Merge pull request #1197 from akohlmey/collected-small-fixes

Collection of small changes and bugfixes for the next release

cmake/presets/all_off.cmake

@@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/all_on.cmake

@@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/manual_selection.cmake

@@ -56,7 +56,8 @@ set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
 set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/user.cmake

@@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

doc/src/Build_basics.txt

@@ -137,9 +137,9 @@ simply loading the appropriate module before building LAMMPS.
 -D CMAKE_C_COMPILER=name              # name of C compiler
 -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre
 
--D CMAKE_CXX_FlAGS=string             # flags to use with C++ compiler
+-D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
--D CMAKE_C_FlAGS=string               # flags to use with C compiler
+-D CMAKE_C_FLAGS=string               # flags to use with C compiler
--D CMAKE_Fortran_FlAGS=string         # flags to use with Fortran compiler :pre
+-D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler :pre
 
 By default CMake will use a compiler it finds and it will add
 optimization flags appropriate to that compiler and any "accelerator

doc/src/compute_ptm_atom.txt

@@ -117,5 +117,5 @@ package"_Build_package.html doc page for more info.
 :line
 
 :link(Larsen)
-[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
+[(Larsen)] Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
 

doc/src/fix_bond_react.txt

@@ -41,7 +41,7 @@ react = mandatory argument indicating new reaction specification :l
       fraction = initiate reaction with this probability if otherwise eligible
       seed = random number seed (positive integer)
     {stabilize_steps} value = timesteps
-      timesteps = number of timesteps to apply internally created nve/limit.html
+      timesteps = number of timesteps to apply internally created nve/limit fix :pre
     {update_edges} value = {none} or {charges} :l
       none = do not update topology near the edges of reaction templates
       charges = update atomic charges of all atoms in reaction templates

src/USER-VTK/dump_vtk.cpp

@@ -93,10 +93,10 @@ enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats
 #define ONEFIELD 32
 #define DELTA 1048576
 
-#if VTK_MAJOR_VERSION >= 7
+#if (VTK_MAJOR_VERSION < 5) || (VTK_MAJOR_VERSION > 8)
-#define InsertNextTupleValue InsertNextTypedTuple
-#elif VTK_MAJOR_VERSION > 8
 #error This code has only been tested with VTK 5, 6, 7, and 8
+#elif VTK_MAJOR_VERSION > 6
+#define InsertNextTupleValue InsertNextTypedTuple
 #endif
 
 /* ---------------------------------------------------------------------- */

src/bond_hybrid.cpp

@@ -33,6 +33,7 @@ BondHybrid::BondHybrid(LAMMPS *lmp) : Bond(lmp)
 {
   writedata = 0;
   nstyles = 0;
+  has_quartic = -1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -171,6 +172,7 @@ void BondHybrid::settings(int narg, char **arg)
     delete [] styles;
     for (int i = 0; i < nstyles; i++) delete [] keywords[i];
     delete [] keywords;
+    has_quartic = -1;
   }
 
   if (allocated) {
@@ -214,14 +216,23 @@ void BondHybrid::settings(int narg, char **arg)
   i = 0;
 
   while (i < narg) {
+
     for (m = 0; m < nstyles; m++)
       if (strcmp(arg[i],keywords[m]) == 0)
         error->all(FLERR,"Bond style hybrid cannot use same bond style twice");
+
     if (strcmp(arg[i],"hybrid") == 0)
       error->all(FLERR,"Bond style hybrid cannot have hybrid as an argument");
+
     if (strcmp(arg[i],"none") == 0)
       error->all(FLERR,"Bond style hybrid cannot have none as an argument");
 
+    // register index of quartic bond type,
+    // so that bond type 0 can be mapped to it
+
+    if (strncmp(arg[i],"quartic",7) == 0)
+      has_quartic = m;
+
     styles[nstyles] = force->new_bond(arg[i],1,dummy);
     force->store_style(keywords[nstyles],arg[i],0);
 
@@ -283,6 +294,12 @@ void BondHybrid::init_style()
 {
   for (int m = 0; m < nstyles; m++)
     if (styles[m]) styles[m]->init_style();
+
+  // bond style quartic will set broken bonds to bond type 0, so we need
+  // to create an entry for it in the bond type to sub-style map
+
+  if (has_quartic >= 0)
+    map[0] = has_quartic;
 }
 
 /* ----------------------------------------------------------------------

src/bond_hybrid.h

@@ -47,7 +47,7 @@ class BondHybrid : public Bond {
 
  private:
   int *map;                     // which style each bond type points to
-
+  int has_quartic;              // which style, if any is a quartic bond style
   int *nbondlist;               // # of bonds in sub-style bondlists
   int *maxbond;                 // max # of bonds sub-style lists can store
   int ***bondlist;              // bondlist for each sub-style

tools/msi2lmp/src/MakeLists.c

@@ -363,7 +363,7 @@ int count_dihedrals()
               if (i != k) {
                 for (ll=0; ll < atoms[k].no_connect; ll++) {
                   l = atoms[k].conn_no[ll];
-                  if ((l != j) && (i != l)) n++
+                  if ((l != j) && (i != l)) n++;
                 }
               }
             }

tools/msi2lmp/src/ReadCarFile.c

@@ -77,7 +77,6 @@ void ReadCarFile(void)
   double cos_gamma;
   double sin_gamma;
   double cos_beta;
-  double sin_beta;
   double A, B, C;
   double center[3];
   double hmat[6];
@@ -265,7 +264,6 @@ void ReadCarFile(void)
       cos_gamma = cos(pbc[5]*PI_180);
       sin_gamma = sin(pbc[5]*PI_180);
       cos_beta =  cos(pbc[4]*PI_180);
-      sin_beta =  sin(pbc[4]*PI_180);
       if (pflag > 2) {
         printf(" pbc[3] %f pbc[4] %f pbc[5] %f\n", pbc[3] ,pbc[4] ,pbc[5]);
         printf(" cos_alpha %f cos_beta %f cos_gamma %f\n", cos_alpha ,cos_beta ,cos_gamma);