diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 9021dedc08..b434796d7c 100644 --- a/cmake/presets/all_off.cmake +++ b/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}) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index ef17e38914..3a1100f337 100644 --- a/cmake/presets/all_on.cmake +++ b/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}) diff --git a/cmake/presets/manual_selection.cmake b/cmake/presets/manual_selection.cmake index 35a45a5c87..6db41b708c 100644 --- a/cmake/presets/manual_selection.cmake +++ b/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) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 54db12a851..4c02fb6210 100644 --- a/cmake/presets/nolib.cmake +++ b/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}) diff --git a/cmake/presets/user.cmake b/cmake/presets/user.cmake index afb030d3d6..af606203e9 100644 --- a/cmake/presets/user.cmake +++ b/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}) diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index 4b3a347bf1..b3ff0a55c5 100644 --- a/doc/src/Build_basics.txt +++ b/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_C_FlAGS=string # flags to use with C compiler --D CMAKE_Fortran_FlAGS=string # flags to use with Fortran compiler :pre +-D CMAKE_CXX_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 By default CMake will use a compiler it finds and it will add optimization flags appropriate to that compiler and any "accelerator diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt index 2e22e4e9fb..8f79fe502b 100644 --- a/doc/src/compute_ptm_atom.txt +++ b/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). diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index e88bd198f3..55a5785f7f 100644 --- a/doc/src/fix_bond_react.txt +++ b/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 diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index edbc647a81..88e95dd338 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/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 -#define InsertNextTupleValue InsertNextTypedTuple -#elif VTK_MAJOR_VERSION > 8 +#if (VTK_MAJOR_VERSION < 5) || (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 /* ---------------------------------------------------------------------- */ diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index c3a71ee71c..4e5a26f731 100644 --- a/src/bond_hybrid.cpp +++ b/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; } /* ---------------------------------------------------------------------- diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index a385a2e3f8..e51d467ac1 100644 --- a/src/bond_hybrid.h +++ b/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 diff --git a/tools/msi2lmp/src/MakeLists.c b/tools/msi2lmp/src/MakeLists.c index 44b9bdd0af..18b261a561 100644 --- a/tools/msi2lmp/src/MakeLists.c +++ b/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++; } } } diff --git a/tools/msi2lmp/src/ReadCarFile.c b/tools/msi2lmp/src/ReadCarFile.c index c6db96cf92..7932f7d6e2 100644 --- a/tools/msi2lmp/src/ReadCarFile.c +++ b/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);