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reformat, mention compute dipole

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Axel Kohlmeyer
2021-06-22 11:57:08 -04:00
parent 60e1c2be6d
commit 31011252e3
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61
doc/src/compute_dipole_chunk.rst
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@ -29,37 +29,41 @@ Description
Define a computation that calculates the dipole vector and total dipole
for multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
single chunk (or no chunk). The ID for this command is specified as
chunkID. For example, a single chunk could be the atoms in a molecule
or atoms in a spatial bin. See the :doc:`compute chunk/atom
<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
details of how chunks can be defined and examples of how they can be
used to measure properties of a system.
This compute calculates the x,y,z coordinates of the dipole vector
and the total dipole moment for each chunk, which includes all effects
due to atoms passing through periodic boundaries. For chunks with a net
This compute calculates the x,y,z coordinates of the dipole vector and
the total dipole moment for each chunk, which includes all effects due
to atoms passing through periodic boundaries. For chunks with a net
charge the resulting dipole is made position independent by subtracting
the position vector of the center of mass or geometric center times the
net charge from the computed dipole vector.
net charge from the computed dipole vector. Both per-atom charges and
per-atom dipole moments, if present, contribute to the computed dipole.
Note that only atoms in the specified group contribute to the
calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
"all" group for this command if you simply want to include atoms with
non-zero chunk IDs.
defines its own group; atoms will have a chunk ID = 0 if they are not in
that group, signifying they are not assigned to a chunk, and will thus
also not contribute to this calculation. You can specify the "all"
group for this command if you simply want to include atoms with non-zero
chunk IDs.
.. note::
The coordinates of an atom contribute to the chunk's
dipole in "unwrapped" form, by using the image flags
associated with each atom. See the :doc:`dump custom <dump>` command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the :doc:`read_data <read_data>` command for a discussion of image flags
The coordinates of an atom contribute to the chunk's dipole in
"unwrapped" form, by using the image flags associated with each atom.
See the :doc:`dump custom <dump>` command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
:doc:`read_data <read_data>` command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
(e.g. to 0) before invoking this compute by using the :doc:`set image
<set>` command.
The simplest way to output the results of the compute com/chunk
calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
@ -75,11 +79,12 @@ Output info
"""""""""""
This compute calculates a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
4 for the x,y,z dipole vector components and the total dipole of each
number of chunks *Nchunk* as calculated by the specified :doc:`compute
chunk/atom <compute_chunk_atom>` command. The number of columns = 4 for
the x,y,z dipole vector components and the total dipole of each
chunk. These values can be accessed by any command that uses global
array values from a compute as input. See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
options.
array values from a compute as input. See the :doc:`Howto output
<Howto_output>` doc page for an overview of LAMMPS output options.
The array values are "intensive". The array values will be in
dipole units, i.e. charge units times distance :doc:`units <units>`.
@ -91,9 +96,11 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute com/chunk <compute_com_chunk>`
:doc:`compute com/chunk <compute_com_chunk>`,
:doc:`compute dipole <compute_dipole>`
Default
"""""""
none
Using the center of mass is the default setting for the net charge correction.