[pull] develop from lammps:develop

doc/doxygen/Doxyfile.in

@@ -2,7 +2,7 @@
 
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "LAMMPS Programmer's Guide"
-PROJECT_NUMBER         = "10 December 2025"
+PROJECT_NUMBER         = "11 February 2026"
 PROJECT_BRIEF          = "Documentation of the LAMMPS library interface and Python wrapper"
 PROJECT_LOGO           = lammps-logo.png
 CREATE_SUBDIRS         = NO

doc/src/Manual_version.rst

@@ -79,10 +79,11 @@ About once a year, we release a *stable release* version of LAMMPS.
 This is done after a "stabilization period" where we apply only bug
 fixes and small, non-intrusive changes to the *develop* branch but no
 new features to the core code.  At the same time, the code is subjected
-to more detailed and thorough manual testing than the default automated
-testing.  After such a *stable release*, both the *release* and the
-*stable* branches are updated and two tags are applied, a
-``patch_1May2014`` format and a ``stable_1May2014`` format tag.
+to more detailed and thorough manual testing that goes beyond the
+automated testing done by default.  After such a *stable release*, both
+the *release* and the *stable* branches are updated and two tags are
+applied, a ``patch_1May2014`` format and a ``stable_1May2014`` format
+tag.
 
 Stable Release Updates
 """"""""""""""""""""""
@@ -92,4 +93,5 @@ back-ported from the *develop* branch in a branch called *maintenance*.
 From the *maintenance* branch we make occasional *stable update
 releases* and update the *stable* branch accordingly.  The first update
 to the ``stable_1May2014`` release would be tagged as
-``stable_1May2014_update1``.  These updates contain no new features.
+``stable_1May2014_update1``.  These updates contain no new features
+and are intended to be fully backward compatible.

src/citeme.h

@@ -53,7 +53,8 @@ that implements a published method or algorithm.
 
 \endverbatim
 
-   * \param reference  String containing the citation in BibTeX format with DOI header */
+ *
+ * \param reference  String containing the citation in BibTeX format with DOI header */
   void add(const std::string &reference);
 
   /** Flush accumulated citation buffers to screen and log file

src/label_map.h

@@ -58,7 +58,8 @@ class LabelMap : protected Pointers {
    * \param  nangletypes      Number of angle types in map
    * \param  ndihedraltypes   Number of dihedral types in map
    * \param  nimpropertypes   Number of improper types in map */
-  LabelMap(LAMMPS *lmp, int, int, int, int, int);
+  LabelMap(LAMMPS *lmp, int natomtypes, int nbondtypes, int nangletypes, int ndihedraltypes,
+           int nimpropertypes);
   ~LabelMap() override;
 
   /*! Process labelmap command from input script
@@ -72,7 +73,7 @@ Add or modify type label mappings from the LAMMPS
    *
    * \param  narg  Number of arguments
    * \param  arg   Array of argument strings */
-  void modify_lmap(int, char **);
+  void modify_lmap(int narg, char **arg);
 
   /*! Copy another LabelMap into this one
    *
@@ -87,7 +88,7 @@ Currently used when combining data from multiple sources with
    *
    * \param  lmap  Pointer to source LabelMap
    * \param  mode  Merge mode flag */
-  void merge_lmap(LabelMap *, int);
+  void merge_lmap(LabelMap *lmap, int mode);
 
   /*! Create index mapping between two LabelMaps
    *
@@ -96,7 +97,7 @@ Currently used when combining data from multiple sources with
    *
    * \param  lmap  Pointer to source LabelMap
    * \param  mode  Mapping mode flag */
-  void create_lmap2lmap(LabelMap *, int);
+  void create_lmap2lmap(LabelMap *lmap, int mode);
 
   /*! Find numeric type from type label
    *
@@ -146,7 +147,7 @@ Currently used when combining data from multiple sources with
    * \return         Bond type index if types match in the specified order,
    *                 negative bond type index if types match in reverse order,
    *                 0 if there is no match found */
-  int infer_bondtype(int, int);
+  int infer_bondtype(int atype1, int atype2);
 
   /*! Infer bond type from atom type labels
    *
@@ -158,7 +159,7 @@ Currently used when combining data from multiple sources with
    * \return         Bond type index if types match in the specified order,
    *                 negative bond type index if types match in reverse order,
    *                 0 if there is no match found */
-  int infer_bondtype(const std::vector<std::string> &);
+  int infer_bondtype(const std::vector<std::string> &labels);
 
   /*! Infer angle type from three numeric atom types
    *
@@ -171,7 +172,7 @@ Currently used when combining data from multiple sources with
    * \return         Angle type index if types match in the specified order,
    *                 negative angle type index if types match in reverse order,
    *                 0 if there is no match found */
-  int infer_angletype(int, int, int);
+  int infer_angletype(int atype1, int atype2, int atype3);
 
   /*! Infer angle type from three atom type labels
    *
@@ -183,7 +184,7 @@ Currently used when combining data from multiple sources with
    * \return         Angle type index if types match in the specified order,
    *                 negative angle type index if types match in reverse order,
    *                 0 if there is no match found */
-  int infer_angletype(const std::vector<std::string> &);
+  int infer_angletype(const std::vector<std::string> &labels);
 
   /*! Infer dihedral type from four numeric atom types
    *
@@ -197,7 +198,7 @@ Currently used when combining data from multiple sources with
    * \return         Dihedral type index if types match in the specified order,
    *                 negative dihedral type index if types match in reverse order,
    *                 0 if there is no match found */
-  int infer_dihedraltype(int, int, int, int);
+  int infer_dihedraltype(int atype1, int atype2, int atype3, int atype4);
 
   /*! Infer dihedral type from atom type labels
    *
@@ -209,7 +210,7 @@ Currently used when combining data from multiple sources with
    * \return         Dihedral type index if types match in the specified order,
    *                 negative dihedral type index if types match in reverse order,
    *                 0 if there is no match found */
-  int infer_dihedraltype(const std::vector<std::string> &);
+  int infer_dihedraltype(const std::vector<std::string> &labels);
 
   /*! Infer improper type from four numeric atom types
    *
@@ -224,7 +225,8 @@ Currently used when combining data from multiple sources with
    * \return         Improper type index if types match in the specified order,
    *                 negative improper type index if types match but different order,
    *                 0 if there is no match found */
-  int infer_impropertype(int, int, int, int, std::array<int, 4> *iorder = nullptr);
+  int infer_impropertype(int atype1, int atype2, int atype3, int atype4,
+                         std::array<int, 4> *iorder = nullptr);
 
   /*! Infer improper type from atom type labels
    *
@@ -237,7 +239,8 @@ Currently used when combining data from multiple sources with
    * \return         Improper type index if types match in the specified order,
    *                 negative improper type index if types match but different order,
    *                 0 if there is no match found */
-  int infer_impropertype(const std::vector<std::string> &, std::array<int, 4> *iorder = nullptr);
+  int infer_impropertype(const std::vector<std::string> &labels,
+                         std::array<int, 4> *iorder = nullptr);
 
   /*! @} */
 
@@ -246,11 +249,11 @@ Currently used when combining data from multiple sources with
    * Split a hyphen-delimited label (e.g., "C-N-H") into individual type strings.
    * Validates that the number of components matches the expected count.
    *
-   * \param  ntypes  Expected number of components
-   * \param  label   Hyphen-delimited label string
-   * \param  types   Output vector to store component strings
-   * \return         0 on success, -1 if component count doesn't match ntypes */
-  int parse_typelabel(int, const std::string &, std::vector<std::string> &);
+   * \param       ntypes  Expected number of components
+   * \param       label   Hyphen-delimited label string
+   * \param[out]  types   Output vector to store component strings
+   * \return      0 on success, -1 if component count doesn't match ntypes */
+  int parse_typelabel(int ntypes, const std::string &label, std::vector<std::string> &types);
 
   /*! \name I/O methods for label map persistence
    * @{ */
@@ -260,7 +263,7 @@ Currently used when combining data from multiple sources with
    * Output all type labels as sections to a LAMMPS data file.
    *
    * \param  fp  File pointer for writing */
-  void write_data(FILE *);
+  void write_data(FILE *fp);
 
   /*! Read label map from restart file
    *
@@ -284,11 +287,11 @@ Currently used when combining data from multiple sources with
       atypelabel;                                     //!< Label storage (atoms, bonds, angles)
   std::vector<std::string> dtypelabel, itypelabel;    //!< Label storage (dihedrals, impropers)
 
-  std::unordered_map<std::string, int> typelabel_map;     //!< Atom label → type mapping
-  std::unordered_map<std::string, int> btypelabel_map;    //!< Bond label → type mapping
-  std::unordered_map<std::string, int> atypelabel_map;    //!< Angle label → type mapping
-  std::unordered_map<std::string, int> dtypelabel_map;    //!< Dihedral label → type mapping
-  std::unordered_map<std::string, int> itypelabel_map;    //!< Improper label → type mapping
+  std::unordered_map<std::string, int> typelabel_map;     //!< Atom label -> type mapping
+  std::unordered_map<std::string, int> btypelabel_map;    //!< Bond label -> type mapping
+  std::unordered_map<std::string, int> atypelabel_map;    //!< Angle label -> type mapping
+  std::unordered_map<std::string, int> dtypelabel_map;    //!< Dihedral label -> type mapping
+  std::unordered_map<std::string, int> itypelabel_map;    //!< Improper label -> type mapping
 
   /*! \struct Lmap2Lmap
    *  \brief Mapping structure between two LabelMaps
@@ -307,16 +310,51 @@ Currently used when combining data from multiple sources with
   Lmap2Lmap lmap2lmap;    //!< Instance of inter-map translation data
 
   void reset_type_labels();    //!< Clear all type labels
-  int find_or_create(
-      const std::string &, std::vector<std::string> &,
-      std::unordered_map<std::string, int> &);    //!< Look up type or create new type
-  int search(const std::string &,
-             const std::unordered_map<std::string, int> &) const;    //!< Look up type index
-  char *read_string(FILE *);                         //!< Read string from binary file
-  void write_string(const std::string &, FILE *);    //!< Write string to binary file
-  int read_int(FILE *);                              //!< Read integer from binary file
-
-  void write_map(const std::string &);    //!< Write label map to file for debugging
+
+  /*! Look up type label with given name or create new label if it doesn't exist
+
+   * \param          mylabel     string with type label
+   * \param[in,out]  labels      list of type labels
+   * \param[in,out]  labels_map  label to numeric type hash table
+   * \return numeric type
+   */
+  int find_or_create(const std::string &mylabel, std::vector<std::string> &labels,
+                     std::unordered_map<std::string, int> &labels_map);
+
+  /*! Look up numeric type of type label string in type map
+   *
+   * \param mylabel      type label
+   * \param labels_map   label to type map
+   * \return numeric type or -1 if not found */
+  int search(const std::string &mylabel,
+             const std::unordered_map<std::string, int> &labels_map) const;
+
+  /*! Read a C-style string from a binary file and broadcast to world communicator
+   *
+   * the string buffer is allocated with new and must be freed by the calling code with delete[]
+   *
+   * \param fp  FILE pointer of the openend file
+   * \return pointer to the allocated string buffer */
+  char *read_string(FILE *fp);
+
+  /*! Encode string to binary file.
+   *
+   * Must be only called from MPI rank 0.
+   *
+   * \param str string to write to the file
+   * \param fp  FILE pointer of the opened file */
+  void write_string(const std::string &str, FILE *fp);
+
+  /*! Read integer from binary file and broadcast it to world communicator
+   *
+   * \param fp FILE pointer of the opened file
+   * \return  integer value read from file */
+  int read_int(FILE *fp);
+
+  /*! Write out current label maps to a file for debugging
+   *
+   * \param filename  file name */
+  void write_map(const std::string &filename);
 };
 
 }    // namespace LAMMPS_NS

src/platform.h

@@ -256,12 +256,12 @@ std::string find_exe_path(const std::string &cmd);
 
 int chdir(const std::string &path);
 
-/*! Create a directory
+/*! Create a directory or directory path
  *
- * Unlike the the ``mkdir()`` or ``_mkdir()`` functions of the
- * C library, this function will also try to create non-existing sub-directories
- * in case they don't exist, and thus behaves like the ``mkdir -p`` command rather
- * than plain ``mkdir`` or ``md`.
+ * Unlike the the ``mkdir()`` or ``_mkdir()`` functions of the C library, this
+ * function will also try to create non-existing sub-directories in case they
+ * don't exist, and thus it behaves like the ``mkdir -p`` command rather than
+ * plain ``mkdir`` or ``md`` in a Unix or Windows shell, respectively.
  *
  * \param  path  directory path
  * \return -1 if unsuccessful, otherwise >= 0  */

src/utils.h

@@ -426,13 +426,14 @@ tagint tnumeric(const char *file, int line, const char *str, bool do_abort, LAMM
  * - a single asterisk followed by a number, \*i: nlo = nmin; nhi = i;
  * - two numbers with an asterisk in between. i\*j: nlo = i; nhi = j;
  *
+ * \tparam TYPE    the type of the index that is subject to the wildcard expansion
  * \param file     name of source file for error message
  * \param line     line number in source file for error message
  * \param str      string to be processed
  * \param nmin     smallest possible lower bound
  * \param nmax     largest allowed upper bound
- * \param nlo      lower bound
- * \param nhi      upper bound
+ * \param[out] nlo lower bound
+ * \param[out] nhi upper bound
  * \param error    pointer to Error class for out-of-bounds messages
  * \param failed   argument index with failed expansion (optional) */
 
@@ -452,13 +453,14 @@ This functions adds the following case to :cpp:func:`utils::bounds() <LAMMPS_NS:
 
 \endverbatim
 
+ * \tparam TYPE    the type of the index that is subject to the boundary expansion
  * \param file     name of source file for error message
  * \param line     line number in source file for error message
  * \param str      string to be processed
  * \param nmin     smallest possible lower bound
  * \param nmax     largest allowed upper bound
- * \param nlo      lower bound
- * \param nhi      upper bound
+ * \param[out] nlo lower bound
+ * \param[out] nhi upper bound
  * \param lmp      pointer to top-level LAMMPS class instance
  * \param mode     select labelmap using constants from Atom class */
 
@@ -720,8 +722,7 @@ size_t trim_and_count_words(const std::string &text, const std::string &separato
  * \param sep     separator string (may be empty)
  * \return  string with the concatenated values and separators */
 
-template <typename T>
-std::string join(const std::vector<T> &values, const std::string &sep);
+template <typename T> std::string join(const std::vector<T> &values, const std::string &sep);
 
 /*! Take list of words and join them with a given separator text.
  *