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