Merge branch 'develop' into lammps-gui-improvements

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,7 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-17.0
+                                          clang-format-16.0
                                           clang-format-15.0
                                           clang-format-14.0
                                           clang-format-13.0
@@ -19,7 +21,7 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
+  if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*")
     # Arch Linux output:
     # clang-format version 10.0.0
     #
@@ -32,9 +34,15 @@ if(ClangFormat_EXECUTABLE)
     # Ubuntu 22.04 LTS output:
     # Ubuntu clang-format version 14.0.0-1ubuntu1
     #
+    # Debian 11 output:
+    # Debian clang-format version 11.0.1-2
+    #
+    # Debian 12 output:
+    # Debian clang-format version 14.0.6
+    #
     # Fedora 36 output:
     # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
-    string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
+    string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*"
                          "\\2"
                          ClangFormat_VERSION
                          "${clang_format_version}")

doc/src/Howto_cmake.rst

@@ -1,10 +1,10 @@
-Using CMake with LAMMPS tutorial
+Using CMake with LAMMPS
-================================
+=======================
 
 The support for building LAMMPS with CMake is a recent addition to
 LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard
 Berger (LANL).  One of the key strengths of CMake is that it is not
-tied to a specific platform or build system and thus it generates the
+tied to a specific platform or build system. Instead it generates the
 files necessary to build and develop for different build systems and on
 different platforms.  Note, that this applies to the build system itself
 not the LAMMPS code. In other words, without additional porting effort,
@@ -32,7 +32,8 @@ program ``cmake`` (or ``cmake3``), a text mode interactive user
 interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user
 interface (GUI) program ``cmake-gui``.  All of them are portable
 software available on all supported platforms and can be used
-interchangeably.  The minimum required CMake version is 3.16.
+interchangeably.  As of LAMMPS version 2 August 2023, the minimum
+required CMake version is 3.16.
 
 All details about features and settings for CMake are in the `CMake
 online documentation <https://cmake.org/documentation/>`_. We focus

doc/src/Speed_kokkos.rst

@@ -18,7 +18,7 @@ package was developed primarily by Christian Trott (Sandia) and Stan
 Moore (Sandia) with contributions of various styles by others,
 including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
 (Sandia). For more information on developing using Kokkos abstractions
-see the Kokkos `Wiki <https://github.com/kokkos/kokkos/wiki>`_.
+see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
 
 Kokkos currently provides support for 4 modes of execution (per MPI
 task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
@@ -32,8 +32,9 @@ produce an executable compatible with a specific hardware.
    Kokkos requires using a compiler that supports the c++17 standard. For
    some compilers, it may be necessary to add a flag to enable c++17 support.
    For example, the GNU compiler uses the -std=c++17 flag. For a list of
-   compilers that have been tested with the Kokkos library, see the Kokkos
+   compilers that have been tested with the Kokkos library, see the
-   `Wiki <https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
+   `requirements document of the Kokkos Wiki
+   <https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
 
 .. admonition:: NVIDIA CUDA support
    :class: note

lib/gpu/lal_dpd.cu

@@ -301,9 +301,10 @@ __kernel void k_dpd_fast(const __global numtyp4 *restrict x_,
   __local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
   __local numtyp sp_lj[4];
   __local numtyp sp_sqrt[4];
-  if (tid<4)
+  if (tid<4) {
     sp_lj[tid]=sp_lj_in[tid];
     sp_sqrt[tid]=sp_sqrt_in[tid];
+  }
   if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
     coeff[tid]=coeff_in[tid];
   }

src/compute_global_atom.cpp

@@ -438,8 +438,8 @@ void ComputeGlobalAtom::compute_peratom()
         }
       }
     }
+    ++m;
   }
-  ++m;
 }
 
 /* ----------------------------------------------------------------------

src/fmt/core.h

@@ -13,11 +13,12 @@
 #include <cstring>  // std::strlen
 #include <iterator>
 #include <limits>
+#include <memory>  // std::addressof
 #include <string>
 #include <type_traits>
 
 // The fmt library version in the form major * 10000 + minor * 100 + patch.
-#define FMT_VERSION 100001
+#define FMT_VERSION 100100
 
 #if defined(__clang__) && !defined(__ibmxl__)
 #  define FMT_CLANG_VERSION (__clang_major__ * 100 + __clang_minor__)
@@ -1290,9 +1291,9 @@ template <typename Context> class value {
   FMT_INLINE value(const named_arg_info<char_type>* args, size_t size)
       : named_args{args, size} {}
 
-  template <typename T> FMT_CONSTEXPR FMT_INLINE value(T& val) {
+  template <typename T> FMT_CONSTEXPR20 FMT_INLINE value(T& val) {
     using value_type = remove_const_t<T>;
-    custom.value = const_cast<value_type*>(&val);
+    custom.value = const_cast<value_type*>(std::addressof(val));
     // Get the formatter type through the context to allow different contexts
     // have different extension points, e.g. `formatter<T>` for `format` and
     // `printf_formatter<T>` for `printf`.
@@ -1669,6 +1670,7 @@ template <typename Context> class basic_format_arg {
   ``vis(value)`` will be called with the value of type ``double``.
   \endrst
  */
+// DEPRECATED!
 FMT_EXPORT
 template <typename Visitor, typename Context>
 FMT_CONSTEXPR FMT_INLINE auto visit_format_arg(

src/fmt/format.h

@@ -920,7 +920,7 @@ class basic_memory_buffer final : public detail::buffer<T> {
  private:
   T store_[SIZE];
 
-  // Don't inherit from Allocator avoid generating type_info for it.
+  // Don't inherit from Allocator to avoid generating type_info for it.
   FMT_NO_UNIQUE_ADDRESS Allocator alloc_;
 
   // Deallocate memory allocated by the buffer.
@@ -3178,7 +3178,8 @@ FMT_CONSTEXPR20 inline void format_dragon(basic_fp<uint128_t> value,
       }
       if (buf[0] == overflow) {
         buf[0] = '1';
-        ++exp10;
+        if ((flags & dragon::fixed) != 0) buf.push_back('0');
+        else ++exp10;
       }
       return;
     }

src/fmt/std.h

@@ -8,6 +8,7 @@
 #ifndef FMT_STD_H_
 #define FMT_STD_H_
 
+#include <bitset>
 #include <cstdlib>
 #include <exception>
 #include <memory>
@@ -15,6 +16,7 @@
 #include <type_traits>
 #include <typeinfo>
 #include <utility>
+#include <vector>
 
 #include "format.h"
 #include "ostream.h"
@@ -389,6 +391,50 @@ struct formatter<
 #endif
   }
 };
+
+namespace detail {
+
+template <typename T, typename Enable = void>
+struct has_flip : std::false_type {};
+
+template <typename T>
+struct has_flip<T, void_t<decltype(std::declval<T>().flip())>>
+    : std::true_type {};
+
+template <typename T> struct is_bit_reference_like {
+  static constexpr const bool value =
+      std::is_convertible<T, bool>::value &&
+      std::is_nothrow_assignable<T, bool>::value && has_flip<T>::value;
+};
+
+#ifdef _LIBCPP_VERSION
+
+// Workaround for libc++ incompatibility with C++ standard.
+// According to the Standard, `bitset::operator[] const` returns bool.
+template <typename C>
+struct is_bit_reference_like<std::__bit_const_reference<C>> {
+  static constexpr const bool value = true;
+};
+
+#endif
+
+}  // namespace detail
+
+// We can't use std::vector<bool, Allocator>::reference and
+// std::bitset<N>::reference because the compiler can't deduce Allocator and N
+// in partial specialization.
+FMT_EXPORT
+template <typename BitRef, typename Char>
+struct formatter<BitRef, Char,
+                 enable_if_t<detail::is_bit_reference_like<BitRef>::value>>
+    : formatter<bool, Char> {
+  template <typename FormatContext>
+  FMT_CONSTEXPR auto format(const BitRef& v, FormatContext& ctx) const
+      -> decltype(ctx.out()) {
+    return formatter<bool, Char>::format(v, ctx);
+  }
+};
+
 FMT_END_NAMESPACE
 
 #endif  // FMT_STD_H_

src/image.cpp

@@ -1384,7 +1384,7 @@ double *Image::color2rgb(const char *color, int index)
     {0/255.0, 0/255.0, 139/255.0},
     {0/255.0, 139/255.0, 139/255.0},
     {184/255.0, 134/255.0, 11/255.0},
-    {169/255.0, 169/255.0, 169/255.0},
+    {69/255.0, 69/255.0, 69/255.0},
     {0/255.0, 100/255.0, 0/255.0},
     {189/255.0, 183/255.0, 107/255.0},
     {139/255.0, 0/255.0, 139/255.0},

unittest/formats/CMakeLists.txt

@@ -41,8 +41,6 @@ set_tests_properties(TextFileReader PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${
 add_executable(test_file_operations test_file_operations.cpp)
 target_link_libraries(test_file_operations PRIVATE lammps GTest::GMock)
 add_test(NAME FileOperations COMMAND test_file_operations)
-# try to mitigate possible OpenMPI bug
-set_tests_properties(TextFileReader PROPERTIES ENVIRONMENT "OMPI_MCA_sharedfp=\"^sm\"")
 
 add_executable(test_dump_atom test_dump_atom.cpp)
 target_link_libraries(test_dump_atom PRIVATE lammps GTest::GMock)