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This commit is contained in:
Axel Kohlmeyer
2023-05-04 16:04:08 -04:00
parent 042829c40d
commit 8fe4394ada
3 changed files with 4 additions and 4 deletions
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4
doc/src/Developer_atom.rst
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@ -44,7 +44,7 @@ When referring to individual atoms, they may be indexed by their local
containing first all *owned* atoms (index < `Atom::nlocal`) and then all containing first all *owned* atoms (index < `Atom::nlocal`) and then all
*ghost* atoms. The order of atoms in these arrays can change due to *ghost* atoms. The order of atoms in these arrays can change due to
atoms migrating between between subdomains, atoms being added or atoms migrating between between subdomains, atoms being added or
deleted, or atoms being sorted for better cach efficiency. Atoms are deleted, or atoms being sorted for better cache efficiency. Atoms are
globally uniquely identified by their *atom ID*. There may be multiple globally uniquely identified by their *atom ID*. There may be multiple
atoms with the same atom ID present, but only one of them may be an atoms with the same atom ID present, but only one of them may be an
*owned* atom. *owned* atom.
@ -79,7 +79,7 @@ Atom class versus AtomVec classes
The `Atom` class contains all kinds of flags and counters about atoms in The `Atom` class contains all kinds of flags and counters about atoms in
the system and that includes pointers to **all** per-atom properties the system and that includes pointers to **all** per-atom properties
availabel for atoms. However, only a subset of these pointers are available for atoms. However, only a subset of these pointers are
non-NULL and which those are depends on the atom style. For each atom non-NULL and which those are depends on the atom style. For each atom
style there is a corresponding `AtomVecXXX` class derived from the style there is a corresponding `AtomVecXXX` class derived from the
`AtomVec` base class, where the XXX indicates the atom style. This `AtomVec` base class, where the XXX indicates the atom style. This

2
doc/src/Howto_broken_bonds.rst
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@ -31,7 +31,7 @@ The :doc:`fix bond/break <fix_bond_break>` and :doc:`fix bond/react
<fix_bond_react>` commands allow breaking of bonds within a molecular <fix_bond_react>` commands allow breaking of bonds within a molecular
topology with may also define angles, dihedrals, etc. These commands topology with may also define angles, dihedrals, etc. These commands
update internal topology data structures to remove broken bonds, as update internal topology data structures to remove broken bonds, as
well as the appropriate angle, dihederal, etc interactions which well as the appropriate angle, dihedral, etc interactions which
include the bond. They also trigger a rebuild of the neighbor list include the bond. They also trigger a rebuild of the neighbor list
when this occurs, to turn on the appropriate pairwise forces. when this occurs, to turn on the appropriate pairwise forces.

2
doc/src/package.rst
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@ -561,7 +561,7 @@ The *sort* keyword determines whether the host or device performs atom
sorting, see the :doc:`atom_modify sort <atom_modify>` command. The sorting, see the :doc:`atom_modify sort <atom_modify>` command. The
value options for the *sort* keyword are *no* or *device* similar to the value options for the *sort* keyword are *no* or *device* similar to the
*comm* keywords above. If a value of *host* is used it will be *comm* keywords above. If a value of *host* is used it will be
automatically be changed to *no* since the *sort* keyword doesn't automatically be changed to *no* since the *sort* keyword does not
support *host* mode. The value of *no* will also always be used when support *host* mode. The value of *no* will also always be used when
running on the CPU, i.e. setting the value to *device* will have no running on the CPU, i.e. setting the value to *device* will have no
effect if the simulation is running on the CPU. Not all fix styles with effect if the simulation is running on the CPU. Not all fix styles with