[pull] develop from lammps:develop

doc/src/Developer_code_design.rst

@@ -278,10 +278,10 @@ I/O and output formatting
 C-style stdio versus C++ style iostreams
 ========================================
 
-LAMMPS uses the `stdio <https://en.cppreference.com/w/cpp/io/c.html>`
+LAMMPS uses the `stdio <https://cppreference.com/w/cpp/io/c.html>`
 library of the standard C library for reading from and writing to files
 and console instead of C++ `iostreams
-<https://en.cppreference.com/w/cpp/io.html>`_.  This is mainly motivated
+<https://cppreference.com/w/cpp/io.html>`_.  This is mainly motivated
 by better performance, better control over formatting, and less effort
 to achieve specific formatting.
 
@@ -294,36 +294,43 @@ Furthermore, output should generally only be done by MPI rank 0
 ``logfile`` should use the :cpp:func:`utils::logmesg() convenience
 function <LAMMPS_NS::utils::logmesg>`.
 
-We discourage the use of `stringstreams
-<https://en.cppreference.com/w/cpp/io/basic_stringstream.html>`_ because
-the bundled {fmt} library and the customized tokenizer classes provide
-the same functionality in a cleaner way with better performance.  This
-also helps maintain a consistent programming syntax with code from many
-different contributors.
-
-Formatting with the {fmt} library
-===================================
-
-The LAMMPS source code includes a copy of the `{fmt} library
-<https://fmt.dev>`_, which is preferred over formatting with the
-"printf()" family of functions.  The primary reason is that it allows a
-typesafe default format for any type of supported data.  This is
-particularly useful for formatting integers of a given size (32-bit or
-64-bit) which may require different format strings depending on compile
-time settings or compilers/operating systems.  Furthermore, {fmt} gives
-better performance, has more functionality, a familiar formatting syntax
-that has similarities to ``format()`` in Python, and provides a facility
-that can be used to integrate format strings and a variable number of
+We strongly discourage the use of `stringstreams
+<https://cppreference.com/w/cpp/io/basic_stringstream.html>`_ because
+the bundled `{fmt} library <https://fmt.dev>`_ or the `C++ format
+library <https://cppreference.com/w/cpp/utility/format.html>`_ (for
+C++20 and later) and the customized tokenizer classes provide the same
+functionality in a cleaner way with better performance.  This also helps
+maintain a consistent programming syntax with code from many different
+contributors.
+
+Formatting with the {fmt} library and std::format
+=================================================
+
+The LAMMPS source code currently includes a slightly modified copy of
+the `{fmt} library <https://fmt.dev>`_, which is preferred over
+formatting with the "printf()" family of functions.  When compiling for
+C++20 and later we switch to using the `C++ format library
+<https://cppreference.com/w/cpp/utility/format.html>`_.  The namespace
+prefix currently remains ``fmt::`` through a small wrapper.  In the
+future, this will be switched to ``std::`` when LAMMPS requires the
+C++20 standard as the minimum C++ standard.  Thus only functionality
+compatible with the C++ format library for C++20 is accepted.  Using
+``std::format`` requires a fully C++20 compatible compiler (e.g. GCC 13
+and later, Clang 14 and later, or MSVC 16.10 and later) and we `use the
+__cpp_lib_format feature test macro
+<https://cppreference.com/w/cpp/utility/feature_test.html>`_ to confirm
+the availability of ``std::format``.
+
+The primary reason for this choice is that it allows a typesafe default
+format for any type of supported data.  This is particularly useful for
+formatting integers of a given size (32-bit or 64-bit) which may require
+different format strings depending on compile time settings or
+compilers/operating systems.  Furthermore, {fmt} gives better
+performance, has more functionality, a familiar formatting syntax that
+has similarities to ``format()`` in Python, and provides a facility that
+can be used to integrate format strings and a variable number of
 arguments into custom functions in a much simpler way than the varargs
-mechanism of the C library.  Finally, {fmt} has been included into the
-C++20 language standard as ``std::format()``, so changes to adopt it are
-future-proof, for as long as they are not using any extensions that are
-not (yet) included into C++.
-
-The long-term plan is to switch to using ``std::format()`` instead of
-``fmt::format()`` when the minimum C++ standard required for LAMMPS will
-be set to C++20. See the :ref:`basic build instructions <compile>` for
-more details.
+mechanism of the C library.
 
 Formatted strings are frequently created by calling the
 ``fmt::format()`` function, which will return a string as a
@@ -334,15 +341,15 @@ choose the default format based on the data type of the argument.
 Otherwise, the :cpp:func:`utils::print() <LAMMPS_NS::utils::print>`
 function may be used instead of ``printf()`` or ``fprintf()``.  The
 equivalent `std::print() function
-<https://en.cppreference.com/w/cpp/io/print.html>`_ will become
+<https://cppreference.com/w/cpp/io/print.html>`_ will become
 available in C++ 23.  In addition, several LAMMPS output functions, that
 originally accepted a single string as argument have been overloaded to
 accept a format string with optional arguments as well (e.g.,
 ``Error::all()``, ``Error::one()``, :cpp:func:`utils::logmesg()
 <LAMMPS_NS::utils::logmesg>`).
 
-Summary of the {fmt} format syntax
-==================================
+Summary of the {fmt} format and std::format syntax
+==================================================
 
 The syntax of the format string is "{[<argument id>][:<format spec>]}",
 where either the argument id or the format spec (separated by a colon
@@ -404,11 +411,13 @@ value, for example "{:{}d}" will consume two integer arguments, the
 first will be the value shown and the second the minimum width.
 
 For more details and examples, please consult the `{fmt} syntax
-documentation <https://fmt.dev/latest/syntax/>`_ website.  Since we
-plan to eventually transition from {fmt} to using ``std::format()``
+documentation <https://fmt.dev/latest/syntax/>`_ website or the
+`corresponding C++ syntax reference
+<https://cppreference.com/w/cpp/utility/format/spec.html>`_.  Since
+we plan to eventually transition from {fmt} to using ``std::format()``
 of the C++ standard library, it is advisable to avoid using any
 extensions beyond what the `C++20 standard offers
-<https://en.cppreference.com/w/cpp/utility/format/format.html>`_.
+<https://cppreference.com/w/cpp/utility/format/format.html>`_.
 
 JSON format input and output
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Developer_notes.rst

@@ -290,8 +290,10 @@ all three signatures, the single string "Error message" may be replaced
 with a format string using '{}' placeholders and followed by a variable
 number of arguments, one for each placeholder. This format string and
 the arguments are then handed for formatting to the `{fmt} library
-<https://fmt.dev>`_ (which is bundled with LAMMPS) and thus allow
-processing similar to the "format()" functionality in Python.
+<https://fmt.dev>`_ (which is bundled with LAMMPS) or the `C++ format
+library <https://cppreference.com/w/cpp/utility/format.html>`_ (for
+C++20 and later) and thus allow processing similar to the "format()"
+functionality in Python.
 
 .. note::
 

doc/src/Developer_platform.rst

@@ -51,12 +51,12 @@ File and path functions and global constants
 
 Since we are requiring C++17 to compile LAMMPS, you can also make use of
 the functionality of the `C++ filesystem library
-<https://en.cppreference.com/w/cpp/filesystem.html>`_.  The following
+<https://cppreference.com/w/cpp/filesystem.html>`_.  The following
 functions are in part convenience functions or emulate the behavior of
 similar Python functions or Unix shell commands.  Please note that the
 you need to use the ``string()`` member function of the
 `std::filesystem::path class
-<https://en.cppreference.com/w/cpp/filesystem/path.html>`_ to get access
+<https://cppreference.com/w/cpp/filesystem/path.html>`_ to get access
 to the path as a C++ string class instance.
 
 .. doxygenvariable:: filepathsep

doc/src/Developer_unittest.rst

@@ -55,7 +55,7 @@ available:
      - Tests for ``ArgInfo`` class used by LAMMPS
    * - ``test_fmtlib.cpp``
      - FmtLib
-     - Tests for ``fmtlib::`` functions used by LAMMPS
+     - Tests for ``{fmt}`` or ``std::format`` functions used by LAMMPS
    * - ``test_math_eigen_impl.cpp``
      - MathEigen
      - Tests for ``MathEigen::`` classes and functions

doc/src/Developer_utils.rst

@@ -160,6 +160,9 @@ and parsing files or arguments.
 .. doxygenfunction:: trim_and_count_words
    :project: progguide
 
+.. doxygenfunction:: join
+   :project: progguide
+
 .. doxygenfunction:: join_words
    :project: progguide
 

doc/src/Modify_requirements.rst

@@ -313,10 +313,15 @@ so that one could look up the cause by reading the source code.
 
 The new policy encourages more specific error messages that ideally
 indicate the cause directly, and requiring no further lookup. This is
-aided by the `{fmt} library <https://fmt.dev>`_ enabling Error class
-methods that take a variable number of arguments and an error text that
-will be treated like a {fmt} syntax format string.  Error messages should
-still preferably be kept to a single line or two lines at most.
+aided by either the `{fmt} library <https://fmt.dev>`_ or the `C++
+format library
+<https://cppreference.com/w/cpp/utility/format.html>`_ (for C++20
+and later) enabling :cpp:class:`LAMMPS_NS::Error` class methods that
+take a variable number of arguments and an error text that will be
+treated like a `C++ format string
+<https://cppreference.com/w/cpp/utility/format/spec.html>`_. Error
+messages should still preferably be kept to a single line or two lines
+at most.
 
 For more complex explanations or errors that have multiple possible
 reasons, a paragraph should be added to the `Error_details` page with an

doc/src/Modify_style.rst

@@ -39,8 +39,9 @@ Include files (varied)
   derived from it), certain headers will *always* be included and thus
   do not need to be explicitly specified.  These are: `mpi.h`,
   `cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`, `vector`,
-  `fmt/format.h`, `climits`, `cinttypes`.  This also means any such file
-  can assume that `FILE`, `NULL`, and `INT_MAX` are defined.
+  `fmt/format.h` (or `format` when using C++20 and later), `climits`,
+  `cinttypes`.  This also means any such file can assume that `FILE`,
+  `NULL`, and `INT_MAX` are defined.
 
 - Class members variables should not be initialized in the header file,
   but instead should be initialized either in the initializer list of

src/APIP/pair_eam_fs_apip.cpp

@@ -24,6 +24,8 @@
 #include "memory.h"
 #include "potential_file_reader.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
@@ -46,12 +48,8 @@ void PairEAMFSAPIP::coeff(int narg, char **arg)
 
   if (!allocated) allocate();
 
-  if (narg != 3 + atom->ntypes) error->all(FLERR, "Incorrect args for pair coefficients");
-
-  // insure I,J args are * *
-
-  if (strcmp(arg[0], "*") != 0 || strcmp(arg[1], "*") != 0)
-    error->all(FLERR, "Incorrect args for pair coefficients");
+  if (narg != 3 + atom->ntypes)
+    error->all(FLERR, "Number of element to type mappings does not match number of atom types");
 
   // read EAM Finnis-Sinclair file
 
@@ -104,7 +102,7 @@ void PairEAMFSAPIP::coeff(int narg, char **arg)
     }
   }
 
-  if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
+  if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21));
 }
 
 /* ----------------------------------------------------------------------
@@ -136,14 +134,8 @@ void PairEAMFSAPIP::read_file(char *filename)
         error->one(FLERR, "Incorrect element names in EAM potential file");
 
       file->elements = new char *[file->nelements];
-      for (int i = 0; i < file->nelements; i++) {
-        const std::string word = values.next_string();
-        const int n = word.length() + 1;
-        file->elements[i] = new char[n];
-        strcpy(file->elements[i], word.c_str());
-      }
-
-      //
+      for (int i = 0; i < file->nelements; i++)
+        file->elements[i] = utils::strdup(values.next_string());
 
       if (he_flag)
         values = reader.next_values(6);

src/EFF/pair_eff_inline.h

@@ -15,6 +15,8 @@
  Contributing authors: Andres Jaramillo-Botero, Hai Xiao, Julius Su (Caltech)
 ------------------------------------------------------------------------- */
 
+#include <cmath>
+
 namespace LAMMPS_NS {
 
 #define PAULI_RE 0.9

src/EXTRA-DUMP/dump_dcd.cpp

@@ -22,7 +22,6 @@
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
-#include "fmt/chrono.h"
 #include "group.h"
 #include "memory.h"
 #include "output.h"
@@ -318,7 +317,7 @@ void DumpDCD::write_dcd_header(const char *remarks)
   float out_float;
   char title_string[200];
   time_t t;
-  std::tm current_time;
+  struct tm *current_time;
 
   int ntimestep = update->ntimestep;
 
@@ -350,14 +349,19 @@ void DumpDCD::write_dcd_header(const char *remarks)
   fwrite_int32(fp,84);
   fwrite_int32(fp,164);
   fwrite_int32(fp,2);
-  strncpy(title_string,remarks,80);
-  title_string[79] = '\0';
+  // pad string with blanks and truncate at 80 chars
+  snprintf(title_string, sizeof(title_string),
+           "%s                                        "
+           "                                        ", remarks);
   fwrite(title_string,80,1,fp);
   t = time(nullptr);
-  current_time = fmt::localtime(t);
-  std::string s = fmt::format("REMARKS Created {:%d %B,%Y at %H:%M}", current_time);
-  memset(title_string,' ',81);
-  memcpy(title_string, s.c_str(), s.size());
+  current_time = localtime(&t);
+  // pad string with blanks and truncate at 80 chars
+  strftime(title_string, sizeof(title_string),
+           "REMARKS Created %d %B,%Y at %H:%M"
+           "                                        "
+           "                                        ",
+           current_time);
   fwrite(title_string,80,1,fp);
   fwrite_int32(fp,164);
   fwrite_int32(fp,4);

src/EXTRA-FIX/fix_addtorque_group.cpp

@@ -30,6 +30,8 @@
 #include "update.h"
 #include "variable.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/GPU/pair_amoeba_gpu.cpp

@@ -33,6 +33,7 @@
 #include "suffix.h"
 
 #include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/INTEL/intel_preprocess.h

@@ -18,6 +18,8 @@
 
 #include "lmptype.h"
 
+#include <cmath>
+
 #ifdef __INTEL_LLVM_COMPILER
 #define USE_OMP_SIMD
 #define __INTEL_COMPILER_BUILD_DATE __INTEL_LLVM_COMPILER

src/INTEL/math_extra_intel.h

@@ -19,6 +19,8 @@
 #ifndef LMP_MATH_EXTRA_INTEL_H
 #define LMP_MATH_EXTRA_INTEL_H
 
+#include <cmath>
+
 #define ME_quat_to_mat_trans(quat, mat)         \
 {                                               \
   flt_t quat_w = quat.w;                        \

src/INTEL/pair_dpd_intel.cpp

@@ -28,6 +28,7 @@
 #include "suffix.h"
 
 #include <cmath>
+#include <cstring>
 
 #if defined(_OPENMP)
 #include <omp.h>

src/INTEL/pppm_intel.cpp

@@ -34,6 +34,7 @@
 #include "suffix.h"
 
 #include <cmath>
+#include <cstring>
 
 #include "omp_compat.h"
 

src/KIM/kim_interactions.cpp

@@ -70,8 +70,6 @@
 #include "modify.h"
 #include "update.h"
 
-#include "fmt/ranges.h"
-
 #include <cstring>
 #include <vector>
 
@@ -130,8 +128,7 @@ void KimInteractions::do_setup(int narg, char **arg)
   if (simulatorModel) {
     auto first_visit = input->variable->find("kim_update");
     if (!fixed_types) {
-      std::string atom_type_sym_list =
-        fmt::format("{}", fmt::join(arg, arg + narg, " "));
+      std::string atom_type_sym_list = utils::join(std::vector(arg, arg + narg), " ");
 
       std::string atom_type_num_list =
         fmt::format("{}", species_to_atomic_no(arg[0]));
@@ -250,7 +247,7 @@ void KimInteractions::do_setup(int narg, char **arg)
 
     auto cmd1 = fmt::format("pair_style kim {}", model_name);
     auto cmd2 =
-      fmt::format("pair_coeff * * {}", fmt::join(arg, arg + narg, " "));
+      fmt::format("pair_coeff * * {}", utils::join(std::vector(arg, arg + narg), " "));
 
     input->one(cmd1);
     input->one(cmd2);
@@ -308,7 +305,7 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con
           if (((species[ia] == words[0]) && (species[ib] == words[1]))
               || ((species[ib] == words[0]) && (species[ia] == words[1])))
             input->one(fmt::format("pair_coeff {} {} {}", ia + 1, ib + 1,
-              fmt::join(words.begin() + 2, words.end(), " ")));
+                                   utils::join(std::vector(words.begin() + 2, words.end()), " ")));
       }
     } else {
       for (int ia = 0; ia < atom->ntypes; ++ia)