for external lapack" >&6;}
 fi
 
 # first look for blas
-if test "$external_blas" == true ; then
+if test "$external_blas" = true ; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether dgemv can be linked with no library" >&5
 $as_echo_n "checking whether dgemv can be linked with no library... " >&6; }
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -5842,7 +5842,7 @@ else
       { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
 $as_echo "no" >&6; }
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv" >&5
 $as_echo_n "checking for library containing dgemv... " >&6; }
 if ${ac_cv_search_dgemv+:} false; then :
@@ -5900,7 +5900,7 @@ if test "$ac_res" != no; then :
 else
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv_" >&5
 $as_echo_n "checking for library containing dgemv_... " >&6; }
 if ${ac_cv_search_dgemv_+:} false; then :
@@ -6077,7 +6077,7 @@ if test "$ac_res" != no; then :
 else
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv_" >&5
 $as_echo_n "checking for library containing dgemv_... " >&6; }
 if ${ac_cv_search_dgemv_+:} false; then :
@@ -6220,14 +6220,14 @@ if test -n "$blas_found" ; then
 $as_echo "#define __PLUMED_HAS_EXTERNAL_BLAS 1" >>confdefs.h
 
 
-if test "$external_lapack" == true ; then
+if test "$external_lapack" = true ; then
 # Then we look for lapack using same underscoring
 case "$blas_found" in
 (underscore) search_for=dsyevr_ ;;
 (nounderscore) search_for=dsyevr ;;
 esac
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     as_ac_Search=`$as_echo "ac_cv_search_$search_for" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing $search_for" >&5
 $as_echo_n "checking for library containing $search_for... " >&6; }
@@ -6363,7 +6363,7 @@ fi
 # in case external blas have been found, take note of their underscoring
 # notice that this applies also when external blas are used with internal lapack
 # in the latter case, also (internal) lapack names will be underscored consistently
-if test "$blas_found" == nounderscore
+if test "$blas_found" = nounderscore
 then
   $as_echo "#define F77_NO_UNDERSCORE 1" >>confdefs.h
 
@@ -6419,7 +6419,7 @@ rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
 fi
 
 
-if test "$sdot_returns_float" == no ;
+if test "$sdot_returns_float" = no ;
 then
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether sdot returns double" >&5
@@ -6505,7 +6505,7 @@ $as_echo "$as_me: Now we will check for optional headers and libraries" >&6;}
 # GB
 #############################################################
 
-if test $molfile_plugins == true ; then
+if test $molfile_plugins = true ; then
 
 # Check for molfile_plugins and use internal fallback if not found. TG
 
@@ -6513,7 +6513,7 @@ if test $molfile_plugins == true ; then
 $as_echo "#define __PLUMED_HAS_MOLFILE_PLUGINS 1" >>confdefs.h
 
 
-  if test "$external_molfile_plugins" == true ; then
+  if test "$external_molfile_plugins" = true ; then
 
     found=ko
     __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS=no
@@ -6521,7 +6521,7 @@ $as_echo "#define __PLUMED_HAS_MOLFILE_PLUGINS 1" >>confdefs.h
 if test "x$ac_cv_header_libmolfile_plugin_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing molfile_dcdplugin_init" >&5
 $as_echo_n "checking for library containing molfile_dcdplugin_init... " >&6; }
 if ${ac_cv_search_molfile_dcdplugin_init+:} false; then :
@@ -6641,7 +6641,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS 1" >>confdefs.h
 
        __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS=yes
@@ -6706,7 +6706,7 @@ fi
 
 mpi_found=ko
 # optional libraries follow
-if test $mpi == true ; then
+if test $mpi = true ; then
 
     found=ko
     __PLUMED_HAS_MPI=no
@@ -6714,7 +6714,7 @@ if test $mpi == true ; then
 if test "x$ac_cv_header_mpi_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing MPI_Init" >&5
 $as_echo_n "checking for library containing MPI_Init... " >&6; }
 if ${ac_cv_search_MPI_Init+:} false; then :
@@ -6834,7 +6834,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_MPI 1" >>confdefs.h
 
        __PLUMED_HAS_MPI=yes
@@ -6919,12 +6919,12 @@ $as_echo "$ac_cv_prog_cxx_openmp" >&6; }
 
 
 
-if test $asmjit == true ; then
+if test $asmjit = true ; then
   found=ko
 # asmjit calls clock_gettime and thus should be linked to rt on Linux
   if test `(uname)` = Linux ; then
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing clock_gettime" >&5
 $as_echo_n "checking for library containing clock_gettime... " >&6; }
 if ${ac_cv_search_clock_gettime+:} false; then :
@@ -7055,7 +7055,7 @@ $as_echo "$as_me: WARNING: cannot link clock_gettime on this Linux, asmjit will
 fi
 
 
-if test $readdir_r == true ; then
+if test $readdir_r = true ; then
 
     found=ko
     __PLUMED_HAS_READDIR_R=no
@@ -7063,7 +7063,7 @@ if test $readdir_r == true ; then
 if test "x$ac_cv_header_dirent_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing readdir_r" >&5
 $as_echo_n "checking for library containing readdir_r... " >&6; }
 if ${ac_cv_search_readdir_r+:} false; then :
@@ -7183,7 +7183,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_READDIR_R 1" >>confdefs.h
 
        __PLUMED_HAS_READDIR_R=yes
@@ -7193,7 +7193,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_READDIR_R" >&2;}
     fi
 
 fi
-if test $cregex == true ; then
+if test $cregex = true ; then
 
     found=ko
     __PLUMED_HAS_CREGEX=no
@@ -7201,7 +7201,7 @@ if test $cregex == true ; then
 if test "x$ac_cv_header_regex_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing regcomp" >&5
 $as_echo_n "checking for library containing regcomp... " >&6; }
 if ${ac_cv_search_regcomp+:} false; then :
@@ -7321,7 +7321,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_CREGEX 1" >>confdefs.h
 
        __PLUMED_HAS_CREGEX=yes
@@ -7331,7 +7331,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_CREGEX" >&2;}
     fi
 
 fi
-if test $dlopen == true ; then
+if test $dlopen = true ; then
 
     found=ko
     __PLUMED_HAS_DLOPEN=no
@@ -7339,7 +7339,7 @@ if test $dlopen == true ; then
 if test "x$ac_cv_header_dlfcn_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dlopen" >&5
 $as_echo_n "checking for library containing dlopen... " >&6; }
 if ${ac_cv_search_dlopen+:} false; then :
@@ -7459,7 +7459,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_DLOPEN 1" >>confdefs.h
 
        __PLUMED_HAS_DLOPEN=yes
@@ -7470,11 +7470,11 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_DLOPEN" >&2;}
 
 fi
 
-if test $rtld_default == true ; then
+if test $rtld_default = true ; then
 
     found=ko
     __PLUMED_HAS_RTLD_DEFAULT=no
-    if test "${libsearch}" == true ; then
+    if test "${libsearch}" = true ; then
       testlibs=""
     else
       testlibs=""
@@ -7513,12 +7513,12 @@ $as_echo "no" >&6; }
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
-      if test $found == ok ; then
+      if test $found = ok ; then
         break
       fi
       LIBS="$save_LIBS"
     done
-    if test $found == ok ; then
+    if test $found = ok ; then
       $as_echo "#define __PLUMED_HAS_RTLD_DEFAULT 1" >>confdefs.h
 
       __PLUMED_HAS_RTLD_DEFAULT=yes
@@ -7530,7 +7530,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_RTLD_DEFAULT" >&2;}
 
 fi
 
-if test $chdir == true ; then
+if test $chdir = true ; then
 
     found=ko
     __PLUMED_HAS_CHDIR=no
@@ -7538,7 +7538,7 @@ if test $chdir == true ; then
 if test "x$ac_cv_header_unistd_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing chdir" >&5
 $as_echo_n "checking for library containing chdir... " >&6; }
 if ${ac_cv_search_chdir+:} false; then :
@@ -7658,7 +7658,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_CHDIR 1" >>confdefs.h
 
        __PLUMED_HAS_CHDIR=yes
@@ -7669,11 +7669,11 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_CHDIR" >&2;}
 
 fi
 
-if test $subprocess == true ; then
+if test $subprocess = true ; then
 
     found=ko
     __PLUMED_HAS_SUBPROCESS=no
-    if test "${libsearch}" == true ; then
+    if test "${libsearch}" = true ; then
       testlibs=""
     else
       testlibs=""
@@ -7735,12 +7735,12 @@ $as_echo "no" >&6; }
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
-      if test $found == ok ; then
+      if test $found = ok ; then
         break
       fi
       LIBS="$save_LIBS"
     done
-    if test $found == ok ; then
+    if test $found = ok ; then
       $as_echo "#define __PLUMED_HAS_SUBPROCESS 1" >>confdefs.h
 
       __PLUMED_HAS_SUBPROCESS=yes
@@ -7752,7 +7752,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_SUBPROCESS" >&2;}
 
 fi
 
-if test $getcwd == true ; then
+if test $getcwd = true ; then
 
     found=ko
     __PLUMED_HAS_GETCWD=no
@@ -7760,7 +7760,7 @@ if test $getcwd == true ; then
 if test "x$ac_cv_header_unistd_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing getcwd" >&5
 $as_echo_n "checking for library containing getcwd... " >&6; }
 if ${ac_cv_search_getcwd+:} false; then :
@@ -7880,7 +7880,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_GETCWD 1" >>confdefs.h
 
        __PLUMED_HAS_GETCWD=yes
@@ -7891,7 +7891,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_GETCWD" >&2;}
 
 fi
 
-if test $execinfo == true ; then
+if test $execinfo = true ; then
 
     found=ko
     __PLUMED_HAS_EXECINFO=no
@@ -7899,7 +7899,7 @@ if test $execinfo == true ; then
 if test "x$ac_cv_header_execinfo_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing backtrace" >&5
 $as_echo_n "checking for library containing backtrace... " >&6; }
 if ${ac_cv_search_backtrace+:} false; then :
@@ -8019,7 +8019,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_EXECINFO 1" >>confdefs.h
 
        __PLUMED_HAS_EXECINFO=yes
@@ -8029,7 +8029,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_EXECINFO" >&2;}
     fi
 
 fi
-if test $zlib == true ; then
+if test $zlib = true ; then
 
     found=ko
     __PLUMED_HAS_ZLIB=no
@@ -8037,7 +8037,7 @@ if test $zlib == true ; then
 if test "x$ac_cv_header_zlib_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gzopen" >&5
 $as_echo_n "checking for library containing gzopen... " >&6; }
 if ${ac_cv_search_gzopen+:} false; then :
@@ -8157,7 +8157,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_ZLIB 1" >>confdefs.h
 
        __PLUMED_HAS_ZLIB=yes
@@ -8168,10 +8168,10 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_ZLIB" >&2;}
 
 fi
 
-if test $gsl == true ; then
+if test $gsl = true ; then
   found=ko
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing cblas_dgemv" >&5
 $as_echo_n "checking for library containing cblas_dgemv... " >&6; }
 if ${ac_cv_search_cblas_dgemv+:} false; then :
@@ -8230,7 +8230,7 @@ if test "$ac_res" != no; then :
 if test "x$ac_cv_header_gsl_gsl_vector_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gsl_vector_alloc" >&5
 $as_echo_n "checking for library containing gsl_vector_alloc... " >&6; }
 if ${ac_cv_search_gsl_vector_alloc+:} false; then :
@@ -8412,7 +8412,7 @@ if test "$ac_res" != no; then :
 if test "x$ac_cv_header_gsl_gsl_vector_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gsl_vector_alloc" >&5
 $as_echo_n "checking for library containing gsl_vector_alloc... " >&6; }
 if ${ac_cv_search_gsl_vector_alloc+:} false; then :
@@ -8537,7 +8537,7 @@ fi
 
   fi
 
-  if test $found == ok ; then
+  if test $found = ok ; then
     $as_echo "#define __PLUMED_HAS_GSL 1" >>confdefs.h
 
   else
@@ -8546,7 +8546,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_GSL" >&2;}
   fi
 fi
 
-if test $xdrfile == true ; then
+if test $xdrfile = true ; then
 
     found=ko
     __PLUMED_HAS_XDRFILE=no
@@ -8554,7 +8554,7 @@ if test $xdrfile == true ; then
 if test "x$ac_cv_header_xdrfile_xdrfile_xtc_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing write_xtc" >&5
 $as_echo_n "checking for library containing write_xtc... " >&6; }
 if ${ac_cv_search_write_xtc+:} false; then :
@@ -8674,7 +8674,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_XDRFILE 1" >>confdefs.h
 
        __PLUMED_HAS_XDRFILE=yes
@@ -8685,11 +8685,11 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_XDRFILE" >&2;}
 
 fi
 
-if test $boost_graph == true ; then
+if test $boost_graph = true ; then
 
     found=ko
     __PLUMED_HAS_BOOST_GRAPH=no
-    if test "${libsearch}" == true ; then
+    if test "${libsearch}" = true ; then
       testlibs=""
     else
       testlibs=""
@@ -8730,12 +8730,12 @@ $as_echo "no" >&6; }
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
-      if test $found == ok ; then
+      if test $found = ok ; then
         break
       fi
       LIBS="$save_LIBS"
     done
-    if test $found == ok ; then
+    if test $found = ok ; then
       $as_echo "#define __PLUMED_HAS_BOOST_GRAPH 1" >>confdefs.h
 
       __PLUMED_HAS_BOOST_GRAPH=yes
@@ -8747,11 +8747,11 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_BOOST_GRAPH" >&2;}
 
 fi
 
-if test $boost_serialization == true ; then
+if test $boost_serialization = true ; then
 
     found=ko
     __PLUMED_HAS_BOOST_SERIALIZATION=no
-    if test "${libsearch}" == true ; then
+    if test "${libsearch}" = true ; then
       testlibs="boost_serialization boost_serialization-mt"
     else
       testlibs=""
@@ -8790,12 +8790,12 @@ $as_echo "no" >&6; }
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
-      if test $found == ok ; then
+      if test $found = ok ; then
         break
       fi
       LIBS="$save_LIBS"
     done
-    if test $found == ok ; then
+    if test $found = ok ; then
       $as_echo "#define __PLUMED_HAS_BOOST_SERIALIZATION 1" >>confdefs.h
 
       __PLUMED_HAS_BOOST_SERIALIZATION=yes
@@ -8808,7 +8808,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_BOOST_SERIALIZATION" >&2;}
 # notice: macports install libraries with -mt suffix
 fi
 
-if test $fftw == true ; then
+if test $fftw = true ; then
 
     found=ko
     __PLUMED_HAS_FFTW=no
@@ -8816,7 +8816,7 @@ if test $fftw == true ; then
 if test "x$ac_cv_header_fftw3_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing fftw_execute" >&5
 $as_echo_n "checking for library containing fftw_execute... " >&6; }
 if ${ac_cv_search_fftw_execute+:} false; then :
@@ -8936,7 +8936,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_FFTW 1" >>confdefs.h
 
        __PLUMED_HAS_FFTW=yes
@@ -8947,7 +8947,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_FFTW" >&2;}
 
 fi
 
-if test $python == true  ; then
+if test $python = true  ; then
 # if PYTHON_BIN is defined, it is expected to be the full path to python
 # Otherwise, search from a list of names:
   if test -z "$PYTHON_BIN" ; then
@@ -9030,7 +9030,7 @@ $as_echo "$as_me: WARNING: cannot enable python interface" >&2;}
   fi
 fi
 
-if test "$af_ocl" == true ; then
+if test "$af_ocl" = true ; then
 
     found=ko
     __PLUMED_HAS_ARRAYFIRE=no
@@ -9038,7 +9038,7 @@ if test "$af_ocl" == true ; then
 if test "x$ac_cv_header_arrayfire_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5
 $as_echo_n "checking for library containing af_is_double... " >&6; }
 if ${ac_cv_search_af_is_double+:} false; then :
@@ -9158,7 +9158,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h
 
        __PLUMED_HAS_ARRAYFIRE=yes
@@ -9168,7 +9168,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_ARRAYFIRE" >&2;}
     fi
 
 fi
-if test "$af_cuda" == true ; then
+if test "$af_cuda" = true ; then
 
     found=ko
     __PLUMED_HAS_ARRAYFIRE=no
@@ -9176,7 +9176,7 @@ if test "$af_cuda" == true ; then
 if test "x$ac_cv_header_arrayfire_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5
 $as_echo_n "checking for library containing af_is_double... " >&6; }
 if ${ac_cv_search_af_is_double+:} false; then :
@@ -9296,7 +9296,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h
 
        __PLUMED_HAS_ARRAYFIRE=yes
@@ -9306,7 +9306,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_ARRAYFIRE" >&2;}
     fi
 
 fi
-if test "$af_cpu" == true ; then
+if test "$af_cpu" = true ; then
 
     found=ko
     __PLUMED_HAS_ARRAYFIRE=no
@@ -9314,7 +9314,7 @@ if test "$af_cpu" == true ; then
 if test "x$ac_cv_header_arrayfire_h" = xyes; then :
 
 
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5
 $as_echo_n "checking for library containing af_is_double... " >&6; }
 if ${ac_cv_search_af_is_double+:} false; then :
@@ -9434,7 +9434,7 @@ fi
 fi
 
 
-    if test $found == ok ; then
+    if test $found = ok ; then
        $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h
 
        __PLUMED_HAS_ARRAYFIRE=yes
@@ -9446,7 +9446,7 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_ARRAYFIRE" >&2;}
 fi
 
 # in non-debug mode, add -DNDEBUG
-if test "$debug" == false ; then
+if test "$debug" = false ; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: Release mode, adding -DNDEBUG" >&5
 $as_echo "$as_me: Release mode, adding -DNDEBUG" >&6;}
   $as_echo "#define NDEBUG 1" >>confdefs.h
@@ -9454,7 +9454,7 @@ $as_echo "$as_me: Release mode, adding -DNDEBUG" >&6;}
 fi
 
 # in debug-glibcxx mode, add -D_GLIBCXX_DEBUG
-if test "$debug_glibcxx" == true ; then
+if test "$debug_glibcxx" = true ; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: Check boundaries, adding -D_GLIBCXX_DEBUG" >&5
 $as_echo "$as_me: Check boundaries, adding -D_GLIBCXX_DEBUG" >&6;}
   $as_echo "#define _GLIBCXX_DEBUG 1" >>confdefs.h
@@ -9476,7 +9476,7 @@ $as_echo "#define _REENTRANT 1" >>confdefs.h
 
 
 
-if test "$shared" == true ; then
+if test "$shared" = true ; then
   case `(uname)` in
   (Darwin)
     { $as_echo "$as_me:${as_lineno-$LINENO}: *** Special settings for dynamic libraries on OSX ***" >&5
@@ -9528,7 +9528,7 @@ fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
 
-    if test "$bsymbolic" == true ; then
+    if test "$bsymbolic" = true ; then
 
   save_LDFLAGS="$LDFLAGS"
   LDFLAGS="$LDFLAGS -Wl,-Bsymbolic"
@@ -9627,7 +9627,7 @@ $as_echo "no" >&6; }
 fi
 
 
-    if test "$readelf" == found ; then
+    if test "$readelf" = found ; then
       test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/"
       $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null
       if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then
@@ -9647,7 +9647,7 @@ fi
 
 
 make_doc=no
-if test "$doc" == true
+if test "$doc" = true
 then
 
 make_doc=yes
@@ -9690,10 +9690,10 @@ $as_echo "no" >&6; }
 fi
 
 
-if test "$doxygen" == found
+if test "$doxygen" = found
 then
   doxygen_version=`doxygen --version | awk 'BEGIN{FS="."}{if($1>1 || ($1==1 && $2>=8)) print "ok"}'`
-  if test "$doxygen_version" == ok
+  if test "$doxygen_version" = ok
   then
     { $as_echo "$as_me:${as_lineno-$LINENO}: Doxygen version is fine" >&5
 $as_echo "$as_me: Doxygen version is fine" >&6;}
@@ -9760,7 +9760,7 @@ fi
 
 
 make_pdfdoc=""
-if test "$pdfdoc" == true && test "$make_doc" == yes
+if test "$pdfdoc" = true && test "$make_doc" = yes
 then
   { $as_echo "$as_me:${as_lineno-$LINENO}: A PDF version of the manual will be generated" >&5
 $as_echo "$as_me: A PDF version of the manual will be generated" >&6;}
@@ -9855,7 +9855,7 @@ rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
 fi
 
 
-if test $mpi_found == ok ; then
+if test $mpi_found = ok ; then
 
 program_can_run_mpi=""
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program compiled with mpi can be run on this machine" >&5
@@ -9894,7 +9894,7 @@ fi
 
 fi
 
-if test $mpi_found == ok ; then
+if test $mpi_found = ok ; then
   if test -n "$MPIEXEC" ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: Regtest suite will use $MPIEXEC command to run MPI tests" >&5
 $as_echo "$as_me: Regtest suite will use $MPIEXEC command to run MPI tests" >&6;}
@@ -9904,15 +9904,15 @@ $as_echo "$as_me: Regtest suite will use env var PLUMED_MPIRUN to run MPI tests
   fi
 fi
 
-if test "$SOEXT" == "dylib" ; then
+if test "$SOEXT" = "dylib" ; then
   use_absolute_soname=yes
 else
   use_absolute_soname=no
 fi
 
 
-if test "$absolute_soname" == true ; then
-  if test "$SOEXT" == "dylib" ; then
+if test "$absolute_soname" = true ; then
+  if test "$SOEXT" = "dylib" ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: --enable-absolute-soname has no effect on OSX" >&5
 $as_echo "$as_me: WARNING: --enable-absolute-soname has no effect on OSX" >&2;}
   else
@@ -9922,8 +9922,8 @@ $as_echo "$as_me: enabling absolute soname. Full path will be hardcoded in plume
   fi
 fi
 
-if test "$absolute_install_name" == false ; then
-  if test "$SOEXT" == "so" ; then
+if test "$absolute_install_name" = false ; then
+  if test "$SOEXT" = "so" ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: --disable-absolute-install-name has no effect on Linux" >&5
 $as_echo "$as_me: WARNING: --disable-absolute-install-name has no effect on Linux" >&2;}
   else
@@ -9934,8 +9934,8 @@ $as_echo "$as_me: enabling relative install_name. You will have to set DYLD_LIBR
 fi
 
 
-if test "$SOEXT" == "dylib" ; then
-  if test "$loader_path" == true ; then
+if test "$SOEXT" = "dylib" ; then
+  if test "$loader_path" = true ; then
     use_loader_path=yes
   else
     use_loader_path=no
@@ -9951,7 +9951,7 @@ $as_echo "$as_me: PLUMED seems to be configured properly!" >&6;}
 $as_echo "$as_me: **************************" >&6;}
 
 LD_RO=
-if test "$ld_r" == true ; then
+if test "$ld_r" = true ; then
 for test_LD_RO in "$($CXX --print-prog-name=ld) -r -o" "$CXX -Wl,-r -o" "ld -r -o"
 do
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C++ objects can be grouped with $test_LD_RO" >&5
@@ -9995,7 +9995,7 @@ fi
 
 
 AR_CR=
-if test "$ar_cr" == true ; then
+if test "$ar_cr" = true ; then
 for test_AR_CR in "$($CXX --print-prog-name=ar) cr" "ar cr"
 do
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether static libraries can be created with $test_AR_CR" >&5
@@ -10040,7 +10040,7 @@ fi
 make_static_archive=no
 
 
-if test "${static_archive}" == true ; then
+if test "${static_archive}" = true ; then
   if test -z "$LD_RO" || test -z "$AR_CR" ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: no way to create a static archive if ld -ro or ar cr do not work" >&5
 $as_echo "$as_me: WARNING: no way to create a static archive if ld -ro or ar cr do not work" >&2;}
@@ -10048,7 +10048,7 @@ $as_echo "$as_me: WARNING: no way to create a static archive if ld -ro or ar cr
   fi
 fi
 
-if test "${static_archive}" == true ; then
+if test "${static_archive}" = true ; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether static-object constructors can be linked from a static archive" >&5
 $as_echo_n "checking whether static-object constructors can be linked from a static archive... " >&6; }
 
@@ -10091,7 +10091,7 @@ $as_echo "no" >&6; }
   fi
 fi
 
-if test "${static_patch}" == true ; then
+if test "${static_patch}" = true ; then
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: I will now check if C++ objects can be linked by C/Fortran compilers" >&5
 $as_echo "$as_me: I will now check if C++ objects can be linked by C/Fortran compilers" >&6;}
@@ -10132,7 +10132,7 @@ EOF
     $CXX $CXXFLAGS -c conftest.cpp
 # start search:
     found=
-    if test "${libsearch}" == true ; then
+    if test "${libsearch}" = true ; then
       testlibs="-lstdc++ -lc++ -lmpi_cxx"
     else
       testlibs=""
@@ -10173,7 +10173,7 @@ else
 $as_echo "$as_me: Static patching is disabled, thus tests required for static patching will be skipped" >&6;}
 fi
 
-if test "$prefix" == NONE
+if test "$prefix" = NONE
 then
   prefix=/usr/local
 fi
@@ -10227,7 +10227,7 @@ done
 
 
 if test -z "$BASH_COMPLETION_DIR" && test -n "$pkgconfig_bin"; then
-  if test "$prefix" == "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
+  if test "$prefix" = "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
   then
     { $as_echo "$as_me:${as_lineno-$LINENO}: bash-completion is installed on the same prefix where plumed will be installed" >&5
 $as_echo "$as_me: bash-completion is installed on the same prefix where plumed will be installed" >&6;}
@@ -10323,8 +10323,8 @@ $as_echo "$as_me: WARNING: **** _$program_name() { eval \"\$($program_name --no-
 $as_echo "$as_me: WARNING: **** complete -F _$program_name -o default $program_name" >&2;}
 fi
 
-if test $mpi == true; then
-  if test $mpi_found == ok; then
+if test $mpi = true; then
+  if test $mpi_found = ok; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: **** PLUMED will be compiled using MPI" >&5
 $as_echo "$as_me: **** PLUMED will be compiled using MPI" >&6;}
   else
@@ -10336,13 +10336,13 @@ else
 $as_echo "$as_me: **** PLUMED will be compiled without MPI" >&6;}
 fi
 
-if test $program_can_run == no ; then
+if test $program_can_run = no ; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: plumed executable will not run on this machine" >&5
 $as_echo "$as_me: WARNING: plumed executable will not run on this machine" >&2;}
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: to patch an MD code use 'plumed-patch'" >&5
 $as_echo "$as_me: WARNING: to patch an MD code use 'plumed-patch'" >&2;}
-elif test $mpi_found == ok ; then
-  if test $program_can_run_mpi == no ; then
+elif test $mpi_found = ok ; then
+  if test $program_can_run_mpi = no ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: plumed executable will not run on this machine" >&5
 $as_echo "$as_me: WARNING: plumed executable will not run on this machine" >&2;}
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unless you invoke it as 'plumed --no-mpi'" >&5
diff --git a/configure.ac b/configure.ac
index 8ca5640986..5a4ca463a5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -86,10 +86,10 @@ AC_DEFUN([PLUMED_CHECK_LDFLAGS], [
 ])
 
 # PLUMED_SEARCH_LIBS(function,search-libs[,action-if-found][,action-if-not-found][,other-libraries])
-# same as AC_SEARCH_LIBS, but does not try any library unless $libsearch==true
+# same as AC_SEARCH_LIBS, but does not try any library unless $libsearch=true
 # Should be used instead of AC_SEARCH_LIBS in order to make --disable-libsearch work correctly
 AC_DEFUN([PLUMED_SEARCH_LIBS], [
-  if test "${libsearch}" == true ; then
+  if test "${libsearch}" = true ; then
     AC_SEARCH_LIBS([$1],[$2],[$3],[$4],[$5])
   else
     AC_SEARCH_LIBS([$1],[],[$3],[$4],[])
@@ -106,7 +106,7 @@ AC_DEFUN([PLUMED_CHECK_PACKAGE], [
     AC_CHECK_HEADER( [$1],[
       PLUMED_SEARCH_LIBS([$2],[$4],[found=ok])
     ])
-    if test $found == ok ; then
+    if test $found = ok ; then
        AC_DEFINE([$3])
        $3=yes
     else
@@ -122,7 +122,7 @@ AC_DEFUN([PLUMED_CHECK_PACKAGE], [
 AC_DEFUN([PLUMED_CHECK_CXX_PACKAGE], [
     found=ko
     $3=no
-    if test "${libsearch}" == true ; then
+    if test "${libsearch}" = true ; then
       testlibs="$4"
     else
       testlibs=""
@@ -141,12 +141,12 @@ AC_DEFUN([PLUMED_CHECK_CXX_PACKAGE], [
           [AC_MSG_RESULT([yes])],
           [AC_MSG_RESULT([no])]
       )
-      if test $found == ok ; then
+      if test $found = ok ; then
         break
       fi
       LIBS="$save_LIBS"
     done
-    if test $found == ok ; then
+    if test $found = ok ; then
       AC_DEFINE([$3])
       $3=yes
     else
@@ -164,10 +164,10 @@ AC_ARG_ENABLE([modules],
   AS_HELP_STRING([--enable-modules], [all/none/reset or : separated list such as +crystallization:-bias default: reset]),
   [
    rm -f src/*.on src/*.off
-   if test "${enableval}" == yes ; then
+   if test "${enableval}" = yes ; then
      enableval=reset
    fi
-   if test "${enableval}" == no ; then
+   if test "${enableval}" = no ; then
      enableval=none
    fi
    for modules_mod in `echo "${enableval}" | sed 's/:/ /g' | sed 's/+/ +/g' | sed 's/-/ -/g'`
@@ -301,7 +301,7 @@ case `(uname)` in
 esac
 
 # if searching for MPI, try first mpi-like compilers
-if test $mpi == true ; then
+if test $mpi = true ; then
 compilers="mpic++ mpicxx mpiicpc openmpic++ openmpicxx $compilers"
 fi
 
@@ -334,25 +334,25 @@ AC_MSG_NOTICE([Initial LDSHARED:    $LDSHARED])
 AC_MSG_NOTICE([Initial SOEXT:       $SOEXT])
 
 # check C++ flags
-if test $shared == true
+if test $shared = true
 then
   PLUMED_CHECK_CXXFLAG([-fPIC])
   PLUMED_CHECK_CFLAG([-fPIC])
 fi
 
-if test $basic_warnings == true
+if test $basic_warnings = true
 then
   PLUMED_CHECK_CXXFLAG([-Wall])
   PLUMED_CHECK_CXXFLAG([-pedantic])
   PLUMED_CHECK_CXXFLAG([-std=c++11])
 fi
 
-if test $debug == true
+if test $debug = true
 then
   PLUMED_CHECK_CXXFLAG([-g])
 fi
 
-if test $gcov == true
+if test $gcov = true
 then
   CXX="$CXX --coverage"
   LDSHARED="$LDSHARED --coverage"
@@ -361,7 +361,7 @@ then
   STATIC_LIBS="$STATIC_LIBS --coverage"
 fi
 
-if test $fussy == true
+if test $fussy = true
 then
   PLUMED_CHECK_CXXFLAG([-Wextra])
   PLUMED_CHECK_CXXFLAG([-Wfloat-equal])
@@ -483,14 +483,14 @@ lapack_found=
 
 # external lapack can only work with external blas
 # thus, if external blas are disabled also external lapack should be disabled
-if test "$external_blas" == false && test "$external_lapack" == true ; then
+if test "$external_blas" = false && test "$external_lapack" = true ; then
   AC_MSG_NOTICE([Internal blas can only be used with internal lapack])
   AC_MSG_NOTICE([Will not search for external lapack])
   external_lapack=false
 fi
 
 # first look for blas
-if test "$external_blas" == true ; then
+if test "$external_blas" = true ; then
   AC_MSG_CHECKING([whether dgemv can be linked with no library])
   AC_LINK_IFELSE([AC_LANG_CALL([], [dgemv])],[
     AC_MSG_RESULT([yes])
@@ -520,7 +520,7 @@ if test -n "$blas_found" ; then
 
 AC_DEFINE([__PLUMED_HAS_EXTERNAL_BLAS])
 
-if test "$external_lapack" == true ; then
+if test "$external_lapack" = true ; then
 # Then we look for lapack using same underscoring
 case "$blas_found" in
 (underscore) search_for=dsyevr_ ;;
@@ -541,7 +541,7 @@ fi
 # in case external blas have been found, take note of their underscoring
 # notice that this applies also when external blas are used with internal lapack
 # in the latter case, also (internal) lapack names will be underscored consistently
-if test "$blas_found" == nounderscore
+if test "$blas_found" = nounderscore
 then
   AC_DEFINE([F77_NO_UNDERSCORE])
 fi
@@ -580,7 +580,7 @@ AC_RUN_IFELSE([AC_LANG_SOURCE([PLUMED_TEST_SDOT([float])])],
   [ AC_MSG_RESULT([not checked (cross compiling)]) ]
 )
 
-if test "$sdot_returns_float" == no ;
+if test "$sdot_returns_float" = no ;
 then
 
 AC_MSG_CHECKING([whether sdot returns double])
@@ -622,14 +622,14 @@ AC_MSG_NOTICE([Now we will check for optional headers and libraries])
 # GB
 #############################################################
 
-if test $molfile_plugins == true ; then
+if test $molfile_plugins = true ; then
 
 # Check for molfile_plugins and use internal fallback if not found. TG
 
 # We always have molfile, now
 AC_DEFINE([__PLUMED_HAS_MOLFILE_PLUGINS])
 
-  if test "$external_molfile_plugins" == true ; then
+  if test "$external_molfile_plugins" = true ; then
     PLUMED_CHECK_PACKAGE([libmolfile_plugin.h],[molfile_dcdplugin_init],[__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS],molfile_plugin)
     if test "$__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS" != yes ; then
       AC_MSG_WARN([using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files])
@@ -646,7 +646,7 @@ AC_CHECK_LIB([dl],dlopen, [STATIC_LIBS="-ldl $STATIC_LIBS"] [LIBS="-ldl $LIBS"])
 
 mpi_found=ko
 # optional libraries follow
-if test $mpi == true ; then
+if test $mpi = true ; then
   PLUMED_CHECK_PACKAGE([mpi.h],[MPI_Init],[__PLUMED_HAS_MPI])
   if test "$__PLUMED_HAS_MPI" = yes; then
     mpi_found=ok
@@ -659,7 +659,7 @@ fi
 # when configuring with --disable-openmp
 AC_OPENMP
 
-if test $asmjit == true ; then
+if test $asmjit = true ; then
   found=ko
 # asmjit calls clock_gettime and thus should be linked to rt on Linux
   if test `(uname)` = Linux ; then
@@ -676,17 +676,17 @@ if test $asmjit == true ; then
 fi
 
 
-if test $readdir_r == true ; then
+if test $readdir_r = true ; then
   PLUMED_CHECK_PACKAGE([dirent.h],[readdir_r],[__PLUMED_HAS_READDIR_R])
 fi
-if test $cregex == true ; then
+if test $cregex = true ; then
   PLUMED_CHECK_PACKAGE([regex.h],[regcomp],[__PLUMED_HAS_CREGEX])
 fi
-if test $dlopen == true ; then
+if test $dlopen = true ; then
   PLUMED_CHECK_PACKAGE([dlfcn.h],[dlopen],[__PLUMED_HAS_DLOPEN])
 fi
 
-if test $rtld_default == true ; then
+if test $rtld_default = true ; then
   PLUMED_CHECK_CXX_PACKAGE([RTLD_DEFAULT],[
 #include <dlfcn.h>
 int
@@ -698,11 +698,11 @@ main ()
   ], [__PLUMED_HAS_RTLD_DEFAULT])
 fi
 
-if test $chdir == true ; then
+if test $chdir = true ; then
   PLUMED_CHECK_PACKAGE([unistd.h],[chdir],[__PLUMED_HAS_CHDIR])
 fi
 
-if test $subprocess == true ; then
+if test $subprocess = true ; then
   PLUMED_CHECK_CXX_PACKAGE([subprocess],[
 /* random program calling all the functions needed to manage a subprocess */
 #include <cstdio>
@@ -737,36 +737,36 @@ main ()
   ], [__PLUMED_HAS_SUBPROCESS])
 fi
 
-if test $getcwd == true ; then
+if test $getcwd = true ; then
   PLUMED_CHECK_PACKAGE([unistd.h],[getcwd],[__PLUMED_HAS_GETCWD])
 fi
 
-if test $execinfo == true ; then
+if test $execinfo = true ; then
   PLUMED_CHECK_PACKAGE([execinfo.h],[backtrace],[__PLUMED_HAS_EXECINFO])
 fi
-if test $zlib == true ; then
+if test $zlib = true ; then
   PLUMED_CHECK_PACKAGE([zlib.h],[gzopen],[__PLUMED_HAS_ZLIB],[z])
 fi
 
-if test $gsl == true ; then
+if test $gsl = true ; then
   found=ko
   PLUMED_SEARCH_LIBS([cblas_dgemv],[gslcblas], [
     AC_CHECK_HEADER(  [gsl/gsl_vector.h], [
       PLUMED_SEARCH_LIBS([gsl_vector_alloc],[gsl],[found=ok])
     ])
   ])
-  if test $found == ok ; then
+  if test $found = ok ; then
     AC_DEFINE([__PLUMED_HAS_GSL])
   else
     AC_MSG_WARN([cannot enable __PLUMED_HAS_GSL])
   fi
 fi
 
-if test $xdrfile == true ; then
+if test $xdrfile = true ; then
   PLUMED_CHECK_PACKAGE([xdrfile/xdrfile_xtc.h],[write_xtc],[__PLUMED_HAS_XDRFILE],[xdrfile])
 fi
 
-if test $boost_graph == true ; then
+if test $boost_graph = true ; then
   PLUMED_CHECK_CXX_PACKAGE([boost graph],[
 #include <boost/graph/graph_utility.hpp>
 #include <boost/graph/adjacency_matrix.hpp>
@@ -780,7 +780,7 @@ main ()
   ], [__PLUMED_HAS_BOOST_GRAPH])
 fi
 
-if test $boost_serialization == true ; then
+if test $boost_serialization = true ; then
   PLUMED_CHECK_CXX_PACKAGE([boost serialization],[
 #include <fstream>
 #include <boost/archive/text_oarchive.hpp>
@@ -793,11 +793,11 @@ int main() {
 # notice: macports install libraries with -mt suffix
 fi
 
-if test $fftw == true ; then
+if test $fftw = true ; then
   PLUMED_CHECK_PACKAGE([fftw3.h],[fftw_execute],[__PLUMED_HAS_FFTW],[fftw3])
 fi
 
-if test $python == true  ; then
+if test $python = true  ; then
 # if PYTHON_BIN is defined, it is expected to be the full path to python
 # Otherwise, search from a list of names:
   if test -z "$PYTHON_BIN" ; then
@@ -832,24 +832,24 @@ if sys.version_info < (3,):
   fi
 fi
 
-if test "$af_ocl" == true ; then
+if test "$af_ocl" = true ; then
   PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afopencl])
 fi
-if test "$af_cuda" == true ; then
+if test "$af_cuda" = true ; then
   PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afcuda])
 fi
-if test "$af_cpu" == true ; then
+if test "$af_cpu" = true ; then
   PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afcpu])
 fi
 
 # in non-debug mode, add -DNDEBUG
-if test "$debug" == false ; then
+if test "$debug" = false ; then
   AC_MSG_NOTICE([Release mode, adding -DNDEBUG])
   AC_DEFINE([NDEBUG])
 fi
 
 # in debug-glibcxx mode, add -D_GLIBCXX_DEBUG
-if test "$debug_glibcxx" == true ; then
+if test "$debug_glibcxx" = true ; then
   AC_MSG_NOTICE([Check boundaries, adding -D_GLIBCXX_DEBUG])
   AC_DEFINE([_GLIBCXX_DEBUG])
 fi
@@ -868,7 +868,7 @@ AC_SUBST(PYTHON_BIN)
 
 AC_SUBST(MPIEXEC)
 
-if test "$shared" == true ; then
+if test "$shared" = true ; then
   case `(uname)` in
   (Darwin)
     AC_MSG_NOTICE([*** Special settings for dynamic libraries on OSX ***])
@@ -888,7 +888,7 @@ if test "$shared" == true ; then
     SOEXT=so
     LDSHARED="$LDSHARED -shared"
     PLUMED_CHECK_LDFLAGS([-rdynamic])
-    if test "$bsymbolic" == true ; then
+    if test "$bsymbolic" = true ; then
       PLUMED_CHECK_LDFLAGS([-Wl,-Bsymbolic])
     fi
   ;;
@@ -919,7 +919,7 @@ then
     rm -f conftest.$SOEXT
     readelf=""
     AC_CHECK_PROG([readelf],[readelf],[found])
-    if test "$readelf" == found ; then
+    if test "$readelf" = found ; then
       test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/"
       $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null
       if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then
@@ -937,17 +937,17 @@ fi
 
 AC_SUBST(make_doc)
 make_doc=no
-if test "$doc" == true
+if test "$doc" = true
 then
 
 make_doc=yes
 
 ### Look for doxygen
 AC_CHECK_PROG([doxygen],[doxygen],[found])
-if test "$doxygen" == found
+if test "$doxygen" = found
 then
   doxygen_version=`doxygen --version | awk 'BEGIN{FS="."}{if($1>1 || ($1==1 && $2>=8)) print "ok"}'`
-  if test "$doxygen_version" == ok
+  if test "$doxygen_version" = ok
   then
     AC_MSG_NOTICE([Doxygen version is fine])
   else
@@ -973,7 +973,7 @@ fi
 
 AC_SUBST(make_pdfdoc)
 make_pdfdoc=""
-if test "$pdfdoc" == true && test "$make_doc" == yes
+if test "$pdfdoc" = true && test "$make_doc" = yes
 then
   AC_MSG_NOTICE([A PDF version of the manual will be generated])
   make_pdfdoc=yes
@@ -1014,7 +1014,7 @@ int main(int argc,char*argv[[]]){
   [ program_can_run=no ; AC_MSG_RESULT([no (cross compiling)]) ]
 )
 
-if test $mpi_found == ok ; then
+if test $mpi_found = ok ; then
 AC_SUBST(program_can_run_mpi)
 program_can_run_mpi=""
 AC_MSG_CHECKING([whether a program compiled with mpi can be run on this machine])
@@ -1037,7 +1037,7 @@ int main(int argc,char*argv[[]]){
 )
 fi
 
-if test $mpi_found == ok ; then
+if test $mpi_found = ok ; then
   if test -n "$MPIEXEC" ; then
     AC_MSG_NOTICE([Regtest suite will use $MPIEXEC command to run MPI tests])
   else
@@ -1045,15 +1045,15 @@ if test $mpi_found == ok ; then
   fi
 fi
 
-if test "$SOEXT" == "dylib" ; then
+if test "$SOEXT" = "dylib" ; then
   use_absolute_soname=yes
 else
   use_absolute_soname=no
 fi
 
 AC_SUBST(use_absolute_soname)
-if test "$absolute_soname" == true ; then
-  if test "$SOEXT" == "dylib" ; then
+if test "$absolute_soname" = true ; then
+  if test "$SOEXT" = "dylib" ; then
     AC_MSG_WARN([--enable-absolute-soname has no effect on OSX])
   else
     AC_MSG_NOTICE([enabling absolute soname. Full path will be hardcoded in plumed library soname])
@@ -1061,8 +1061,8 @@ if test "$absolute_soname" == true ; then
   fi
 fi
 
-if test "$absolute_install_name" == false ; then
-  if test "$SOEXT" == "so" ; then
+if test "$absolute_install_name" = false ; then
+  if test "$SOEXT" = "so" ; then
     AC_MSG_WARN([--disable-absolute-install-name has no effect on Linux])
   else
     AC_MSG_NOTICE([enabling relative install_name. You will have to set DYLD_LIBRARY_PATH yor plumed libraries to be found at runtime])
@@ -1071,8 +1071,8 @@ if test "$absolute_install_name" == false ; then
 fi
 
 AC_SUBST(use_loader_path)
-if test "$SOEXT" == "dylib" ; then
-  if test "$loader_path" == true ; then
+if test "$SOEXT" = "dylib" ; then
+  if test "$loader_path" = true ; then
     use_loader_path=yes
   else
     use_loader_path=no
@@ -1086,7 +1086,7 @@ AC_MSG_NOTICE([PLUMED seems to be configured properly!])
 AC_MSG_NOTICE([**************************])
 AC_SUBST(LD_RO)
 LD_RO=
-if test "$ld_r" == true ; then
+if test "$ld_r" = true ; then
 for test_LD_RO in "$($CXX --print-prog-name=ld) -r -o" "$CXX -Wl,-r -o" "ld -r -o"
 do
   AC_MSG_CHECKING([whether C++ objects can be grouped with $test_LD_RO])
@@ -1127,7 +1127,7 @@ fi
 
 AC_SUBST(AR_CR)
 AR_CR=
-if test "$ar_cr" == true ; then
+if test "$ar_cr" = true ; then
 for test_AR_CR in "$($CXX --print-prog-name=ar) cr" "ar cr"
 do
   AC_MSG_CHECKING([whether static libraries can be created with $test_AR_CR])
@@ -1169,14 +1169,14 @@ fi
 make_static_archive=no
 AC_SUBST(make_static_archive)
 
-if test "${static_archive}" == true ; then
+if test "${static_archive}" = true ; then
   if test -z "$LD_RO" || test -z "$AR_CR" ; then
     AC_MSG_WARN([no way to create a static archive if ld -ro or ar cr do not work])
     static_archive=false
   fi
 fi
 
-if test "${static_archive}" == true ; then
+if test "${static_archive}" = true ; then
   AC_MSG_CHECKING([whether static-object constructors can be linked from a static archive])
 
   magic_token=c1bc476d093a3a5c67b4530e6c54c633593fe9aa
@@ -1216,7 +1216,7 @@ EOF
   fi
 fi
 
-if test "${static_patch}" == true ; then
+if test "${static_patch}" = true ; then
 
 AC_MSG_NOTICE([I will now check if C++ objects can be linked by C/Fortran compilers])
 AC_MSG_NOTICE([This is relevant if you want to use plumed patch --static on a non-C++ code])
@@ -1255,7 +1255,7 @@ EOF
     $CXX $CXXFLAGS -c conftest.cpp 
 # start search:
     found=
-    if test "${libsearch}" == true ; then
+    if test "${libsearch}" = true ; then
       testlibs="-lstdc++ -lc++ -lmpi_cxx"
     else
       testlibs=""
@@ -1289,7 +1289,7 @@ else
 AC_MSG_NOTICE([Static patching is disabled, thus tests required for static patching will be skipped])
 fi
 
-if test "$prefix" == NONE
+if test "$prefix" = NONE
 then
   prefix=/usr/local
 fi
@@ -1299,7 +1299,7 @@ pkgconfig_bin=""
 AC_PATH_PROGS(pkgconfig_bin,pkg-config)
 
 if test -z "$BASH_COMPLETION_DIR" && test -n "$pkgconfig_bin"; then
-  if test "$prefix" == "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
+  if test "$prefix" = "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
   then
     AC_MSG_NOTICE([bash-completion is installed on the same prefix where plumed will be installed])
     if pkg-config --variable=completionsdir bash-completion 2>/dev/null >/dev/null ; then
@@ -1366,8 +1366,8 @@ if test -z "$BASH_COMPLETION_DIR" ; then
   AC_MSG_WARN([**** complete -F _$program_name -o default $program_name])
 fi
 
-if test $mpi == true; then
-  if test $mpi_found == ok; then
+if test $mpi = true; then
+  if test $mpi_found = ok; then
     AC_MSG_NOTICE([**** PLUMED will be compiled using MPI])
   else 
     AC_MSG_WARN([**** PLUMED will NOT be compiled using MPI because MPI have not been found!])
@@ -1376,11 +1376,11 @@ else
     AC_MSG_NOTICE([**** PLUMED will be compiled without MPI])
 fi
 
-if test $program_can_run == no ; then
+if test $program_can_run = no ; then
   AC_MSG_WARN([plumed executable will not run on this machine])
   AC_MSG_WARN([to patch an MD code use 'plumed-patch'])
-elif test $mpi_found == ok ; then
-  if test $program_can_run_mpi == no ; then
+elif test $mpi_found = ok ; then
+  if test $program_can_run_mpi = no ; then
     AC_MSG_WARN([plumed executable will not run on this machine])
     AC_MSG_WARN([unless you invoke it as 'plumed --no-mpi'])
     AC_MSG_WARN([all command line tools are thus available as 'plumed --no-mpi name-of-the-tool'])