From 4ee8dea4b36b2b8d5b8102ba919c5c54651391d2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 24 Dec 2022 23:05:47 -0500 Subject: [PATCH] improve bond_write docs and fix minor issues --- doc/src/bond_write.rst | 45 ++++++++++++++++++++++-------------------- 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index 4170029239..47982303ee 100644 --- a/doc/src/bond_write.rst +++ b/doc/src/bond_write.rst @@ -10,7 +10,7 @@ Syntax bond_write btype N inner outer file keyword itype jtype -* btype = bond types +* btype = bond type * N = # of values * inner,outer = inner and outer bond length (distance units) * file = name of file to write values to @@ -29,31 +29,34 @@ Description """"""""""" Write energy and force values to a file as a function of distance for -the currently defined bond potential. This is useful for plotting the -potential function or otherwise debugging its values. If the file -already exists, the table of values is appended to the end of the file -to allow multiple tables of energy and force to be included in one -file. +the currently defined :doc:`bond style ` for a selected bond +type. This is useful for plotting the potential function or otherwise +debugging its values. The resulting file can also be used as input for +use with :doc:`bond style table `. -The energy and force values are computed at distances from inner to -outer for 2 interacting atoms forming a bond of type btype, using the -appropriate :doc:`bond_coeff ` coefficients. N evenly spaced -distances are used. +If the file already exists, the table of values is appended to the end +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 +the appropriate :doc:`bond_coeff ` coefficients. N evenly +spaced distances are used. For example, for N = 7, inner = 1.0, and outer = 4.0, values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. -The file is written in the format used as input for the -:doc:`bond_style ` *table* option with *keyword* as the -section name. Each line written to the file lists an index number -(1-N), a distance (in distance units), an energy (in energy units), -and a force (in force units). In case a new file is created, the first -line will be a comment with a "DATE:" and "UNITS:" tag with the current -date and :doc:`units ` settings. For subsequent invocations of -the bond_write command for the same file, data will be appended and the -current units settings will be compared to the data from the header, if -present, and bond_write will refuse to add a table if the units are not -the same. +The file is written in the format used as input for the :doc:`bond_style +table ` option with *keyword* as the section name. Each +line written to the file lists an index number (1-N), a distance (in +distance units), an energy (in energy units), and a force (in force +units). In case a new file is created, the first line will be a comment +with a "DATE:" and "UNITS:" tag with the current date and :doc:`units +` settings. For subsequent invocations of the *bond_write* +command for the same file, data will be appended and the current units +settings will be compared to the data from the header, if present. The +*bond_write* command will refuse to add a table to an existing file if +the units are not the same. Restrictions """"""""""""