update text for MOLECULE package

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megmcca
2025-02-10 09:26:08 -07:00
parent 3b8139d428
commit 75fd76aaa6

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@ -15,7 +15,7 @@ following are discussions of such cases.
- :ref:`Too many neighbor bins <err0009>`
- :ref:`Cannot use neighbor bins - box size \<\< cutoff <err0015>`
- :ref:`Domain too large for neighbor bins <err0017>`
- :ref:`Incorrect args for pair coefficients <err0021>`
- :ref:`Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients) <err0021>`
- :ref:`Molecule topology/atom exceeds system topology/atom <err0024>`
- :ref:`Molecule topology type exceeds system topology type <err0025>`
- :ref:`Molecule attributes do not match system attributes <err0026>`
@ -288,7 +288,7 @@ Too many neighbor bins
The simulation box has become too large relative to the size of a
neighbor bin and LAMMPS is unable to store the needed number of
bins. This typically implies the simulation box has expanded too far.
This can happen when some atoms move rapidly apart with shrinkwrap
This can happen when some atoms move rapidly apart with shrink-wrap
boundaries or when a fix (like fix deform or a barostat) excessively
grows the simulation box.
@ -319,15 +319,22 @@ excessively grown the simulation box.
.. _err0021:
Incorrect args for pair coefficients
------------------------------------
Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients)
-------------------------------------------------------------------------------------
The parameters in the :doc:`pair_coeff <pair_coeff>`, command for a specified
:doc:`pair_style <pair_style>` have a missing or erroneous argument. Outside of
normal typos, this error can have several sources. In all cases, the first step
is to compare the command arguments to the expected format found in the
corresponding :doc:`pair_style <pair_style>` page. This can reveal cases where,
for example, a pair style was changed, but the pair coefficients were not
The parameters in the :doc:`pair_coeff <pair_coeff>` command for a specified
:doc:`pair_style <pair_style>` have a missing or erroneous argument. The same
applies when seeing this error for :doc:`bond_coeff <bond_coeff>`,
:doc:`angle_coeff <angle_coeff>`, :doc:`dihedral_coeff <dihedral_coeff>`, or
:doc:`improper_coeff <improper_coeff>` and their respective style commands when
using the MOLECULE or EXTRA-MOLECULE packages. The cases below will describe
some ways to approach pair coefficient errors, but the same strategies will
apply to bonded systems as well.
Outside of normal typos, this error can have several sources. In all cases, the
first step is to compare the command arguments to the expected format found in
the corresponding :doc:`pair_style <pair_style>` page. This can reveal cases
where, for example, a pair style was changed, but the pair coefficients were not
updated. This can happen especially with pair style variants such as
:doc:`pair_style eam <pair_eam>` vs. :doc:`pair_style eam/alloy <pair_style>`
that look very similar but accept different parameters (the latter 'eam/alloy'
@ -345,10 +352,10 @@ files that are read in by the input script, such as data files or restart files.
Molecule topology/atom exceeds system topology/atom
---------------------------------------------------
LAMMPS uses :doc:`domain decomposition <Developer_par_part>` to
distribute data (i.e. atoms) across the MPI processes in parallel runs.
This includes topology data, that is data about bonds, angles,
dihedrals, impropers and :doc:`"special" neighbors <special_bonds>`.
LAMMPS uses :doc:`domain decomposition <Developer_par_part>` to distribute data
(i.e. atoms) across the MPI processes in parallel runs. This includes topology
data, that is data about bonds, angles, dihedrals, impropers and :doc:`"special"
neighbors <special_bonds>`.
This information is stored with either one or all atoms involved in such
a topology entry (which of the two option applies depends on the
:doc:`newton <newton>` setting for bonds. When reading a data file,