diff --git a/doc/src/Developer_grid.rst b/doc/src/Developer_grid.rst index 22eadd5da8..1661524f90 100644 --- a/doc/src/Developer_grid.rst +++ b/doc/src/Developer_grid.rst @@ -433,7 +433,7 @@ from owned to ghost cells, or ghost to owned cells, respectively, as described above. The *caller* argument should be one of these values -- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR -- depending on the style of the caller class. The *ptr* argument is the -"this" pointer to the caller class. These 2 arguments are used to +"this" pointer to the caller class. These two arguments are used to call back to pack()/unpack() functions in the caller class, as explained below. diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 2e6a6e1cbe..7a48234d5f 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -419,7 +419,7 @@ showing the use of the *template* atom style versus *molecular*. ` that contains multiple molecules, you should ensure the atom types, bond types, angle_types, etc in all the molecules are consistent. E.g. if one molecule represents H2O and another CO2, - then you probably do not want each molecule file to define 2 atom + then you probably do not want each molecule file to define two atom types and a single bond type, because they will conflict with each other when a mixture system of H2O and CO2 molecules is defined, e.g. by the :doc:`read_data ` command. Rather the H2O diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index da56fe7fbb..590f7c8cba 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -59,10 +59,10 @@ coefficients need to be re-specified. When both a bond and pair style is defined, the :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise - exist between 2 bonded atoms. + exist between two bonded atoms. In the formulas listed for each bond style, *r* is the distance -between the 2 atoms in the bond. +between the two atoms in the bond. ---------- diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index bd63ebea29..750f7b5339 100644 --- a/doc/src/bond_write.rst +++ b/doc/src/bond_write.rst @@ -15,7 +15,7 @@ Syntax * inner,outer = inner and outer bond length (distance units) * file = name of file to write values to * keyword = section name in file for this set of tabulated values -* itype,jtype = 2 atom types (optional) +* itype,jtype = two atom types (optional) Examples """""""" @@ -39,7 +39,7 @@ of the file to allow multiple tables of energy and force to be included in one file. The individual sections may be identified by the *keyword*. The energy and force values are computed at distances from *inner* to -*outer* for 2 interacting atoms forming a bond of type *btype*, using +*outer* for two interacting atoms forming a bond of type *btype*, using the appropriate :doc:`bond_coeff ` coefficients. N evenly spaced distances are used. diff --git a/doc/src/clear.rst b/doc/src/clear.rst index fba3b69f47..a362a62109 100644 --- a/doc/src/clear.rst +++ b/doc/src/clear.rst @@ -36,7 +36,8 @@ script variables except for *atomfile* style variables (:doc:`variable Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/comm_style.rst b/doc/src/comm_style.rst index 73e341b191..ee296ea93f 100644 --- a/doc/src/comm_style.rst +++ b/doc/src/comm_style.rst @@ -55,7 +55,7 @@ commands. The decomposition can be changed via the Restrictions """""""""""" -None +none Related commands """""""""""""""" diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 0690ec57c3..082f93a6c4 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -362,7 +362,8 @@ The individual style names on the :doc:`Commands compute ` pag Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index c863d0c7d2..296a12dc5c 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -73,7 +73,7 @@ keyword discussion below. For style *overlap* pairs of atoms whose distance of separation is within the specified cutoff distance are searched for, and one of the -2 atoms is deleted. Only pairs where one of the two atoms is in the +two atoms is deleted. Only pairs where one of the two atoms is in the first group specified and the other atom is in the second group are considered. The atom that is in the first group is the one that is deleted. diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index d7350c4e9b..2336a5889a 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -389,7 +389,7 @@ cylinders with that diameter, e.g. 1.0, which is in whatever distance If *atom* is specified for the *width* value, then each bond will be drawn with a width corresponding to the minimum diameter -of the 2 atoms in the bond. +of the two atoms in the bond. If *type* is specified for the *width* value then the diameter of each bond is determined by its bond type. By default all types have diff --git a/doc/src/if.rst b/doc/src/if.rst index 8aaee39f61..1f3696df66 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -206,7 +206,8 @@ FALSE. Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index 3fd7eeb1e8..8b24378b78 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -76,7 +76,6 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`none ` - turn off improper interactions * :doc:`zero ` - topology but no interactions * :doc:`hybrid ` - define multiple styles of improper interactions - * :doc:`amoeba ` - AMOEBA out-of-plane improper * :doc:`class2 ` - COMPASS (class 2) improper * :doc:`cossq ` - improper with a cosine squared term @@ -88,8 +87,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`inversion/harmonic ` - harmonic improper with Wilson-Decius out-of-plane definition * :doc:`ring ` - improper which prevents planar conformations * :doc:`umbrella ` - DREIDING improper - -:doc:`sqdistharm ` - improper that is harmonic in the square of the out-of-plane distance +* :doc:`sqdistharm ` - improper that is harmonic in the square of the out-of-plane distance ---------- diff --git a/doc/src/include.rst b/doc/src/include.rst index 5e19f4a377..d141d90642 100644 --- a/doc/src/include.rst +++ b/doc/src/include.rst @@ -35,7 +35,8 @@ scripts. Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/info.rst b/doc/src/info.rst index ef0bedc6e4..757ea94a6c 100644 --- a/doc/src/info.rst +++ b/doc/src/info.rst @@ -130,7 +130,8 @@ process that writes output (usually MPI rank 0). Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 07490ecf64..ab9b4486a2 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -428,7 +428,7 @@ Syntax * variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command -* formatarg = *list, split, or index* (optional): +* formatarg = *list* or *split* or *index* (optional) .. parsed-literal:: @@ -697,17 +697,18 @@ Syntax * variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command -* formatarg = *list, split, or explicit* (optional): +* formatarg = *list* or *split* or *explicit* (optional) + .. parsed-literal:: *list* = returns a single string with a list of space separated values (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as - defined by the *variable* argument. + defined by the *variable* argument *split* = returns the values separately in new variables with names based on the prefix specified in *variable* and a number appended to indicate which element in the list of values is in the variable *explicit* = returns the values separately in one more more variable names - provided as arguments that precede *formatarg*\ . [default] + provided as arguments that precede *formatarg* (default) * values = new value(s) to replace the current value(s) of a KIM portable model parameter diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index 351e387c0f..c40ba70ef0 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -459,7 +459,7 @@ The option defaults are as follows: * diff = ik (PPPM) * disp/auto = no * fftbench = no (PPPM) -* force = -1.0, +* force = -1.0 * force/disp/kspace = -1.0 * force/disp/real = -1.0 * gewald = gewald/disp = 0.0 diff --git a/doc/src/log.rst b/doc/src/log.rst index 46784f6ea6..b45e451b88 100644 --- a/doc/src/log.rst +++ b/doc/src/log.rst @@ -39,7 +39,8 @@ name of the initial log file can also be set by the :doc:`-log command-line swit Restrictions """""""""""" - none + +none Related commands """"""""""""""""