From 2fed3fa0031d31d33139d8a7f0336ba6480e01a3 Mon Sep 17 00:00:00 2001 From: Karl Hammond Date: Thu, 6 Oct 2022 22:12:33 -0500 Subject: [PATCH] Minor documentation edits --- doc/src/thermo_modify.rst | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index b3f8cade1d..1bee26c289 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -66,10 +66,10 @@ atom can be "lost" if it moves across a non-periodic simulation box :doc:`boundary ` or if it moves more than a box length outside the simulation domain (or more than a processor sub-domain length) before reneighboring occurs. The latter case is typically due to bad -dynamics, e.g. too large a timestep or huge forces and velocities. If +dynamics (e.g., too large a time step and/or huge forces and velocities). If the value is *ignore*, LAMMPS does not check for lost atoms. If the value is *error* or *warn*, LAMMPS checks and either issues an error or -warning. The code will exit with an error and continue with a warning. +warning. The simulation will exit with an error and continue with a warning. A warning will only be issued once, the first time an atom is lost. This can be a useful debugging option. @@ -90,10 +90,10 @@ that should be investigated, but LAMMPS cannot determine for certain whether they are an indication of an error. Some warning messages are printed during a run (or immediately before) -each time a specific MPI rank encounters the issue, e.g. bonds that are -stretched too far or dihedrals in extreme configurations. These number +each time a specific MPI rank encounters the issue (e.g., bonds that are +stretched too far or dihedrals in extreme configurations). These number of these can quickly blow up the size of the log file and screen output. -Thus a limit of 100 warning messages is applied by default. The warning +Thus, a limit of 100 warning messages is applied by default. The warning count is applied to the entire input unless reset with a ``thermo_modify warn reset`` command. If there are more warnings than the limit, LAMMPS will print one final warning that it will not print any additional @@ -161,8 +161,8 @@ for a column or field of thermodynamic output. The setting for *ID string* replaces the default text with the provided string. *ID* can be a positive integer when it represents the column number counting from the left, a negative integer when it represents the column number from -the right (i.e. -1 is the last column/keyword), or a thermo keyword (or -compute, fix, property, or variable reference) and then it replaces the +the right (i.e., :math:`-1` is the last column/keyword), or a thermo keyword +(or compute, fix, property, or variable reference) and then it replaces the string for that specific thermo keyword. The *colname* keyword can be used multiple times. If multiple *colname* @@ -172,10 +172,10 @@ to their default values. The *format* keyword can be used to change the default numeric format of any of quantities the :doc:`thermo_style ` command -outputs. All the specified format strings are C-style formats, e.g. as -used by the C/C++ printf() command. The *line* keyword takes a single +outputs. All the specified format strings are C-style formats (i.e., as +used by the C/C++ printf() command). The *line* keyword takes a single argument which is the format string for the entire line of thermo -output, with N fields, which you must enclose in quotes if it is more +output, with :math:`N` fields, which you must enclose in quotes if it is more than one field. The *int* and *float* keywords take a single format argument and are applied to all integer or floating-point quantities output. The setting for *ID string* also takes a single format argument @@ -205,8 +205,8 @@ settings, reverting all values to their default format. to the corresponding 8-byte form when it is applied to those keywords. However, when specifying the *line* option or *format ID string* option for *step* and *natoms*, you should specify a format - string appropriate for an 8-byte signed integer, e.g. one with "%ld" - or "%lld" depending on the platform. + string appropriate for an 8-byte signed integer (i.e., one with "%ld" + or "%lld", depending on the platform). The *temp* keyword is used to determine how thermodynamic temperature is calculated, which is used by all thermo quantities that require a