diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index e2aea82abb..a9d7d0395b 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -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 ` 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 -` command or in a section of a data file read by the -:doc:`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 ` command or in a section of a data file read +by the :doc:`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 ` 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 ` 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 ` 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 ` doc page. They are also listed in more -compact form on the :ref:`Commands angle ` doc -page. +compact form on the :ref:`Commands 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 diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 0cd38f181a..f5b7f01e38 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -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 ` 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 -` command or in a section of a data file read by the -:doc:`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 ` command or in a section of a data file read +by the :doc:`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:: diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index 20d8ebb4b6..8af6b64a5f 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -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 ` 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 ` 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 -` command or in a corresponding section of a data file read by -the :doc:`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 ` command or in a corresponding section of a +data file read by the :doc:`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 diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index 9320054abc..e894eda005 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -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 ` command or in a restart -file. +improper style. Improper coefficients can also be set in the data file +read by the :doc:`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 -` command or in a section of a data file read by the -:doc:`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 ` command or in a section of a data file read +by the :doc:`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:: diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 5cbd210bac..83519a2051 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -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::