Merge pull request #2624 from rbberger/collected_small_changes

Collection of small changes

cmake/Modules/OpenCLLoader.cmake

@@ -1,11 +1,5 @@
 message(STATUS "Downloading and building OpenCL loader library")
 
-if(CMAKE_BUILD_TYPE STREQUAL Debug)
-  set(OPENCL_LOADER_LIB_POSTFIX d)
-else()
-  set(OPENCL_LOADER_LIB_POSTFIX)
-endif()
-
 include(ExternalProject)
 set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
@@ -20,7 +14,7 @@ ExternalProject_Add(opencl_loader
                                     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
                                     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
                                     -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-                    BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${OPENCL_LOADER_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
                     LOG_DOWNLOAD ON
                     LOG_CONFIGURE ON
                     LOG_BUILD ON
@@ -34,7 +28,7 @@ set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
 file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
 
 ExternalProject_Get_Property(opencl_loader BINARY_DIR)
-set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${OPENCL_LOADER_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
+set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
 
 find_package(Threads QUIET)
 if(NOT WIN32)

doc/src/fix_wall_body_polygon.rst

@@ -15,7 +15,7 @@ Syntax
 * k_n = normal repulsion strength (force/distance or pressure units)
 * c_n = normal damping coefficient (force/distance or pressure units)
 * c_t = tangential damping coefficient (force/distance or pressure units)
-* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder*
+* wallstyle = *xplane* or *yplane* or *zcylinder*
 * args = list of arguments for a particular style
 
   .. parsed-literal::

doc/src/fix_wall_gran.rst

@@ -199,11 +199,11 @@ the following table:
 |     1 | 1.0 if particle is in contact with wall,           |                |
 |       | 0.0 otherwise                                      |                |
 +-------+----------------------------------------------------+----------------+
-|     2 | Force :math:`f_x` exerted on the wall              | force units    |
+|     2 | Force :math:`f_x` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     3 | Force :math:`f_y` exerted on the wall              | force units    |
+|     3 | Force :math:`f_y` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     4 | Force :math:`f_z` exerted on the wall              | force units    |
+|     4 | Force :math:`f_z` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
 |     5 | :math:`x`-coordinate of contact point on wall      | distance units |
 +-------+----------------------------------------------------+----------------+

doc/src/fix_wall_gran_region.rst

@@ -240,11 +240,11 @@ the following table:
 |     1 | 1.0 if particle is in contact with wall,           |                |
 |       | 0.0 otherwise                                      |                |
 +-------+----------------------------------------------------+----------------+
-|     2 | Force :math:`f_x` exerted on the wall              | force units    |
+|     2 | Force :math:`f_x` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     3 | Force :math:`f_y` exerted on the wall              | force units    |
+|     3 | Force :math:`f_y` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     4 | Force :math:`f_z` exerted on the wall              | force units    |
+|     4 | Force :math:`f_z` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
 |     5 | :math:`x`-coordinate of contact point on wall      | distance units |
 +-------+----------------------------------------------------+----------------+

src/BODY/fix_wall_body_polygon.cpp

@@ -59,6 +59,7 @@ FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) :
 
   restart_peratom = 1;
   create_attribute = 1;
+  wallstyle = -1;
 
   // wall/particle coefficients
 
@@ -96,7 +97,7 @@ FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) :
     lo = hi = 0.0;
     cylradius = utils::numeric(FLERR,arg[iarg+1],false,lmp);
     iarg += 2;
-  }
+  } else error->all(FLERR,fmt::format("Unknown wall style {}",arg[iarg]));
 
   // check for trailing keyword/values
 

src/BODY/fix_wall_body_polyhedron.cpp

@@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;
 
-enum{XPLANE=0,YPLANE=1,ZPLANE};    // XYZ PLANE need to be 0,1,2
+enum{XPLANE=0,YPLANE=1,ZPLANE=2};    // XYZ PLANE need to be 0,1,2
 enum{HOOKE,HOOKE_HISTORY};
 
 enum {INVALID=0,NONE=1,VERTEX=2};
@@ -59,6 +59,7 @@ FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg)
 
   restart_peratom = 1;
   create_attribute = 1;
+  wallstyle = -1;
 
   // wall/particle coefficients
 
@@ -98,7 +99,7 @@ FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg)
     if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
     else hi = utils::numeric(FLERR,arg[iarg+2],false,lmp);
     iarg += 3;
-  }
+  } else error->all(FLERR,fmt::format("Unknown wall style {}",arg[iarg]));
 
   // check for trailing keyword/values
 

src/BODY/pair_body_rounded_polygon.cpp

@@ -569,6 +569,10 @@ void PairBodyRoundedPolygon::body2space(int i)
     memory->grow(edge,edmax,5,"pair:edge");
   }
 
+  if ((body_num_edges > 0) && (edge_ends == nullptr))
+    error->one(FLERR,fmt::format("Inconsistent edge data for body of atom {}",
+                                 atom->tag[i]));
+
   for (int m = 0; m < body_num_edges; m++) {
     edge[nedge][0] = static_cast<int>(edge_ends[2*m+0]);
     edge[nedge][1] = static_cast<int>(edge_ends[2*m+1]);

src/BODY/pair_body_rounded_polyhedron.cpp

@@ -556,6 +556,10 @@ void PairBodyRoundedPolyhedron::body2space(int i)
     memory->grow(edge,edmax,6,"pair:edge");
   }
 
+  if ((body_num_edges > 0) && (edge_ends == nullptr))
+    error->one(FLERR,fmt::format("Inconsistent edge data for body of atom {}",
+                                 atom->tag[i]));
+
   for (int m = 0; m < body_num_edges; m++) {
     edge[nedge][0] = static_cast<int>(edge_ends[2*m+0]);
     edge[nedge][1] = static_cast<int>(edge_ends[2*m+1]);
@@ -579,6 +583,10 @@ void PairBodyRoundedPolyhedron::body2space(int i)
     memory->grow(face,facmax,MAX_FACE_SIZE,"pair:face");
   }
 
+  if ((body_num_faces > 0) && (face_pts == nullptr))
+    error->one(FLERR,fmt::format("Inconsistent face data for body of atom {}",
+                                 atom->tag[i]));
+
   for (int m = 0; m < body_num_faces; m++) {
     for (int k = 0; k < MAX_FACE_SIZE; k++)
       face[nface][k] = static_cast<int>(face_pts[MAX_FACE_SIZE*m+k]);

src/COLLOID/pair_colloid.cpp

@@ -473,6 +473,7 @@ double PairColloid::single(int /*i*/, int /*j*/, int itype, int jtype, double rs
   double K[9],h[4],g[4];
   double r,r2inv,r6inv,forcelj,c1,c2,phi,fR,dUR,dUA;
 
+  phi = 0.0;
   switch (form[itype][jtype]) {
   case SMALL_SMALL:
     r2inv = 1.0/rsq;

src/GPU/fix_gpu.cpp

@@ -270,7 +270,7 @@ void FixGPU::init()
 
   // give a warning if no pair style is defined
 
-  if (!force->pair)
+  if (!force->pair && (comm->me == 0))
     error->warning(FLERR,"Using package gpu without any pair style defined");
 
   // make sure fdotr virial is not accumulated multiple times
@@ -293,7 +293,7 @@ void FixGPU::init()
 void FixGPU::setup(int vflag)
 {
   if (_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH)
-    if (neighbor->exclude_setting()!=0)
+    if (neighbor->exclude_setting() != 0)
       error->all(FLERR,
                  "Cannot use neigh_modify exclude with GPU neighbor builds");
 

src/MC/fix_tfmc.cpp

@@ -56,6 +56,7 @@ FixTFMC::FixTFMC(LAMMPS *lmp, int narg, char **arg) :
 
   comflag = 0;
   rotflag = 0;
+  xflag = yflag = zflag = 0;
 
   int iarg = 6;
   while (iarg < narg) {

src/SHOCK/fix_append_atoms.cpp

@@ -49,6 +49,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
   scaleflag = 1;
   spatflag=0;
   spatialid = nullptr;
+  size = 0.0;
   xloflag = xhiflag = yloflag = yhiflag = zloflag = zhiflag = 0;
 
   tempflag = 0;

src/SHOCK/fix_wall_piston.cpp

@@ -43,6 +43,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
   tempflag = 0;
   scaleflag = 1;
   roughflag = 0;
+  roughdist = 0.0;
   rampflag = 0;
   rampNL1flag = 0;
   rampNL2flag = 0;

src/USER-REACTION/fix_bond_react.cpp

@@ -1368,11 +1368,11 @@ void FixBondReact::superimpose_algorithm()
         }
 
         // reaction site found successfully!
-        if (status == ACCEPT)
+        if (status == ACCEPT) {
           if (fraction[rxnID] < 1.0 &&
               random[rxnID]->uniform() >= fraction[rxnID]) status = REJECT;
           else glove_ghostcheck();
-
+        }
         hang_catch++;
         // let's go ahead and catch the simplest of hangs
         //if (hang_catch > onemol->natoms*4)

src/compute_chunk_atom.cpp

@@ -386,7 +386,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
   // apply scaling factors and cylinder dims orthogonal to axis
 
   if (binflag) {
-    double scale;
+    double scale = 1.0;
     if (which == ArgInfo::BIN1D || which == ArgInfo::BIN2D
         || which == ArgInfo::BIN3D || which == ArgInfo::BINCYLINDER) {
       if (which == ArgInfo::BIN1D || which == ArgInfo::BINCYLINDER) ndim = 1;

src/compute_global_atom.cpp

@@ -50,7 +50,7 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
   indexref = argi.get_index1();
   idref = argi.copy_name();
 
-  if ((whichref == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE)
+  if ((whichref == ArgInfo::UNKNOWN) || (whichref == ArgInfo::NONE)
       || (argi.get_dim() > 1))
     error->all(FLERR,"Illegal compute global/atom command");
 

src/error.cpp

@@ -52,8 +52,11 @@ Error::Error(LAMMPS *lmp) : Pointers(lmp) {
 void Error::universe_all(const std::string &file, int line, const std::string &str)
 {
   MPI_Barrier(universe->uworld);
-  std::string mesg = fmt::format("ERROR: {} ({}:{})\n",
+  std::string mesg = "ERROR: " + str;
-                                 str,truncpath(file),line);
+  try {
+    mesg += fmt::format(" ({}:{})\n",truncpath(file),line);
+  } catch (fmt::format_error &e) {
+  }
   if (universe->me == 0) {
     if (universe->uscreen)  fputs(mesg.c_str(),universe->uscreen);
     if (universe->ulogfile) fputs(mesg.c_str(),universe->ulogfile);
@@ -135,9 +138,14 @@ void Error::all(const std::string &file, int line, const std::string &str)
   MPI_Comm_rank(world,&me);
 
   if (me == 0) {
+    std::string mesg = "ERROR: " + str;
     if (input && input->line) lastcmd = input->line;
-    utils::logmesg(lmp,fmt::format("ERROR: {} ({}:{})\nLast command: {}\n",
+    try {
-                                   str,truncpath(file),line,lastcmd));
+      mesg += fmt::format(" ({}:{})\nLast command: {}\n",
+                          truncpath(file),line,lastcmd);
+    } catch (fmt::format_error &e) {
+    }
+    utils::logmesg(lmp,mesg);
   }
 
 #ifdef LAMMPS_EXCEPTIONS

src/fix_ave_histo_weight.cpp

@@ -51,7 +51,7 @@ FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) :
 
   // check that length of 2 values is the same
 
-  int size[2];
+  int size[2] = {0,0};
 
   for (int i = 0; i < nvalues; i++) {
     if (which[i] == ArgInfo::X || which[i] == ArgInfo::V || which[i] == ArgInfo::F) {

src/main.cpp

@@ -58,6 +58,10 @@ int main(int argc, char **argv)
     MPI_Barrier(MPI_COMM_WORLD);
     MPI_Finalize();
     exit(1);
+  } catch(fmt::format_error &fe) {
+    fprintf(stderr,"fmt::format_error: %s\n", fe.what());
+    MPI_Abort(MPI_COMM_WORLD, 1);
+    exit(1);
   }
 #else
   LAMMPS *lammps = new LAMMPS(argc,argv,MPI_COMM_WORLD);

src/update.cpp

@@ -54,6 +54,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
   eflag_atom = vflag_atom = 0;
 
   dt_default = 1;
+  dt = 0.0;
   unit_style = nullptr;
   set_units("lj");