remove backslash escapes for underscore in doc references
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@ -45,7 +45,7 @@ Define a computation that calculates the radial distribution function
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(RDF), also called g(r), and the coordination number for a group of
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particles. Both are calculated in histogram form by binning pairwise
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distances into *Nbin* bins from 0.0 to the maximum force cutoff
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defined by the :doc:`pair\_style <pair_style>` command or the cutoff
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defined by the :doc:`pair_style <pair_style>` command or the cutoff
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distance *Rcut* specified via the *cutoff* keyword. The bins are of
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uniform size in radial distance. Thus a single bin encompasses a thin
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shell of distances in 3d and a thin ring of distances in 2d.
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@ -53,9 +53,9 @@ shell of distances in 3d and a thin ring of distances in 2d.
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.. note::
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If you have a bonded system, then the settings of
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:doc:`special\_bonds <special_bonds>` command can remove pairwise
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:doc:`special_bonds <special_bonds>` command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the :doc:`special\_bonds <special_bonds>`
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is the default setting for the :doc:`special_bonds <special_bonds>`
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses a neighbor list, it also means
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those pairs will not be included in the RDF. This does not apply when
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@ -65,11 +65,11 @@ shell of distances in 3d and a thin ring of distances in 2d.
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zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
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use the :doc:`rerun <rerun>` command to compute the RDF for snapshots in
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the dump file. The rerun script can use a
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:doc:`special\_bonds <special_bonds>` command that includes all pairs in
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:doc:`special_bonds <special_bonds>` command that includes all pairs in
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the neighbor list.
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By default the RDF is computed out to the maximum force cutoff defined
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by the :doc:`pair\_style <pair_style>` command. If the *cutoff* keyword
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by the :doc:`pair_style <pair_style>` command. If the *cutoff* keyword
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is used, then the RDF is computed accurately out to the *Rcut* > 0.0
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distance specified.
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@ -87,7 +87,7 @@ distance specified.
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timestep, whichever is less frequent), which is inefficient. LAMMPS
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will warn you if this is the case. If you specify a *Rcut* > force
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cutoff, you must insure ghost atom information out to *Rcut* + *skin*
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is communicated, via the :doc:`comm\_modify cutoff <comm_modify>`
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is communicated, via the :doc:`comm_modify cutoff <comm_modify>`
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command, else the RDF computation cannot be performed, and LAMMPS will
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give an error message. The *skin* value is what is specified with the
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:doc:`neighbor <neighbor>` command. In this case, you are forcing a
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@ -120,7 +120,7 @@ by *itypeN* are the central atom, and atoms of any of the range of
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types represented by *jtypeN* are the distribution atom.
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Pairwise distances are generated by looping over a pairwise neighbor
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list, just as they would be in a :doc:`pair\_style <pair_style>`
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list, just as they would be in a :doc:`pair_style <pair_style>`
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computation. The distance between two atoms I and J is included in a
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specific histogram if the following criteria are met:
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@ -205,12 +205,12 @@ change from zero to one at the location of the spike in g(r).
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parallel efficiency and scaling. For systems, where only the type
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of atoms changes (e.g. when using :doc:`fix atom/swap <fix_atom_swap>`),
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you need to explicitly request the dynamic normalization updates
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via :doc:`compute\_modify dynamic yes <compute_modify>`
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via :doc:`compute_modify dynamic yes <compute_modify>`
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Related commands
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""""""""""""""""
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:doc:`fix ave/time <fix_ave_time>`, :doc:`compute\_modify <compute_modify>`,
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:doc:`fix ave/time <fix_ave_time>`, :doc:`compute_modify <compute_modify>`,
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:doc:`compute adf <compute_adf>`
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Default
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