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improve bond_write docs and fix minor issues

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Axel Kohlmeyer
2022-12-24 23:05:47 -05:00
parent 1c223f7ce6
commit 4ee8dea4b3
1 changed files with 24 additions and 21 deletions
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doc/src/bond_write.rst
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@ -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 <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 <bond_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 <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 <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 <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 <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 <bond_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
<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
""""""""""""