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add comments/warnings to docs of fix property/atom and fix store/state about restarting

This commit is contained in:
Axel Kohlmeyer 2020-09-04 00:14:01 -04:00
parent cb618e19d1
commit 87dfdb8723
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2 changed files with 32 additions and 13 deletions
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36
doc/src/fix_property_atom.rst
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@ -105,7 +105,7 @@ keyword with a value of *yes*\ . This will invoke extra communication
when ghost atoms are created (at every re-neighboring) to insure the
new properties are also defined for the ghost atoms.
.. note::
.. admonition:: Properties on ghost atoms
If you use this command with the *mol*\ , *q* or *rmass* vectors,
then you most likely want to set *ghost* yes, since these properties
@ -115,7 +115,7 @@ new properties are also defined for the ghost atoms.
atoms to have these values. LAMMPS will issue a warning it you define
those vectors but do not set *ghost* yes.
.. note::
.. admonition:: Limitations on ghost atom properties
The properties for ghost atoms are not updated every timestep,
but only once every few steps when neighbor lists are re-built. Thus
@ -126,12 +126,6 @@ new properties are also defined for the ghost atoms.
that can be invoked from within a :doc:`pair style <pair_style>` or
:doc:`fix <fix>` or :doc:`compute <compute>` that you write.
.. note::
If this fix is defined **after** the simulation box is created,
a 'run 0' command should be issued to properly initialize the storage
created by this fix.
----------
This fix is one of a small number that can be defined in an input
@ -139,6 +133,12 @@ script before the simulation box is created or atoms are defined.
This is so it can be used with the :doc:`read_data <read_data>` command
as described below.
.. note::
If this fix is defined **after** the simulation box is created,
a 'run 0' command may be needed to properly initialize the storage
created by this fix.
Per-atom properties that are defined by the :doc:`atom style <atom_style>` are initialized when atoms are created, e.g. by
the :doc:`read_data <read_data>` or :doc:`create_atoms <create_atoms>`
commands. The per-atom properties defined by this fix are not. So
@ -271,11 +271,21 @@ example to heavy water:
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a
simulation is restarted. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
This fix writes the per-atom values it stores to :doc:`binary restart
files <restart>`, so that the values can be restored when a simulation
is restarted. See the :doc:`read_restart <read_restart>` command for
info on how to re-specify a fix in an input script that reads a restart
file, so that the operation of the fix continues in an uninterrupted
fashion.
.. warning::
When reading data from a restart, the fix command has to be specified
**exactly** the same way as before. LAMMPS will only check whether a
fix is of the same style and has the same fix ID and in case of a match
will then try to initialize the fix with the data stored in the binary
restart file. If the fix property/atom command does not match exactly,
data can be corrupted or LAMMPS may crash.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for

9
doc/src/fix_store_state.rst
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@ -111,6 +111,15 @@ command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
.. warning::
When reading data from a restart, the fix command has to be specified
**exactly** the same way as before. LAMMPS will only check whether a
fix is of the same style and has the same fix ID and in case of a match
will then try to initialize the fix with the data stored in the binary
restart file. If the fix store/state command does not match exactly,
data can be corrupted or LAMMPS may crash.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix.