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Merge branch 'develop' of https://github.com/lammps/lammps into kk_occupancy

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Stan Moore
2022-12-23 08:54:23 -07:00
parent ae1dc7b52c 07fe2fa29d
commit ea0a91f2bc
3 changed files with 25 additions and 6 deletions
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19
doc/src/dump.rst
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@ -250,13 +250,20 @@ the :doc:`dump_modify <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 <https://www.ks.uiuc.edu/Research/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 <https://www.ks.uiuc.edu/Research/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 <https://www.ovito.org>`_,
popular for materials modeling, can read the *atom*, *custom*, and
*grid* style dump files.
Likewise the `OVITO visualization package <https://www.ovito.org>`_,
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 <dump_modify>`
command can also alter the format of individual values and content of

2
src/create_atoms.cpp
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@ -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();

10
src/read_data.cpp
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@ -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