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This commit is contained in:
Axel Kohlmeyer
2024-03-17 15:13:13 -04:00
parent 1bbe87d9d2
commit d97c7fffac
3 changed files with 29 additions and 27 deletions
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29
doc/src/fix_electrode.rst
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@ -255,23 +255,24 @@ and the fix will issue an error in that case.
.. versionadded:: TBD .. versionadded:: TBD
The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo* The keyword *qtotal* causes *fix electrode/conp* and *fix
to add an overall potential to all electrodes so that the total charge on electrode/thermo* to add an overall potential to all electrodes so that
the electrodes is a specified amount (which may be an equal-style variable). the total charge on the electrodes is a specified amount (which may be
For example, if a user wanted to simulate a solution of excess cations an equal-style variable). For example, if a user wanted to simulate a
such that the total electrolyte charge is +2, setting *qtotal -2* would cause solution of excess cations such that the total electrolyte charge is +2,
the total electrode charge to be -2, so that the simulation box remains overall setting *qtotal -2* would cause the total electrode charge to be -2, so
electroneutral. Since *fix electrode/conq* constrains the total charges of that the simulation box remains overall electroneutral. Since *fix
individual electrodes, and since *symm on* constrains the total charge of all electrode/conq* constrains the total charges of individual electrodes,
electrodes to be zero, either option is incompatible with the *qtotal* keyword and since *symm on* constrains the total charge of all electrodes to be
(even if *qtotal* is set to zero). zero, either option is incompatible with the *qtotal* keyword (even if
*qtotal* is set to zero).
.. versionadded:: TBD .. versionadded:: TBD
The keyword *eta* takes the name of a custom double vector defined via fix The keyword *eta* takes the name of a custom double vector defined via
property/atom. The values will be used instead of the standard eta value. The fix property/atom. The values will be used instead of the standard eta
property/atom fix must be for vector of double values and use the *ghost on* value. The property/atom fix must be for vector of double values and
option. use the *ghost on* option.
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""

26
doc/src/processors.rst
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@ -159,17 +159,17 @@ surface-to-volume ratio of each processor's subdomain.
for most MPI implementations, but some MPIs provide options for this for most MPI implementations, but some MPIs provide options for this
ordering, e.g. via environment variable settings. ordering, e.g. via environment variable settings.
The *numa* style operates similar to the *twolevel* keyword except The *numa* style operates similar to the *twolevel* keyword except that
that it auto-detects which cores are running on which nodes. it auto-detects which cores are running on which nodes. It will also
It will also subdivide the cores into numa domains. Currently, the subdivide the cores into numa domains. Currently, the number of numa
number of numa domains is not autodetected and must be specified using domains is not auto-detected and must be specified using the
the *numa_nodes* keyword; otherwise, the default value is used. The *numa_nodes* keyword; otherwise, the default value is used. The *numa*
*numa* style uses a different algorithm than the *twolevel* keyword for style uses a different algorithm than the *twolevel* keyword for doing
doing the two-level factorization of the simulation box into a 3d the two-level factorization of the simulation box into a 3d processor
processor grid to minimize off-node communication and communication grid to minimize off-node communication and communication across numa
across numa domains. It does its own MPI-based mapping of nodes and domains. It does its own MPI-based mapping of nodes and cores to the
cores to the regular 3d grid. Thus it may produce a different layout regular 3d grid. Thus it may produce a different layout of the
of the processors than the *twolevel* options. processors than the *twolevel* options.
The *numa* style will give an error if the number of MPI processes is The *numa* style will give an error if the number of MPI processes is
not divisible by the number of cores used per node, or any of the Px not divisible by the number of cores used per node, or any of the Px
@ -182,7 +182,7 @@ or Py or Pz values is greater than 1.
is because it auto-detects which processes are running on which nodes. is because it auto-detects which processes are running on which nodes.
However, it assumes that the lowest ranks are in the first numa However, it assumes that the lowest ranks are in the first numa
domain, and so forth. MPI rank orderings that do not preserve this domain, and so forth. MPI rank orderings that do not preserve this
property might result in more intranode communication between CPUs. property might result in more intra-node communication between CPUs.
The *custom* style uses the file *infile* to define both the 3d The *custom* style uses the file *infile* to define both the 3d
factorization and the mapping of processors to the grid. factorization and the mapping of processors to the grid.
@ -213,7 +213,7 @@ any order, but no processor ID should appear more than once.
---------- ----------
The *numa_nodes* keyword is used to specifiy the number of numa domains The *numa_nodes* keyword is used to specify the number of numa domains
per node. It is currently only used by the *numa* style for two-level per node. It is currently only used by the *numa* style for two-level
factorization to reduce the amount of MPI communications between CPUs. factorization to reduce the amount of MPI communications between CPUs.
A good setting for this will typically be equal to the number of CPU A good setting for this will typically be equal to the number of CPU

1
doc/utils/sphinx-config/false_positives.txt
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@ -947,6 +947,7 @@ elastance
Electroneg Electroneg
electronegative electronegative
electronegativity electronegativity
electroneutral
electroneutrality electroneutrality
Eleftheriou Eleftheriou
ElementN ElementN