Merge pull request lammps#4212 from akohlmey/collected-small-changes

Collected small changes and fixes

cmake/presets/mingw-cross.cmake

@@ -33,7 +33,6 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
-  INTEL
   INTERLAYER
   KSPACE
   LEPTON

doc/src/Developer_write_pair.rst

@@ -50,6 +50,30 @@ We are looking at the following cases:
 - `Case 3: a potential requiring communication`_
 - `Case 4: potentials without a compute() function`_
 
+Package and build system considerations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In general, new pair styles should be added to the :ref:`EXTRA-PAIR
+package <PKG-EXTRA-PAIR>` unless they are an accelerated pair style and
+then they should be added to the corresponding accelerator package
+(:ref:`GPU <PKG-GPU>`, :ref:`INTEL <PKG-INTEL>`, :ref:`KOKKOS
+<PKG-KOKKOS>`, :ref:`OPENMP <PKG-OPENMP>`, :ref:`OPT <PKG-OPT>`).  If
+you feel that your contribution should be added to a different package,
+please consult with the LAMMPS developers first.
+
+The contributed code needs to support the :doc:`traditional GNU make
+build process <Build_make>` **and** the :doc:`CMake build process
+<Build_cmake>`.  For the GNU make process and if the package has an
+``Install.sh`` file, most likely that file needs to be updated to
+correctly copy the sources when installing the package and properly
+delete them when uninstalling.  This is particularly important when
+added a new pair style that is a derived class from an existing pair
+style in a package, so that its installation depends on the the
+installation status of the package of the derived class.  For the CMake
+process, it is sometimes necessary to make changes to the package
+specific CMake scripting in ``cmake/Modules/Packages``.
+
+
 ----
 
 Case 1: a pairwise additive model

doc/src/variable.rst

@@ -67,7 +67,7 @@ Syntax
                            bound(group,dir,region), gyration(group,region), ke(group,reigon),
                            angmom(group,dim,region), torque(group,dim,region),
                            inertia(group,dimdim,region), omega(group,dim,region)
-         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label)
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()
          feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
@@ -547,7 +547,7 @@ variables.
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Region functions       | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)                                                                                                                |
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Special functions      | sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label)                                                                                                                               |
+| Special functions      | sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()                                                                                                                 |
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Feature functions      | is_available(category,feature), is_active(category,feature), is_defined(category,id)                                                                                                                                                                                                                                                              |
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -1042,6 +1042,20 @@ label2type(), but returns 1 if the type label has been assigned,
 otherwise it returns 0.  This function can be used to check if a
 particular type label already exists in the simulation.
 
+.. versionadded:: TBD
+
+The is_timeout() function returns 1 when the :doc:`timer timeout
+<timer>` has expired otherwise it returns 0.  This function can be used
+to check inputs in combination with the :doc:`if command <if>` to
+execute commands after the timer has expired. Example:
+
+.. code-block:: LAMMPS
+
+   variable timeout equal is_timeout()
+   timer timeout 0:10:00 every 10
+   run 10000
+   if ${timeout} then "print 'Timer has expired'"
+
 ----------
 
 Feature Functions

src/REPLICA/neb.cpp

@@ -198,7 +198,7 @@ void NEB::run()
   if (me == 0)
     color = 0;
   else
-    color = 1;
+    color = MPI_UNDEFINED;
   MPI_Comm_split(uworld, color, 0, &roots);
 
   auto fixes = modify->get_fix_by_style("^neb$");
@@ -608,17 +608,20 @@ void NEB::open(char *file)
 void NEB::print_status()
 {
   double fnorm2 = sqrt(update->minimize->fnorm_sqr());
-  double fmaxreplica;
-  MPI_Allreduce(&fnorm2, &fmaxreplica, 1, MPI_DOUBLE, MPI_MAX, roots);
   double fnorminf = update->minimize->fnorm_inf();
-  double fmaxatom;
-  MPI_Allreduce(&fnorminf, &fmaxatom, 1, MPI_DOUBLE, MPI_MAX, roots);
+  double fmaxreplica = 0.0;
+  double fmaxatom = 0.0;
 
-  if (print_mode == VERBOSE) {
-    freplica = new double[nreplica];
-    MPI_Allgather(&fnorm2, 1, MPI_DOUBLE, &freplica[0], 1, MPI_DOUBLE, roots);
-    fmaxatomInRepl = new double[nreplica];
-    MPI_Allgather(&fnorminf, 1, MPI_DOUBLE, &fmaxatomInRepl[0], 1, MPI_DOUBLE, roots);
+  if (me == 0) {
+    MPI_Allreduce(&fnorm2, &fmaxreplica, 1, MPI_DOUBLE, MPI_MAX, roots);
+    MPI_Allreduce(&fnorminf, &fmaxatom, 1, MPI_DOUBLE, MPI_MAX, roots);
+
+    if (print_mode == VERBOSE) {
+      freplica = new double[nreplica];
+      MPI_Allgather(&fnorm2, 1, MPI_DOUBLE, &freplica[0], 1, MPI_DOUBLE, roots);
+      fmaxatomInRepl = new double[nreplica];
+      MPI_Allgather(&fnorminf, 1, MPI_DOUBLE, &fmaxatomInRepl[0], 1, MPI_DOUBLE, roots);
+    }
   }
 
   double one[7];
@@ -703,7 +706,7 @@ void NEB::print_status()
       fflush(universe->ulogfile);
     }
   }
-  if (print_mode == VERBOSE) {
+  if ((me == 0) && (print_mode == VERBOSE)) {
     delete[] freplica;
     delete[] fmaxatomInRepl;
   }

src/library.cpp

@@ -2420,7 +2420,7 @@ use to avoid a memory leak. Example:
 
 .. code-block:: c
 
-   double *dptr = (double *) lammps_extract_variable(handle,name,NULL);
+   double *dptr = (double *) lammps_extract_variable(handle, name, NULL);
    double value = *dptr;
    lammps_free((void *)dptr);
 
@@ -2431,16 +2431,25 @@ content will not be updated in case the variable is re-evaluated.
 To avoid a memory leak, this pointer needs to be freed after use in
 the calling program.
 
-For *vector*\ -style variables, the returned pointer is to actual LAMMPS data.
-The pointer should not be deallocated. Its length depends on the variable,
-compute, or fix data used to construct the *vector*\ -style variable.
-This length can be fetched by calling this function with *group* set to the
-constant "LMP_SIZE_VECTOR", which returns a ``void *`` pointer that can be
-dereferenced to an integer that is the length of the vector. This pointer
-needs to be deallocated when finished with it to avoid memory leaks.
+For *vector*\ -style variables, the returned pointer points to actual
+LAMMPS data and thus it should **not** be deallocated.  Its length
+depends on the variable, compute, or fix data used to construct the
+*vector*\ -style variable.  This length can be fetched by calling this
+function with *group* set to a non-NULL pointer (NULL returns the vector).
+In that case it will return the vector length as an allocated int
+pointer cast to a ``void *`` pointer.  That pointer can be recast and
+dereferenced to an integer yielding the length of the vector. This pointer
+must be deallocated when finished with it to avoid memory leaks. Example:
+
+.. code-block:: c
+
+   double *vectvals = (double *) lammps_extract_variable(handle, name, NULL);
+   int *intptr = (int *) lammps_extract_variable(handle, name, 1);
+   int vectlen = *intptr;
+   lammps_free((void *)intptr);
 
 For other variable styles the returned pointer needs to be cast to
-a char pointer. It should not be deallocated.
+a char pointer and it should **not** be deallocated. Example:
 
 .. code-block:: c
 
@@ -2452,7 +2461,7 @@ a char pointer. It should not be deallocated.
    LAMMPS cannot easily check if it is valid to access the data
    referenced by the variables (e.g., computes, fixes, or thermodynamic
    info), so it may fail with an error.  The caller has to make certain
-   that the data are extracted only when it safe to evaluate the variable
+   that the data is extracted only when it safe to evaluate the variable
    and thus an error or crash are avoided.
 
 \endverbatim
@@ -2487,7 +2496,7 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group)
     } else if (lmp->input->variable->vectorstyle(ivar)) {
       double *values = nullptr;
       int nvector = lmp->input->variable->compute_vector(ivar, &values);
-      if (group != nullptr && strcmp(group,"LMP_SIZE_VECTOR") == 0) {
+      if (group) {
           int* nvecptr = (int *) malloc(sizeof(int));
           *nvecptr = nvector;
           return (void *) nvecptr;

src/library.h

@@ -175,9 +175,9 @@ void *lammps_extract_atom(void *handle, const char *name);
  * Library functions to access data from computes, fixes, variables in LAMMPS
  * ---------------------------------------------------------------------- */
 
-void *lammps_extract_compute(void *handle, const char *, int, int);
-void *lammps_extract_fix(void *handle, const char *, int, int, int, int);
-void *lammps_extract_variable(void *handle, const char *, const char *);
+void *lammps_extract_compute(void *handle, const char *id, int style, int type);
+void *lammps_extract_fix(void *handle, const char *id, int style, int type, int nrow, int ncol);
+void *lammps_extract_variable(void *handle, const char *name, const char *group);
 int lammps_extract_variable_datatype(void *handle, const char *name);
 int lammps_set_variable(void *handle, const char *name, const char *str);
 int lammps_set_string_variable(void *handle, const char *name, const char *str);

src/timer.cpp

@@ -28,8 +28,8 @@ Timer::Timer(LAMMPS *_lmp) : Pointers(_lmp)
 {
   _level = NORMAL;
   _sync = OFF;
-  _timeout = -1;
-  _s_timeout = -1;
+  _timeout = -1.0;
+  _s_timeout = -1.0;
   _checkfreq = 10;
   _nextcheck = -1;
   this->_stamp(RESET);
@@ -251,7 +251,7 @@ void Timer::modify_params(int narg, char **arg)
 
     // format timeout setting
     std::string timeout = "off";
-    if (_timeout >= 0) {
+    if (_timeout >= 0.0) {
       std::tm tv = fmt::gmtime((std::time_t) _timeout);
       timeout = fmt::format("{:02d}:{:%M:%S}", tv.tm_yday * 24 + tv.tm_hour, tv);
     }

src/timer.h

@@ -110,12 +110,12 @@ class Timer : protected Pointers {
   double previous_cpu;
   double previous_wall;
   double timeout_start;
-  int _level;        // level of detail: off=0,loop=1,normal=2,full=3
-  int _sync;         // if nonzero, synchronize tasks before setting the timer
-  int _timeout;      // max allowed wall time in seconds. infinity if negative
-  int _s_timeout;    // copy of timeout for restoring after a forced timeout
-  int _checkfreq;    // frequency of timeout checking
-  int _nextcheck;    // loop number of next timeout check
+  double _timeout;      // max allowed wall time in seconds. infinity if negative
+  double _s_timeout;    // copy of timeout for restoring after a forced timeout
+  int _level;           // level of detail: off=0,loop=1,normal=2,full=3
+  int _sync;            // if nonzero, synchronize tasks before setting the timer
+  int _checkfreq;       // frequency of timeout checking
+  int _nextcheck;       // loop number of next timeout check
 
   // update one specific timer array
   void _stamp(enum ttype);

src/utils.cpp

@@ -1677,7 +1677,7 @@ double utils::timespec2seconds(const std::string &timespec)
   try {
     for (i = 0; i < 3; i++) {
       if (!values.has_next()) break;
-      vals[i] = values.next_int();
+      vals[i] = values.next_double();
     }
   } catch (TokenizerException &) {
     return -1.0;

src/variable.cpp

@@ -34,6 +34,7 @@
 #include "random_mars.h"
 #include "region.h"
 #include "thermo.h"
+#include "timer.h"
 #include "tokenizer.h"
 #include "universe.h"
 #include "update.h"
@@ -4276,8 +4277,9 @@ Region *Variable::region_function(char *id, int ivar)
    return 0 if not a match, 1 if successfully processed
    customize by adding a special function:
      sum(x),min(x),max(x),ave(x),trap(x),slope(x),
-     gmask(x),rmask(x),grmask(x,y),next(x),is_file(x),is_ox(x),
-     extract_setting(x),label2type(x,y),is_typelabel(x,y)
+     gmask(x),rmask(x),grmask(x,y),next(x),is_file(x),is_os(x),
+     extract_setting(x),label2type(x,y),is_tpelabel(x,y)
+     is_timeout()
 ------------------------------------------------------------------------- */
 
 // to simplify finding matches and assigning constants for functions operating on vectors
@@ -4286,7 +4288,7 @@ static const std::unordered_map<std::string,int> special_function_map = {
   {"sum", SUM}, {"min", XMIN}, {"max", XMAX}, {"ave", AVE}, {"trap", TRAP}, {"slope", SLOPE},
   {"sort", SORT}, {"rsort", RSORT}, {"gmask", NOVECTOR}, {"rmask", NOVECTOR}, {"grmask", NOVECTOR},
   {"next", NOVECTOR}, {"is_file", NOVECTOR}, {"is_os", NOVECTOR}, {"extract_setting", NOVECTOR},
-  {"label2type", NOVECTOR}, {"is_typelabel", NOVECTOR} };
+  {"label2type", NOVECTOR}, {"is_typelabel", NOVECTOR}, {"is_timeout", NOVECTOR} };
 
 int Variable::special_function(const std::string &word, char *contents, Tree **tree,
                                Tree **treestack, int &ntreestack, double *argstack,
@@ -4765,6 +4767,21 @@ int Variable::special_function(const std::string &word, char *contents, Tree **t
       newtree->value = value;
       treestack[ntreestack++] = newtree;
     } else argstack[nargstack++] = value;
+
+  } else if (word == "is_timeout") {
+    if ((narg != 1) || (std::string(args[0]).size() != 0))
+      print_var_error(FLERR,"Invalid is_timeout() function in variable formula",ivar);
+    value = timer->is_timeout() ? 1.0 : 0.0;
+
+    // save value in tree or on argstack
+
+    if (tree) {
+      auto newtree = new Tree();
+      newtree->type = VALUE;
+      newtree->value = value;
+      treestack[ntreestack++] = newtree;
+    } else argstack[nargstack++] = value;
+
   }
 
   // delete stored args

unittest/c-library/CMakeLists.txt

@@ -18,6 +18,12 @@ target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=$
 add_test(NAME LibraryProperties COMMAND test_library_properties)
 set_tests_properties(LibraryProperties PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
 
+add_executable(test_library_objects test_library_objects.cpp test_main.cpp)
+target_link_libraries(test_library_objects PRIVATE lammps GTest::GMock)
+target_compile_definitions(test_library_objects PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
+add_test(NAME LibraryObjects COMMAND test_library_objects)
+set_tests_properties(LibraryObjects PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
+
 add_executable(test_library_scatter_gather test_library_scatter_gather.cpp test_main.cpp)
 target_link_libraries(test_library_scatter_gather PRIVATE lammps GTest::GMock)
 target_compile_definitions(test_library_scatter_gather PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})