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add some docs for the special treatment of image flags

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This commit is contained in:
Axel Kohlmeyer
2017-03-28 02:22:45 -04:00
parent 443ea13eff
commit fc51c38abb
2 changed files with 15 additions and 1 deletions
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5
doc/src/Section_howto.txt
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@ -2013,6 +2013,11 @@ Both methods are thus a means to extract or assign (overwrite) any
peratom quantities within LAMMPS. See the extract() method in the peratom quantities within LAMMPS. See the extract() method in the
src/atom.cpp file for a list of valid per-atom properties. New names src/atom.cpp file for a list of valid per-atom properties. New names
could easily be added if the property you want is not listed. could easily be added if the property you want is not listed.
A special treatment is applied for accessing image flags via the
"image" property. Image flags are stored in a packed format with all
three image flags stored in a single integer. When signaling to access
the image flags as 3 individual values per atom instead of 1, the data
is transparently packed or unpacked by the library interface.
The lammps_create_atoms() function takes a list of N atoms as input The lammps_create_atoms() function takes a list of N atoms as input
with atom types and coords (required), an optionally atom IDs and with atom types and coords (required), an optionally atom IDs and

11
doc/src/Section_python.txt
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@ -698,7 +698,12 @@ method in the src/atom.cpp file for a list of valid names. Again, new
names could easily be added if the property you want is missing. The names could easily be added if the property you want is missing. The
vector can be used via normal Python subscripting. If atom IDs are vector can be used via normal Python subscripting. If atom IDs are
not consecutively ordered within LAMMPS, a None is returned as not consecutively ordered within LAMMPS, a None is returned as
indication of an error. indication of an error. A special treatment is applied for image flags
stored in the "image" property. All three image flags are stored in
a packed format in a single integer, so count would be 1 to retrieve
that integer, however also a count value of 3 can be used and then
the image flags will be unpacked into 3 individual integers, ordered
in a similar fashion as coordinates.
Note that the data structure gather_atoms("x") returns is different Note that the data structure gather_atoms("x") returns is different
from the data structure returned by extract_atom("x") in four ways. from the data structure returned by extract_atom("x") in four ways.
@ -727,6 +732,10 @@ corresponding properties for each atom inside LAMMPS. This requires
LAMMPS to have its "map" option enabled; see the LAMMPS to have its "map" option enabled; see the
"atom_modify"_atom_modify.html command for details. If it is not, or "atom_modify"_atom_modify.html command for details. If it is not, or
if atom IDs are not consecutively ordered, no coordinates are reset. if atom IDs are not consecutively ordered, no coordinates are reset.
Similar as for gather_atoms() a special treatment is applied for image
flags, which can be provided in packed (count = 1) or unpacked (count = 3)
format and in the latter case, they will be packed before applied to
atoms.
The array of coordinates passed to scatter_atoms() must be a ctypes The array of coordinates passed to scatter_atoms() must be a ctypes
vector of ints or doubles, allocated and initialized something like vector of ints or doubles, allocated and initialized something like