diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index f22fa401a2..6fb2f0c65e 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -102,31 +102,31 @@ include(CheckIncludeFileCXX)
 if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
     if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
+      set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} /Qrestrict")
     endif()
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
+      set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} /QxCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "/QxHost")
+      set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} /QxHost")
     endif()
   else()
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+    set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} -restrict")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
+      set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} -xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
+      set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} -xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
     endif()
   endif()
 endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
+  set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} -fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
 if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "PGI"))
-  set(CMAKE_TUNE_DEFAULT "-Minform=severe")
+  set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} -Minform=severe")
 endif()
 
 # this hack is required to compile fmt lib with CrayClang version 15.0.2
@@ -134,17 +134,17 @@ endif()
 if(CMAKE_VERSION VERSION_LESS 3.28)
   get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
   if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
-    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+    set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} -DFMT_STATIC_THOUSANDS_SEPARATOR")
   endif()
 else()
   if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
-    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+    set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}} -DFMT_STATIC_THOUSANDS_SEPARATOR")
   endif()
 endif()
 
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
-  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
+  set(CMAKE_CXX_FLAGS_${BTYPE} "${CMAKE_CXX_FLAGS_${BTYPE}}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
 # we *require* C++11 without extensions but prefer C++17.
@@ -628,10 +628,6 @@ if(WITH_SWIG)
   add_subdirectory(${LAMMPS_SWIG_DIR} swig)
 endif()
 
-set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
-separate_arguments(CMAKE_TUNE_FLAGS)
-target_compile_options(lammps PRIVATE ${CMAKE_TUNE_FLAGS})
-target_compile_options(lmp PRIVATE ${CMAKE_TUNE_FLAGS})
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
diff --git a/cmake/Modules/Packages/COLVARS.cmake b/cmake/Modules/Packages/COLVARS.cmake
index b943a0345e..8fa0d84f01 100644
--- a/cmake/Modules/Packages/COLVARS.cmake
+++ b/cmake/Modules/Packages/COLVARS.cmake
@@ -14,10 +14,6 @@ endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
 target_compile_definitions(colvars PRIVATE -DCOLVARS_LAMMPS)
-separate_arguments(CMAKE_TUNE_FLAGS)
-foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  target_compile_options(colvars PRIVATE ${_FLAG})
-endforeach()
 set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
 target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 # The line below is needed to locate math_eigen_impl.h
diff --git a/cmake/presets/kokkos-hip.cmake b/cmake/presets/kokkos-hip.cmake
index 38bf27092f..ba1eeb1853 100644
--- a/cmake/presets/kokkos-hip.cmake
+++ b/cmake/presets/kokkos-hip.cmake
@@ -10,7 +10,13 @@ set(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
 
 set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
+if (CMAKE_CXX_FLAGS)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -munsafe-fp-atomics" CACHE STRING "" FORCE)
+endif()
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -munsafe-fp-atomics" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -munsafe-fp-atomics" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -munsafe-fp-atomics" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL} -munsafe-fp-atomics" CACHE STRING "" FORCE)
 
 # If KSPACE is also enabled, use CUFFT for FFTs
 set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE)
diff --git a/cmake/presets/kokkos-sycl-intel.cmake b/cmake/presets/kokkos-sycl-intel.cmake
index eba386564d..163d35e031 100644
--- a/cmake/presets/kokkos-sycl-intel.cmake
+++ b/cmake/presets/kokkos-sycl-intel.cmake
@@ -21,9 +21,16 @@ set(CMAKE_C_COMPILER icx CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
-# Silence everything
-set(CMAKE_CXX_FLAGS "-w" CACHE STRING "" FORCE)
+
+# set(_intel_sycl_flags " -w -fsycl -flink-huge-device-code -fsycl-targets=spir64_gen "
+set(_intel_sycl_flags " -w -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen "
+if (CMAKE_CXX_FLAGS)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+endif()
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+
 #set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-targets=spir64_gen " CACHE STRING "" FORCE)
-#set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)
-set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code " CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel " CACHE STRING "" FORCE)
+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsycl -flink-huge-device-code " CACHE STRING "" FORCE)
diff --git a/cmake/presets/kokkos-sycl-nvidia.cmake b/cmake/presets/kokkos-sycl-nvidia.cmake
index c706aca7d8..678f9f380a 100644
--- a/cmake/presets/kokkos-sycl-nvidia.cmake
+++ b/cmake/presets/kokkos-sycl-nvidia.cmake
@@ -14,5 +14,13 @@ set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
 set(CMAKE_CXX_COMPILER clang++ CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
-set(CMAKE_SHARED_LINKER_FLAGS "-Xsycl-target-frontend -O3" CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-fgpu-inline-threshold=100000 -Xsycl-target-frontend -O3  -Xsycl-target-frontend -ffp-contract=on -Wno-unknown-cuda-version" CACHE STRING "" FORCE)
+set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Xsycl-target-frontend -O3 " CACHE STRING "" FORCE)
+
+set(_intel_sycl_flags "-fgpu-inline-threshold=100000 -Xsycl-target-frontend -O3  -Xsycl-target-frontend -ffp-contract=on -Wno-unknown-cuda-version")
+if (CMAKE_CXX_FLAGS)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+endif()
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake
index 413744b078..dbcd4ef11d 100644
--- a/cmake/presets/mingw-cross.cmake
+++ b/cmake/presets/mingw-cross.cmake
@@ -91,7 +91,13 @@ endif()
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
+if (CMAKE_CXX_FLAGS)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-missing-include-dirs" CACHE STRING "" FORCE)
+endif()
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wno-missing-include-dirs" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -Wno-missing-include-dirs" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -Wno-missing-include-dirs" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL} -Wno-missing-include-dirs" CACHE STRING "" FORCE)
 set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
 set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
 set(BUILD_TOOLS ON CACHE BOOL "" FORCE)
diff --git a/cmake/presets/windows-intel-llvm.cmake b/cmake/presets/windows-intel-llvm.cmake
index e9d88d22fe..cdde3c146a 100644
--- a/cmake/presets/windows-intel-llvm.cmake
+++ b/cmake/presets/windows-intel-llvm.cmake
@@ -5,4 +5,10 @@ set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
 set(INTEL_LRT_MODE "C++11" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
-set(CMAKE_TUNE_FLAGS -Wno-unused-command-line-argument)
+if (CMAKE_CXX_FLAGS)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-command-line-argument" CACHE STRING "" FORCE)
+endif()
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wno-unused-command-line-argument" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -Wno-unused-command-line-argument" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -Wno-unused-command-line-argument" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL} -Wno-unused-command-line-argument" CACHE STRING "" FORCE)
diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst
index be4b312578..f9cf251688 100644
--- a/doc/src/Build_basics.rst
+++ b/doc/src/Build_basics.rst
@@ -212,11 +212,7 @@ LAMMPS.
       You can tell CMake to look for a specific compiler with setting
       CMake variables (listed below) during configuration.  For a few
       common choices, there are also presets in the ``cmake/presets``
-      folder.  For convenience, there is a ``CMAKE_TUNE_FLAGS`` variable
-      that can be set to apply global compiler options (applied to
-      compilation only), to be used for adding compiler or host specific
-      optimization flags in addition to the "flags" variables listed
-      below. You may also specify the corresponding ``CMAKE_*_FLAGS``
+      folder.  You may also specify the corresponding ``CMAKE_*_FLAGS``
       variables individually, if you want to experiment with alternate
       optimization flags.  You should specify all 3 compilers, so that
       the (few) LAMMPS source files written in C or Fortran are built
@@ -266,10 +262,6 @@ LAMMPS.
       ``-C ../cmake/presets/pgi.cmake`` will switch the compiler to the PGI compilers,
       and ``-C ../cmake/presets/nvhpc.cmake`` will switch to the NVHPC compilers.
 
-      Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
-      compiler flags to tune for optimal performance on given hosts.
-      This variable is empty by default.
-
       .. note::
 
          When the cmake command completes, it prints a summary to the
diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst
index 226e19bfc3..7c16409995 100644
--- a/doc/src/Build_settings.rst
+++ b/doc/src/Build_settings.rst
@@ -18,7 +18,6 @@ explains how to do this for building both with CMake and make.
 * `Memory allocation alignment`_
 * `Workaround for long long integers`_
 * `Exception handling when using LAMMPS as a library`_ to capture errors
-* `Trigger selected floating-point exceptions`_
 
 ----------
 
@@ -659,40 +658,3 @@ code has to be set up to *catch* exceptions thrown from within LAMMPS.
    throw an exception and thus other MPI ranks may get stuck waiting for
    messages from the ones with errors.
 
-----------
-
-.. _trap_fpe:
-
-Trigger selected floating-point exceptions
-------------------------------------------
-
-Many kinds of CPUs have the capability to detect when a calculation
-results in an invalid math operation, like a division by zero or calling
-the square root with a negative argument.  The default behavior on
-most operating systems is to continue and have values for ``NaN`` (= not
-a number) or ``Inf`` (= infinity).  This allows software to detect and
-recover from such conditions.  This behavior can be changed, however,
-often through use of compiler flags.  On Linux systems (or more general
-on systems using the GNU C library), these so-called floating-point traps
-can also be selectively enabled through library calls.  LAMMPS supports
-that by setting the ``-DLAMMPS_TRAP_FPE`` pre-processor define.  As it is
-done in the ``main()`` function, this applies only to the standalone
-executable, not the library.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D CMAKE_TUNE_FLAGS=-DLAMMPS_TRAP_FPE
-
-   .. tab:: Traditional make
-
-      .. code-block:: make
-
-         LMP_INC = -DLAMMPS_TRAP_FPE  <other LMP_INC settings>
-
-After compilation with this flag set, the LAMMPS executable will stop
-and produce a core dump when a division by zero, overflow, illegal math
-function argument or other invalid floating point operation is encountered.
diff --git a/doc/src/Howto_cmake.rst b/doc/src/Howto_cmake.rst
index 6b8fc82bad..64acee47dd 100644
--- a/doc/src/Howto_cmake.rst
+++ b/doc/src/Howto_cmake.rst
@@ -285,7 +285,7 @@ when used before the CMake directory, there may be a space between the
 can have boolean values (on/off, yes/no, or 1/0 are all valid) or are
 strings representing a choice, or a path, or are free format. If the
 string would contain whitespace, it must be put in quotes, for example
-``-D CMAKE_TUNE_FLAGS="-ftree-vectorize -ffast-math"``.
+``-D CMAKE_CXX_FLAGS="-O3 -Wall -ftree-vectorize -ffast-math"``.
 
 CMake variables fall into two categories: 1) common CMake variables that
 are used by default for any CMake configuration setup and 2) project
@@ -341,8 +341,6 @@ Some common LAMMPS specific variables
      - compile some additional executables from the ``tools`` folder (default: ``off``)
    * - ``BUILD_DOC``
      - include building the HTML format documentation for packaging/installing (default: ``off``)
-   * - ``CMAKE_TUNE_FLAGS``
-     - common compiler flags, for optimization or instrumentation (default:)
    * - ``LAMMPS_MACHINE``
      - when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
    * - ``FFT``