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more formatting/typesetting consistency

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This commit is contained in:
Axel Kohlmeyer
2022-09-03 04:17:22 -04:00
parent b4eb3e8156
commit b60f144705
5 changed files with 75 additions and 76 deletions
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33
doc/src/angle_coeff.rst
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@ -33,19 +33,19 @@ The number and meaning of the coefficients depends on the angle style.
Angle coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or N can be a type label,
which is an alphanumeric string defined by the :doc:`labelmap
<labelmap>` command or in a section of a data file read by the
:doc:`read_data <read_data>` command.
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple angle types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the number of angle types, then an
asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
"\*n" or "n\*" or "m\*n". If :math:`N` is the number of angle types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an :doc:`angle_coeff <angle_coeff>` command can
override a previous setting for the same angle type. For example,
@ -60,9 +60,9 @@ coeffs for just angle type 2:
A line in a data file that specifies angle coefficients uses the exact
same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
command in an input script, except that wild-card asterisks should not
be used since coefficients for all N types must be listed in the file.
For example, under the "Angle Coeffs" section of a data file, the line
that corresponds to the first example above would be listed as
be used since coefficients for all :math:`N` types must be listed in the
file. For example, under the "Angle Coeffs" section of a data file, the
line that corresponds to the first example above would be listed as
.. parsed-literal::
@ -70,15 +70,14 @@ that corresponds to the first example above would be listed as
The :doc:`angle_style class2 <angle_class2>` is an exception to this
rule, in that an additional argument is used in the input script to
allow specification of the cross-term coefficients. See its
doc page for details.
allow specification of the cross-term coefficients. See its doc page
for details.
----------
The list of all angle styles defined in LAMMPS is given on the
:doc:`angle_style <angle_style>` doc page. They are also listed in more
compact form on the :ref:`Commands angle <angle>` doc
page.
compact form on the :ref:`Commands angle <angle>` doc page.
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated

24
doc/src/bond_coeff.rst
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@ -34,19 +34,19 @@ The number and meaning of the coefficients depends on the bond style.
Bond coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of several ways. An explicit numeric value
can be used, as in the first example above. Or N can be a type label,
which is an alphanumeric string defined by the :doc:`labelmap
<labelmap>` command or in a section of a data file read by the
:doc:`read_data <read_data>` command.
:math:`N` can be specified in one of several ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple bond types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the number of bond types, then an
asterisk with no numeric values means all types from 1 to N. A
coefficients for multiple bond types. This takes the form "\*" or "\*n"
or "n\*" or "m\*n". If :math:`N` is the number of bond types, then an
asterisk with no numeric values means all types from 1 to :math:`N`. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
asterisk means all types from n to :math:`N` (inclusive). A middle
asterisk means all types from m to n (inclusive).
Note that using a bond_coeff command can override a previous setting
for the same bond type. For example, these commands set the coeffs
@ -60,8 +60,8 @@ for all bond types, then overwrite the coeffs for just bond type 2:
A line in a data file that specifies bond coefficients uses the exact
same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Bond Coeffs" section of a data file, the line that
coefficients for all :math:`N` types must be listed in the file. For
example, under the "Bond Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
.. parsed-literal::

29
doc/src/dihedral_coeff.rst
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@ -28,28 +28,29 @@ Examples
Description
"""""""""""
Specify the dihedral force field coefficients for one or more dihedral types.
The number and meaning of the coefficients depends on the dihedral style.
Dihedral coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
Specify the dihedral force field coefficients for one or more dihedral
types. The number and meaning of the coefficients depends on the
dihedral style. Dihedral coefficients can also be set in the data file
read by the :doc:`read_data <read_data>` command or in a restart file.
:math:`N` can be specified in one of two ways. An explicit numeric value
can be used, as in the first example above. Or :math:`N` can be an
alphanumeric type label, which is a string defined by the :doc:`labelmap
<labelmap>` command or in a corresponding section of a data file read by
the :doc:`read_data <read_data>` command.
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be
an alphanumeric type label, which is a string defined by the
:doc:`labelmap <labelmap>` command or in a corresponding section of a
data file read by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple dihedral types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` is the number of dihedral types,
then an asterisk with no numeric values means all types from 1 to :math:`N`.
A leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to :math:`N` (inclusive). A middle asterisk
means all types from m to n (inclusive).
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using a dihedral_coeff command can override a previous setting
for the same dihedral type. For example, these commands set the coeffs
for all dihedral types, then overwrite the coeffs for just dihedral type 2:
for all dihedral types, then overwrite the coeffs for just dihedral type
2:
.. code-block:: LAMMPS

35
doc/src/improper_coeff.rst
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@ -30,27 +30,26 @@ Description
Specify the improper force field coefficients for one or more improper
types. The number and meaning of the coefficients depends on the
improper style. Improper coefficients can also be set in the data
file read by the :doc:`read_data <read_data>` command or in a restart
file.
improper style. Improper coefficients can also be set in the data file
read by the :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or N can be a type label,
which is an alphanumeric string defined by the :doc:`labelmap
<labelmap>` command or in a section of a data file read by the
:doc:`read_data <read_data>` command.
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple improper types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the number of improper types, then
an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
"\*n" or "n\*" or "m\*n". If :math:`N` = the number of improper types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an improper_coeff command can override a previous
setting for the same improper type. For example, these commands set
the coeffs for all improper types, then overwrite the coeffs for just
setting for the same improper type. For example, these commands set the
coeffs for all improper types, then overwrite the coeffs for just
improper type 2:
.. code-block:: LAMMPS
@ -61,9 +60,9 @@ improper type 2:
A line in a data file that specifies improper coefficients uses the
exact same format as the arguments of the improper_coeff command in an
input script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Improper Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
coefficients for all :math:`N` types must be listed in the file. For
example, under the "Improper Coeffs" section of a data file, the line
that corresponds to the first example above would be listed as
.. parsed-literal::

30
doc/src/pair_coeff.rst
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@ -47,18 +47,18 @@ or in a section of a data file read by the :doc:`read_data
Internally, LAMMPS will set coefficients for the symmetric J,I
interaction to the same values as the I,J interaction.
For numeric values only, a wildcard asterisk can be used in place of
or in conjunction with the I,J arguments to set the coefficients for
For numeric values only, a wildcard asterisk can be used in place of or
in conjunction with the I,J arguments to set the coefficients for
multiple pairs of atom types. This takes the form "\*" or "\*n" or
"n\*" or "m\*n". If N = the number of atom types, then an asterisk
with no numeric values means all types from 1 to N. A leading
asterisk means all types from 1 to n (inclusive). A trailing asterisk
means all types from n to N (inclusive). A middle asterisk means all
types from m to n (inclusive). For the asterisk syntax, only type
pairs with I <= J are considered; if asterisks imply type pairs where
J < I, they are ignored. Again internally, LAMMPS will set the
coefficients for the symmetric J,I interactions to the same values as
the I <= J interactions.
"n\*" or "m\*n". If :math:`N` is the number of atom types, then an
asterisk with no numeric values means all types from 1 to :math:`N`. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to :math:`N` (inclusive). A middle
asterisk means all types from m to n (inclusive). For the asterisk
syntax, only type pairs with I <= J are considered; if asterisks imply
type pairs where J < I, they are ignored. Again internally, LAMMPS will
set the coefficients for the symmetric J,I interactions to the same
values as the I <= J interactions.
Note that a pair_coeff command can override a previous setting for the
same I,J pair. For example, these commands set the coeffs for all I,J
@ -74,10 +74,10 @@ same format as the arguments of the pair_coeff command in an input
script, with the exception of the I,J type arguments. In each line of
the "Pair Coeffs" section of a data file, only a single type I is
specified, which sets the coefficients for type I interacting with
type I. This is because the section has exactly N lines, where N =
the number of atom types. For this reason, the wild-card asterisk
should also not be used as part of the I argument. Thus in a data
file, the line corresponding to the first example above would be
type I. This is because the section has exactly :math:`N` lines, where
:math:`N` is the number of atom types. For this reason, the wild-card
asterisk should also not be used as part of the I argument. Thus in a
data file, the line corresponding to the first example above would be
listed as
.. parsed-literal::