diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 4b60a9705e..800542475d 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -250,13 +250,20 @@ the :doc:`dump_modify ` page for details. The *style* keyword determines what kind of data is written to the dump file(s) and in what format. -Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files -can be read directly by `VMD `_, -a popular tool for viewing molecular system. +Note that *atom*, *custom*, *dcd*, *xtc*, *xyz*, and *yaml* style dump +files can be read directly by `VMD `_, +a popular tool for visualizing and analyzing trajectories from atomic +and molecular systems. For reading *netcdf* style dump files, the +netcdf plugin needs to be recompiled from source using a NetCDF version +compatible with the one used by LAMMPS. The bundled plugin binary +uses a very old version of NetCDF that is not compatible with LAMMPS. -Likewise the `OVITO visualization tool `_, -popular for materials modeling, can read the *atom*, *custom*, and -*grid* style dump files. +Likewise the `OVITO visualization package `_, +popular for materials modeling, can read the *atom*, *custom*, +*local*, *xtc*, *cfg*, *netcdf*, and *xyz* style atom dump files +directly. With version 3.8 and above, OVITO can also read and +visualize *grid* style dump files with grid cell data, including +iso-surface images of the grid cell values. Note that settings made via the :doc:`dump_modify ` command can also alter the format of individual values and content of diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 9c66d1d19b..f070d0a53f 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -441,10 +441,12 @@ void CreateAtoms::command(int narg, char **arg) MPI_Barrier(world); double time1 = platform::walltime(); + // clear global->local map for owned and ghost atoms // clear ghost count and any ghost bonus data internal to AtomVec // same logic as beginning of Comm::exchange() // do it now b/c creating atoms will overwrite ghost atoms + if (atom->map_style != Atom::MAP_NONE) atom->map_clear(); atom->nghost = 0; atom->avec->clear_bonus(); diff --git a/src/read_data.cpp b/src/read_data.cpp index 31289cdd82..85f5accc4b 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -375,6 +375,16 @@ void ReadData::command(int narg, char **arg) if (addflag == NONE) { domain->box_exist = 1; update->ntimestep = 0; + } else { + + // clear global->local map for owned and ghost atoms + // clear ghost count and any ghost bonus data internal to AtomVec + // same logic as beginning of Comm::exchange() + // do it now b/c adding atoms will overwrite ghost atoms + + if (atom->map_style != Atom::MAP_NONE) atom->map_clear(); + atom->nghost = 0; + atom->avec->clear_bonus(); } // compute atomID and optionally moleculeID offset for addflag = APPEND