Merge pull request #4550 from akohlmey/collected-small-fixes

Collected small changes and fixes

README

@@ -34,6 +34,7 @@ lib                        additional provided or external libraries
 potentials                 interatomic potential files
 python                     Python module for LAMMPS
 src                        source files
+third_party                Copies of thirdparty software bundled with LAMMPS
 tools                      pre- and post-processing tools
 unittest                   test programs for use with CTest
 .github                    Git and GitHub related files and tools

cmake/CMakeLists.txt

@@ -44,6 +44,7 @@ set(LAMMPS_DOC_DIR        ${LAMMPS_DIR}/doc)
 set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
 set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
 set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
+set(LAMMPS_THIRDPARTY_DIR ${LAMMPS_DIR}/third_party)
 
 set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
 set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
@@ -131,7 +132,7 @@ endif()
 
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
 # we *require* C++11 without extensions but prefer C++17.
@@ -370,6 +371,7 @@ endforeach()
 # packages with special compiler needs or external libs
 ######################################################
 target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
+target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_THIRDPARTY_DIR}>)
 
 if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because

cmake/Modules/LAMMPSUtils.cmake

@@ -30,7 +30,7 @@ function(check_omp_h_include)
   if(OpenMP_CXX_FOUND)
     set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
     set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
-    set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
+    separate_arguments(CMAKE_REQUIRED_LINK_OPTIONS NATIVE_COMMAND ${OpenMP_CXX_FLAGS}) # needs to be a list
     set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
     # there are all kinds of problems with finding omp.h
     # for Clang and derived compilers so we pretend it is there.

cmake/presets/kokkos-sycl-intel.cmake

@@ -23,7 +23,7 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
 
 # set(_intel_sycl_flags " -w -fsycl -flink-huge-device-code -fsycl-targets=spir64_gen "
-set(_intel_sycl_flags " -w -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen "
+set(_intel_sycl_flags " -w -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen ")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
 
 #set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-targets=spir64_gen " CACHE STRING "" FORCE)

doc/src/Install_git.rst

@@ -12,19 +12,10 @@ several advantages:
   LAMMPS.  For that, you should first create your own :doc:`fork on
   GitHub <Howto_github>`, though.
 
-You must have `git <git_>`_ installed on your system to use the
+You must have `git <git_>`_ installed on your system to use the commands
-commands explained below to communicate with the git servers on
+explained below to communicate with the git servers on GitHub.
-GitHub.  For people still using subversion (svn), GitHub also
-provides `limited support for subversion clients <svn_>`_.
-
-.. note::
-
-   As of October 2016, the official home of public LAMMPS development is
-   on GitHub.  The previously advertised LAMMPS git repositories on
-   git.lammps.org and bitbucket.org are now offline or deprecated.
 
 .. _git: https://git-scm.com
-.. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
 
 You can follow the LAMMPS development on 4 different git branches:
 

src/REAXFF/reaxff_tool_box.cpp

@@ -101,6 +101,6 @@ void sfree(void *ptr)
   if (ptr == nullptr) return;
 
   free(ptr);
-  ptr = nullptr;
+  ptr = nullptr;  // NOTE: this has no effect
 }
 }    // namespace ReaxFF

src/displace_atoms.cpp

@@ -125,7 +125,7 @@ void DisplaceAtoms::command(int narg, char **arg)
     else if (strcmp(arg[2],"y") == 0) d_dim = 1;
     else if (strcmp(arg[2],"z") == 0) d_dim = 2;
     else error->all(FLERR, 2, "Unknown displace_atoms ramp dimension {}", arg[2]);
-    if ((domain->dimension == 2) && (d_dim = 2))
+    if ((domain->dimension == 2) && (d_dim == 2))
       error->all(FLERR, 2, "Must not displace atoms in z-direction with 2d system");
 
     double d_lo,d_hi;

src/dump_custom.cpp

@@ -78,8 +78,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
 
   int ioffset = 5;
   expand = 0;
-  nfield = nargnew = utils::expand_args(FLERR,narg-5,&arg[5],1,earg,lmp);
+  nfield = nargnew = utils::expand_args(FLERR,narg-ioffset,&arg[ioffset],1,earg,lmp);
-  if (earg != &arg[5]) expand = 1;
+  if (earg != &arg[ioffset]) expand = 1;
 
   // allocate field vectors
 

src/info.cpp

@@ -44,7 +44,9 @@
 #include "region.h"
 #include "update.h"
 #include "variable.h"
+#ifndef FMT_STATIC_THOUSANDS_SEPARATOR
 #include "fmt/chrono.h"
+#endif
 
 #include <cctype>
 #include <cmath>
@@ -270,8 +272,16 @@ void Info::command(int narg, char **arg)
   if (out == nullptr) return;
 
   fputs("\nInfo-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info\n",out);
+#if defined(FMT_STATIC_THOUSANDS_SEPARATOR)
+  {
+    time_t tv = time(nullptr);
+    struct tm *now = localtime(&tv);
+    utils::print(out, "Printed on {}", asctime(now));
+  }
+#else
   std::tm now = fmt::localtime(std::time(nullptr));
   utils::print(out,"Printed on {}", std::asctime(&now));
+#endif
 
   if (flags & CONFIG) {
     utils::print(out,"\nLAMMPS version: {} / {}\n", lmp->version, lmp->num_ver);

src/json.h

@@ -17,7 +17,7 @@
 // wrapper around including the JSON parsing and writing class
 // Do NOT include in any header file
 
-#include "../third_party/nlohmann/json.hpp"
+#include "nlohmann/json.hpp"
 
 namespace LAMMPS_NS {
 using json = ::nlohmann_lmp::json;

src/library.cpp

@@ -24,6 +24,7 @@
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
+#include "command.h"
 #include "compute.h"
 #include "domain.h"
 #include "dump.h"
@@ -42,6 +43,7 @@
 #include "molecule.h"
 #include "neigh_list.h"
 #include "neighbor.h"
+#include "neigh_request.h"
 #include "output.h"
 #include "pair.h"
 #if defined(LMP_PLUGIN)
@@ -6119,6 +6121,96 @@ int lammps_find_compute_neighlist(void *handle, const char *id, int reqid) {
 
 /* ---------------------------------------------------------------------- */
 
+// helper Command class for a single neighbor list build
+
+namespace LAMMPS_NS {
+  class NeighProxy : protected Command
+  {
+ public:
+  NeighProxy(class LAMMPS *lmp) : Command(lmp), neigh_idx(-1) {};
+
+  void command(int, char **) override;
+  int get_index() const { return neigh_idx; }
+ protected:
+  int neigh_idx;
+};
+}
+
+void NeighProxy::command(int narg, char **arg)
+{
+  neigh_idx = -1;
+  if (narg != 3) return;
+  auto *req = neighbor->add_request(this, arg[0]);
+  int flags = atoi(arg[1]);
+  double cutoff = atof(arg[2]);
+  req->apply_flags(flags);
+  if (cutoff > 0.0) req->set_cutoff(cutoff);
+  lmp->init();
+
+  // setup domain, communication and neighboring
+  // acquire ghosts and build standard neighbor lists
+
+  if (domain->triclinic) domain->x2lamda(atom->nlocal);
+  domain->pbc();
+  domain->reset_box();
+  comm->setup();
+  if (neighbor->style) neighbor->setup_bins();
+  comm->exchange();
+  comm->borders();
+  if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost);
+  neighbor->build(1);
+
+  // build neighbor list this command needs based on earlier request
+
+  auto list = neighbor->find_list(this);
+  neighbor->build_one(list);
+
+  // find neigh list
+  for (int i = 0; i < neighbor->nlist; i++) {
+    NeighList *list = neighbor->lists[i];
+    if (this == list->requestor) {
+      neigh_idx = i;
+      break;
+    }
+  }
+}
+
+/** Build a single neighbor list in between runs and return its index
+ *
+ * A neighbor list request is created and the neighbor list built from a
+ * proxy command. The request ID is typically 0, but will be
+ * > 0 in case a compute has multiple neighbor list requests.
+ *
+ * \param handle   pointer to a previously created LAMMPS instance cast to ``void *``.
+ * \param id       Identifier of neighbor list request
+ * \param flags    Neighbor list flags
+ * \param cutoff   Custom neighbor list cutoff if > 0, use default cutoff if < 0
+ * \return         return neighbor list index if valid, otherwise -1 */
+
+int lammps_request_single_neighlist(void *handle, const char *id, int flags, double cutoff) {
+  auto lmp = (LAMMPS *)handle;
+  int idx = -1;
+  if (!lmp || !lmp->error || !lmp->neighbor) {
+    lammps_last_global_errormessage = fmt::format("ERROR: {}(): Invalid LAMMPS handle\n", FNERR);
+    return -1;
+  }
+
+  BEGIN_CAPTURE
+  {
+    NeighProxy proxy(lmp);
+    std::vector<std::string> args = {id, std::to_string(flags), std::to_string(cutoff)};
+    std::vector<char *> c_args;
+    std::transform(args.begin(), args.end(), std::back_inserter(c_args),
+                   [](const std::string& s) { return (char *)s.c_str(); });
+    proxy.command(static_cast<int>(c_args.size()), c_args.data());
+    idx = proxy.get_index();
+  }
+  END_CAPTURE
+  return idx;
+}
+
+/* ---------------------------------------------------------------------- */
+
 /** Return the number of entries in the neighbor list with given index
  *
  * \param handle   pointer to a previously created LAMMPS instance cast to ``void *``.

src/library.h

@@ -109,6 +109,17 @@ enum _LMP_VAR_CONST {
   LMP_VAR_STRING = 3  /*!< return value will be a string (catch-all) */
 };
 
+/** Neighbor list settings constants
+ *
+ * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``,
+ * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and
+ * ``examples/COUPLE/plugin/liblammpsplugin.h`` */
+
+enum _LMP_NEIGH_CONST {
+  LMP_NEIGH_HALF = 0,  /*!< request (default) half neighbor list */
+  LMP_NEIGH_FULL = 1,  /*!< request full neighbor list */
+};
+
 /* Ifdefs to allow this file to be included in C and C++ programs */
 
 #ifdef __cplusplus
@@ -235,6 +246,7 @@ int lammps_create_atoms(void *handle, int n, const int64_t *id, const int *type,
 int lammps_find_pair_neighlist(void *handle, const char *style, int exact, int nsub, int request);
 int lammps_find_fix_neighlist(void *handle, const char *id, int request);
 int lammps_find_compute_neighlist(void *handle, const char *id, int request);
+int lammps_request_single_neighlist(void *handle, const char *id, int flags, double cutoff);
 int lammps_neighlist_num_elements(void *handle, int idx);
 void lammps_neighlist_element_neighbors(void *handle, int idx, int element, int *iatom,
                                         int *numneigh, int **neighbors);

src/min.cpp

@@ -113,6 +113,9 @@ void Min::init()
   // create fix needed for storing atom-based quantities
   // will delete it at end of run
 
+  if (lmp->kokkos)
+    fix_minimize = dynamic_cast<FixMinimize *>(modify->add_fix("MINIMIZE all MINIMIZE/kk"));
+  else
     fix_minimize = dynamic_cast<FixMinimize *>(modify->add_fix("MINIMIZE all MINIMIZE"));
 
   // clear out extra global and per-atom dof

src/timer.cpp

@@ -15,7 +15,9 @@
 
 #include "comm.h"
 #include "error.h"
+#ifndef FMT_STATIC_THOUSANDS_SEPARATOR
 #include "fmt/chrono.h"
+#endif
 #include "tokenizer.h"
 
 #include <cstring>
@@ -264,8 +266,15 @@ void Timer::modify_params(int narg, char **arg)
     // format timeout setting
     std::string timeout = "off";
     if (_timeout >= 0.0) {
+#if defined(FMT_STATIC_THOUSANDS_SEPARATOR)
+      char outstr[200];
+      struct tm *tv = gmtime(&((time_t) _timeout));
+      strftime(outstr, 200, "%02d:%M:%S", tv);
+      timeout = outstr;
+#else
       std::tm tv = fmt::gmtime((std::time_t) _timeout);
       timeout = fmt::format("{:02d}:{:%M:%S}", tv.tm_yday * 24 + tv.tm_hour, tv);
+#endif
     }
 
     utils::logmesg(lmp, "New timer settings: style={}  mode={}  timeout={}\n", timer_style[_level],

src/utils.cpp

@@ -20,7 +20,9 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
+#ifndef FMT_STATIC_THOUSANDS_SEPARATOR
 #include "fmt/chrono.h"
+#endif
 #include "input.h"
 #include "label_map.h"
 #include "memory.h"
@@ -1953,8 +1955,15 @@ int utils::date2num(const std::string &date)
 std::string utils::current_date()
 {
   time_t tv = time(nullptr);
+#if defined(FMT_STATIC_THOUSANDS_SEPARATOR)
+  char outstr[200];
+  struct tm *today = localtime(&tv);
+  strftime(outstr, 200, "%Y-%m-%d", today);
+  return std::string(outstr);
+#else
   std::tm today = fmt::localtime(tv);
   return fmt::format("{:%Y-%m-%d}", today);
+#endif
 }
 
 /* ----------------------------------------------------------------------

third_party/README

@@ -1 +1,13 @@
-This folder contains copies of third-party software
+This folder contains copies of third-party software.
+These packages may be either included in the source
+code tarball or downloaded on-the-fly during compilation
+as needed.  In some cases, some small customizations
+are made to avoid namespace conflicts where the
+included third party software needs workarounds for
+issues on platforms (OS or compiler related) to
+function consistently with LAMMPS.
+
+The following software source packages are included
+
+Folder:           Package:               Version:   Original URL
+nlohmann/json     JSON for Modern C++    3.12.0     https://github.com/nlohmann/json/releases/tag/v3.12.0

unittest/utils/test_json.cpp

@@ -48,7 +48,11 @@ TEST(JSON, serialize_deserialize)
     j1["nothing"] = nullptr;
 
     std::string expected = "{\"happy\":true,\"name\":\"Niels\",\"nothing\":null,\"pi\":3.141}";
-    std::string dumped   = j1.dump();
+    std::string dumped   = j1.dump(-1);
+    ASSERT_THAT(expected, Eq(dumped));
+
+    expected = "{\n  \"happy\": true,\n  \"name\": \"Niels\",\n  \"nothing\": null,\n  \"pi\": 3.141\n}";
+    dumped   = j1.dump(2, ' ');
     ASSERT_THAT(expected, Eq(dumped));
 
     json j2 = json::parse(expected);