Merge pull request #2336 from akohlmey/collected-small-changes

Collected small changes for the next patch release

cmake/CMakeLists.txt

@@ -218,10 +218,9 @@ if(BUILD_OMP)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
 
-  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9)) OR
-      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 9.99.9)) OR
-      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 18.99.9))
-      )
+  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
     target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4)

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -55,8 +55,8 @@ if(DOWNLOAD_PLUMED)
   endif()
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
-    URL_MD5 204d2edae58d9b10ba3ad460cad64191
+    URL https://github.com/plumed/plumed2/releases/download/v2.6.1/plumed-src-2.6.1.tgz
+    URL_MD5 89a9a450fc6025299fe16af235957163
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}

doc/src/fix_property_atom.rst

@@ -105,7 +105,7 @@ keyword with a value of *yes*\ .  This will invoke extra communication
 when ghost atoms are created (at every re-neighboring) to insure the
 new properties are also defined for the ghost atoms.
 
-.. note::
+.. admonition:: Properties on ghost atoms
 
    If you use this command with the *mol*\ , *q* or *rmass* vectors,
    then you most likely want to set *ghost* yes, since these properties
@@ -115,7 +115,7 @@ new properties are also defined for the ghost atoms.
    atoms to have these values.  LAMMPS will issue a warning it you define
    those vectors but do not set *ghost* yes.
 
-.. note::
+.. admonition:: Limitations on ghost atom properties
 
    The properties for ghost atoms are not updated every timestep,
    but only once every few steps when neighbor lists are re-built.  Thus
@@ -126,12 +126,6 @@ new properties are also defined for the ghost atoms.
    that can be invoked from within a :doc:`pair style <pair_style>` or
    :doc:`fix <fix>` or :doc:`compute <compute>` that you write.
 
-.. note::
-
-   If this fix is defined **after** the simulation box is created,
-   a 'run 0' command should be issued to properly initialize the storage
-   created by this fix.
-
 ----------
 
 This fix is one of a small number that can be defined in an input
@@ -139,6 +133,12 @@ script before the simulation box is created or atoms are defined.
 This is so it can be used with the :doc:`read_data <read_data>` command
 as described below.
 
+.. note::
+
+   If this fix is defined **after** the simulation box is created,
+   a 'run 0' command may be needed to properly initialize the storage
+   created by this fix.
+
 Per-atom properties that are defined by the :doc:`atom style <atom_style>` are initialized when atoms are created, e.g. by
 the :doc:`read_data <read_data>` or :doc:`create_atoms <create_atoms>`
 commands.  The per-atom properties defined by this fix are not.  So
@@ -271,11 +271,21 @@ example to heavy water:
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a
-simulation is restarted.  See the :doc:`read_restart <read_restart>`
-command for info on how to re-specify a fix in an input script that
-reads a restart file, so that the operation of the fix continues in an
-uninterrupted fashion.
+This fix writes the per-atom values it stores to :doc:`binary restart
+files <restart>`, so that the values can be restored when a simulation
+is restarted.  See the :doc:`read_restart <read_restart>` command for
+info on how to re-specify a fix in an input script that reads a restart
+file, so that the operation of the fix continues in an uninterrupted
+fashion.
+
+.. warning::
+
+   When reading data from a restart, the fix command has to be specified
+   **exactly** the same way as before. LAMMPS will only check whether a
+   fix is of the same style and has the same fix ID and in case of a match
+   will then try to initialize the fix with the data stored in the binary
+   restart file.  If the fix property/atom command does not match exactly,
+   data can be corrupted or LAMMPS may crash.
 
 None of the :doc:`fix_modify <fix_modify>` options are relevant to this
 fix.  No global or per-atom quantities are stored by this fix for

doc/src/fix_store_state.rst

@@ -111,6 +111,15 @@ command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
+.. warning::
+
+   When reading data from a restart, the fix command has to be specified
+   **exactly** the same way as before. LAMMPS will only check whether a
+   fix is of the same style and has the same fix ID and in case of a match
+   will then try to initialize the fix with the data stored in the binary
+   restart file.  If the fix store/state command does not match exactly,
+   data can be corrupted or LAMMPS may crash.
+
 None of the :doc:`fix_modify <fix_modify>` options are relevant to this
 fix.
 

doc/src/pg_developer.rst

@@ -909,6 +909,9 @@ Convenience functions
 .. doxygenfunction:: timespec2seconds
    :project: progguide
 
+.. doxygenfunction:: date2num
+   :project: progguide
+
 ---------------------------
 
 Tokenizer classes

doc/src/write_data.rst

@@ -42,16 +42,24 @@ Similar to :doc:`dump <dump>` files, the data filename can contain a "\*"
 wild-card character.  The "\*" is replaced with the current timestep
 value.
 
-.. note::
+.. admonition:: Data in Coeff sections
 
-   The write-data command is not yet fully implemented in two
-   respects.  First, most pair styles do not yet write their coefficient
-   information into the data file.  This means you will need to specify
-   that information in your input script that reads the data file, via
-   the :doc:`pair_coeff <pair_coeff>` command.  Second, a few of the :doc:`atom styles <atom_style>` (body, ellipsoid, line, tri) that store
-   auxiliary "bonus" information about aspherical particles, do not yet
-   write the bonus info into the data file.  Both these functionalities
-   will be added to the write_data command later.
+   The write_data command may not always write all coefficient settings
+   to the corresponding Coeff sections of the data file.  This can have
+   one of multiple reasons. 1) A few styles may be missing the code that
+   would write those sections (if you come across one, please notify
+   the LAMMPS developers). 2) Some pair styles require a single pair_coeff
+   statement and those are not compatible with data files. 3) The
+   default for write_data is to write a PairCoeff section, which has
+   only entries for atom types i == j. The remaining coefficients would
+   be inferred through the currently selected mixing rule.  If there has
+   been a pair_coeff command with i != j, this setting would be lost.
+   LAMMPS will detect this and print a warning message unless *pair ij*
+   is appended to the write_data command.  This will request writing a
+   PairIJCoeff section which has information for all pairs of atom types.
+   In cases where the coefficient data in the data file is incomplete,
+   you will need to re-specify that information in your input script
+   that reads the data file.
 
 Because a data file is in text format, if you use a data file written
 out by this command to restart a simulation, the initial state of the

lib/plumed/Install.py

@@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = "2.6.0"
+version = "2.6.1"
 mode = "static"
 
 # help message
@@ -48,6 +48,7 @@ checksums = { \
         '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \
         '2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \
         '2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \
+        '2.6.1' : '89a9a450fc6025299fe16af235957163', \
         }
 
 # parse and process arguments

src/REPLICA/fix_neb.cpp

@@ -237,7 +237,7 @@ void FixNEB::init()
 
   if (atom->nmax > maxlocal) reallocate();
 
-  if (MULTI_PROC && counts == NULL) {
+  if ((cmode == MULTI_PROC) && (counts == NULL)) {
     memory->create(xsendall,ntotal,3,"neb:xsendall");
     memory->create(xrecvall,ntotal,3,"neb:xrecvall");
     memory->create(fsendall,ntotal,3,"neb:fsendall");

src/universe.cpp

@@ -24,8 +24,6 @@ using namespace LAMMPS_NS;
 
 #define MAXLINE 256
 
-static char *date2num(const char *version);
-
 /* ----------------------------------------------------------------------
    create & initialize the universe of processors in communicator
 ------------------------------------------------------------------------- */
@@ -33,7 +31,9 @@ static char *date2num(const char *version);
 Universe::Universe(LAMMPS *lmp, MPI_Comm communicator) : Pointers(lmp)
 {
   version = (const char *) LAMMPS_VERSION;
-  num_ver = date2num(version);
+  auto tmp_ver = new char[10];
+  snprintf(tmp_ver,10,"%08d",utils::date2num(version));
+  num_ver = tmp_ver;
 
   uworld = uorig = communicator;
   MPI_Comm_rank(uworld,&me);
@@ -234,43 +234,3 @@ int Universe::consistent()
   if (n == nprocs) return 1;
   else return 0;
 }
-
-// helper function to convert the LAMMPS date string to a version id
-// that can be used for both string and numerical comparisons
-// where newer versions are larger than older ones.
-
-char *date2num(const char *version)
-{
-  int day,month,year;
-  day = month = year = 0;
-
-  if (version) {
-
-    day = atoi(version);
-
-    while (*version != '\0' && (isdigit(*version) || *version == ' '))
-      ++version;
-
-    if (strncmp(version,"Jan",3) == 0) month = 1;
-    if (strncmp(version,"Feb",3) == 0) month = 2;
-    if (strncmp(version,"Mar",3) == 0) month = 3;
-    if (strncmp(version,"Apr",3) == 0) month = 4;
-    if (strncmp(version,"May",3) == 0) month = 5;
-    if (strncmp(version,"Jun",3) == 0) month = 6;
-    if (strncmp(version,"Jul",3) == 0) month = 7;
-    if (strncmp(version,"Aug",3) == 0) month = 8;
-    if (strncmp(version,"Sep",3) == 0) month = 9;
-    if (strncmp(version,"Oct",3) == 0) month = 10;
-    if (strncmp(version,"Nov",3) == 0) month = 11;
-    if (strncmp(version,"Dec",3) == 0) month = 12;
-
-    while (*version != '\0' && !isdigit(*version))
-      ++version;
-
-    year = atoi(version);
-  }
-
-  char *ver = new char[12];
-  snprintf(ver,12,"%04d%02d%02d", year % 10000, month, day % 100);
-  return ver;
-}

src/utils.cpp

@@ -983,6 +983,34 @@ double utils::timespec2seconds(const std::string &timespec)
   return vals[0];
 }
 
+/* ----------------------------------------------------------------------
+   convert a LAMMPS version date (1Jan01) to a number
+------------------------------------------------------------------------- */
+
+int utils::date2num(const std::string &date)
+{
+  std::size_t found = date.find_first_not_of("0123456789 ");
+  int num = strtol(date.substr(0,found).c_str(),NULL,10);
+  auto month = date.substr(found);
+  found = month.find_first_of("0123456789 ");
+  num += strtol(month.substr(found).c_str(),NULL,10)*10000;
+  if (num < 1000000) num += 20000000;
+
+  if (strmatch(month,"^Jan")) num += 100;
+  else if (strmatch(month,"^Feb")) num += 200;
+  else if (strmatch(month,"^Mar")) num += 300;
+  else if (strmatch(month,"^Apr")) num += 400;
+  else if (strmatch(month,"^May")) num += 500;
+  else if (strmatch(month,"^Jun")) num += 600;
+  else if (strmatch(month,"^Jul")) num += 700;
+  else if (strmatch(month,"^Aug")) num += 800;
+  else if (strmatch(month,"^Sep")) num += 900;
+  else if (strmatch(month,"^Oct")) num += 1000;
+  else if (strmatch(month,"^Nov")) num += 1100;
+  else if (strmatch(month,"^Dec")) num += 1200;
+  return num;
+}
+
 /* ------------------------------------------------------------------ */
 
 extern "C" {

src/utils.h

@@ -371,6 +371,24 @@ namespace LAMMPS_NS {
      * \return total in seconds
      */
     double timespec2seconds(const std::string &timespec);
+
+    /** Convert a LAMMPS version date to a number
+     *
+     * This will generate a number YYYYMMDD from a date string
+     * (with or without blanks) that is suitable for numerical
+     * comparisons, i.e. later dates will generate a larger number.
+     *
+     * The day may or may not have a leading zero, the month
+     * is identified by the first 3 letters (so there may be more)
+     * and the year may be 2 or 4 digits (the missing 2 digits will
+     * be assumed as 20. That is 04 corresponds to 2004).
+     *
+     * No check is made whether the date is valid.
+     *
+     * \param  date  string in the format (Day Month Year)
+     * \return       date code
+     */
+    int date2num(const std::string &date);
   }
 }
 

unittest/c-library/CMakeLists.txt

@@ -1,13 +1,13 @@
 
-add_executable(library-open library-open.cpp)
-target_link_libraries(library-open PRIVATE lammps GTest::GTest GTest::GTestMain)
-add_test(LibraryOpen library-open)
+add_executable(test_library_open test_library_open.cpp)
+target_link_libraries(test_library_open PRIVATE lammps GTest::GTest GTest::GTestMain)
+add_test(LibraryOpen test_library_open)
 
-add_executable(library-commands library-commands.cpp)
-target_link_libraries(library-commands PRIVATE lammps GTest::GTest GTest::GTestMain)
-add_test(LibraryCommands library-commands)
+add_executable(test_library_commands test_library_commands.cpp)
+target_link_libraries(test_library_commands PRIVATE lammps GTest::GTest GTest::GTestMain)
+add_test(LibraryCommands test_library_commands)
 
-add_executable(library-properties library-properties.cpp)
-target_link_libraries(library-properties PRIVATE lammps GTest::GTest GTest::GTestMain)
-add_test(LibraryProperties library-properties)
+add_executable(test_library_properties test_library_properties.cpp)
+target_link_libraries(test_library_properties PRIVATE lammps GTest::GTest GTest::GTestMain)
+add_test(LibraryProperties test_library_properties)
 

unittest/cplusplus/CMakeLists.txt

@@ -1,8 +1,8 @@
 
-add_executable(lammps-class lammps-class.cpp)
-target_link_libraries(lammps-class PRIVATE lammps GTest::GMockMain GTest::GTest GTest::GMock)
-add_test(LammpsClass lammps-class)
+add_executable(test_lammps_class test_lammps_class.cpp)
+target_link_libraries(test_lammps_class PRIVATE lammps GTest::GMockMain GTest::GTest GTest::GMock)
+add_test(LammpsClass test_lammps_class)
 
-add_executable(input-class input-class.cpp)
-target_link_libraries(input-class PRIVATE lammps GTest::GTest GTest::GTestMain)
-add_test(InputClass input-class)
+add_executable(test_input_class test_input_class.cpp)
+target_link_libraries(test_input_class PRIVATE lammps GTest::GTest GTest::GTestMain)
+add_test(InputClass test_input_class)

unittest/force-styles/tests/mol-pair-coul_streitz_long.yaml

@@ -5,6 +5,7 @@ epsilon: 5e-13
 prerequisites: ! |
   atom full
   pair coul/streitz
+  kspace ewald
 pre_commands: ! |
   variable units index metal
   variable newton_pair delete

unittest/formats/test_dump_cfg_zstd.cpp

@@ -61,7 +61,7 @@ TEST_F(DumpCfgZstdTest, compressed_run0)
     auto compressed_file = "dump_cfg_zstd_compressed_run0.melt.cfg.zst";
     auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz";
 
-    generate_text_and_compressed_dump(text_files, compressed_files, "cfg/gz", fields, "", 0);
+    generate_text_and_compressed_dump(text_files, compressed_files, "cfg/zstd", fields, "", 0);
 
     TearDown();
 

unittest/fortran/CMakeLists.txt

@@ -18,13 +18,13 @@ if(CMAKE_Fortran_COMPILER)
 
   add_library(flammps STATIC ${LAMMPS_FORTRAN_MODULE})
 
-  add_executable(fortran-create wrap-create.cpp fortran-create.f90)
-  target_link_libraries(fortran-create PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTest GTest::GTestMain)
-  add_test(FortranOpen fortran-create)
+  add_executable(test_fortran_create wrap_create.cpp test_fortran_create.f90)
+  target_link_libraries(test_fortran_create PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTest GTest::GTestMain)
+  add_test(FortranOpen test_fortran_create)
 
-  add_executable(fortran-commands wrap-commands.cpp fortran-commands.f90)
-  target_link_libraries(fortran-commands PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTest GTest::GTestMain)
-  add_test(FortranCommands fortran-commands)
+  add_executable(test_fortran_commands wrap_commands.cpp test_fortran_commands.f90)
+  target_link_libraries(test_fortran_commands PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTest GTest::GTestMain)
+  add_test(FortranCommands test_fortran_commands)
 else()
   message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran compiler")
 endif()

unittest/utils/test_utils.cpp

@@ -611,3 +611,20 @@ TEST(Utils, timespec2seconds_hhmmss)
 {
     ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:10:45"), 7845.0);
 }
+
+
+TEST(Utils, date2num)
+{
+    ASSERT_EQ(utils::date2num("1Jan05"),20050101);
+    ASSERT_EQ(utils::date2num("10Feb2005"),20050210);
+    ASSERT_EQ(utils::date2num("02Mar10"),20100302);
+    ASSERT_EQ(utils::date2num(" 5Apr1900"),19000405);
+    ASSERT_EQ(utils::date2num("10May22 "),20220510);
+    ASSERT_EQ(utils::date2num("1 Jun 05"),20050601);
+    ASSERT_EQ(utils::date2num("10 Jul 2005"),20050710);
+    ASSERT_EQ(utils::date2num("02 Aug 10"),20100802);
+    ASSERT_EQ(utils::date2num("  5  September  99"),20990905);
+    ASSERT_EQ(utils::date2num("10October22 "),20221010);
+    ASSERT_EQ(utils::date2num("30November 02"),20021130);
+    ASSERT_EQ(utils::date2num("31December100"),1001231);
+}