diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index eddf36c44c..275ad26325 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -702,7 +702,7 @@ The *skip* keyword can be used with all dump styles. It allows a dump snapshot to be skipped (not written to the dump file), if a condition is met. The condition is computed by an :doc:`equal-style variable `, which should be specified as v_name, where name is the -variable name. If the variable evaulation returns a non-zero value, +variable name. If the variable evaluation returns a non-zero value, then the dump snapshot is skipped. If it returns zero, the dump proceeds as usual. Note that :doc:`equal-style variable ` can contain Boolean operators which effectively evaluate as a true @@ -718,12 +718,12 @@ value. The *sort* keyword determines whether lines of per-atom output in a snapshot are sorted or not. A sort value of *off* means they will typically be written in indeterminate order, either in serial or -parallel. This is the case even in serial if the :doc:`atom_modify -sort ` option is turned on, which it is by default, to -improve performance. A sort value of *id* means sort the output by -atom ID. A sort value of N or -N means sort the output by the value -in the Nth column of per-atom info in either ascending or descending -order. +parallel. This is the case even in serial if the :doc:`atom_modify sort +` option is turned on, which it is by default, to improve +performance. A sort value of *id* means sort the output by atom ID. A +sort value of :math:`N` or :math:`-N` means sort the output by the value +in the :math:`N`\ th column of per-atom info in either ascending or +descending order. The dump *local* style cannot be sorted by atom ID, since there are typically multiple lines of output per atom. Some dump styles, such @@ -766,7 +766,7 @@ attributes that can be tested for are the same as those that can be specified in the :doc:`dump custom ` command, with the exception of the *element* attribute, since it is not a numeric value. Note that a different attributes can be used than those output by the -:doc:`dump custom ` command. E.g. you can output the +:doc:`dump custom ` command. For example, you can output the coordinates and stress of atoms whose energy is above some threshold. If an atom-style variable is used as the attribute, then it can diff --git a/doc/src/fix_pair.rst b/doc/src/fix_pair.rst index b1d3010be0..0718be5d3c 100644 --- a/doc/src/fix_pair.rst +++ b/doc/src/fix_pair.rst @@ -8,12 +8,12 @@ Syntax .. parsed-literal:: - fix ID group-ID pair N pairstyle name flag ... + fix ID group-ID pair N pstyle name flag ... * ID, group-ID are documented in :doc:`fix ` command * pair = style name of this fix command * N = invoke this fix once every N timesteps -* pairstyle = name of pair style to extract info from (e.g. eam) +* pstyle = name of pair style to extract info from (e.g. eam) * one or more name/flag pairs can be listed * name = name of quantity the pair style allows extraction of * flag = 1 if pair style needs to be triggered to produce data for name, 0 if not @@ -46,7 +46,7 @@ These are example use cases: The *N* argument determines how often the fix is invoked. -The *pairstyle* argument is the name of the pair style. It can be a +The *pstyle* argument is the name of the pair style. It can be a sub-style used in a :doc:`pair_style hybrid ` command. One or more *name/flag* pairs of arguments follow. Each *name* is a @@ -55,11 +55,11 @@ request. See the doc pages for individual :doc:`pair_styles ` to see what fix pair requests (if any) they support. The *flag* setting determines whether this fix will also trigger the -pair style to compute the named quantity so it can be extracted. If -the quantity is always computed by the pair style, no trigger is -needed; specify *flag* = 0. If the quantity is not always computed -(e.g. it is expensive to calculate), then specify *flag* = 1. This -will trigger the quantity to be calculated only on timesteps it is +pair style to compute the named quantity so it can be extracted. If the +quantity is always computed by the pair style, no trigger is needed; +specify *flag* = 0. If the quantity is not always computed +(e.g. because it is expensive to calculate), then specify *flag* = 1. +This will trigger the quantity to be calculated only on timesteps it is needed. Again, see the doc pages for individual :doc:`pair_styles ` to determine which fix pair requests (if any) need to be triggered with a *flag* = 1 setting. @@ -71,12 +71,16 @@ atom, then this fix stores it as a per-atom vector. Otherwise a per-atom array is created, with its data in the order of the *name* arguments. -For example, :doc:`pair_style amoeba ` allows extraction -of two named quantities: "uind" and "uinp", both of which are -3-vectors for each atom, i.e. dipole moments. If this fix specifies -"uind" and "uinp" (in that order), then a 6-column per-atom array will -be created. Columns 1-3 will store the "uind" values; columns 4-6 -will store the "uinp" values. +For example, :doc:`pair_style amoeba ` allows extraction of +two named quantities: "uind" and "uinp", both of which are 3-vectors for +each atom, i.e. dipole moments. In the example below a 6-column per-atom +array will be created. Columns 1-3 will store the "uind" values; +columns 4-6 will store the "uinp" values. + +.. code-block:: LAMMPS + + pair_style amoeba + fix ex all pair amoeba 10 uind 0 uinp 0 Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/pair_amoeba.rst b/doc/src/pair_amoeba.rst index 22ec2281dd..44a14f0f45 100644 --- a/doc/src/pair_amoeba.rst +++ b/doc/src/pair_amoeba.rst @@ -158,15 +158,15 @@ settings. .. versionadded:: TBD -The *amoeba* and *hippo* pair styles support extraction of two -per-atom quantities by the :doc:`fix pair ` command. This -allows the quantities to be output to files by the :doc:`dump ` -or otherwise processed by other LAMMPS commamds. +The *amoeba* and *hippo* pair styles support extraction of two per-atom +quantities by the :doc:`fix pair ` command. This allows the +quantities to be output to files by the :doc:`dump ` or otherwise +processed by other LAMMPS commands. -The names of the two quantites are "uind" and "uinp" for the induced -dipole moments for each atom. Neither quantity needs to be triggered -by the :doc:`fix pair ` command in order for these pair -styles to calculate it. +The names of the two quantities are "uind" and "uinp" for the induced +dipole moments for each atom. Neither quantity needs to be triggered by +the :doc:`fix pair ` command in order for these pair styles to +calculate it. ---------- diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index bb8433f101..af936a6bc9 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -447,15 +447,14 @@ identical to the FS EAM files (see above). .. versionadded:: TBD The *eam*, *eam/alloy*, *eam/fs*, and *eam/he* pair styles support -extraction of two per-atom quantities by the :doc:`fix pair -` command. This allows the quantities to be output to files -by the :doc:`dump ` or otherwise processed by other LAMMPS -commamds. +extraction of two per-atom quantities by the :doc:`fix pair ` +command. This allows the quantities to be output to files by the +:doc:`dump ` or otherwise processed by other LAMMPS commands. -The names of the two quantites are "rho" and "fp" for the density and +The names of the two quantities are "rho" and "fp" for the density and derivative of the embedding energy for each atom. Neither quantity -needs to be triggered by the :doc:`fix pair ` command in -order for these pair styles to calculate it. +needs to be triggered by the :doc:`fix pair ` command in order +for these pair styles to calculate it. ---------- diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index c6c6a2de6a..15316b4f09 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -3581,7 +3581,9 @@ UEF ufm Uhlenbeck Ui +uind uInfParallel +uinp uk ul ulb