diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 1009eb5089..fb99077137 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -181,7 +181,7 @@ include Coulomb interactions, for instance *lj/cut/coul/long* with As compared to the non-polarizable input file, *pair\_coeff* lines need to be added for the DPs. Since the DPs have no Lennard-Jones -interactions, their *epsilon* is 0. so the only *pair\_coeff* line +interactions, their :math:`\epsilon` is 0. so the only *pair\_coeff* line that needs to be added is diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 9f9b1ee532..c15fd635b7 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -35,13 +35,14 @@ The *sdk* angle style is a combination of the harmonic angle potential, E = K (\theta - \theta_0)^2 -where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor, -with the *repulsive* part of the non-bonded *lj/sdk* pair style -between the atoms 1 and 3. This angle potential is intended for -coarse grained MD simulations with the CMM parameterization using the -:doc:`pair_style lj/sdk `. Relative to the pair\_style -*lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden -jumps. Note that the usual 1/2 factor is included in :math:`K`. +where :math:`\theta_0` is the equilibrium value of the angle and +:math:`K` a prefactor, with the *repulsive* part of the non-bonded +*lj/sdk* pair style between the atoms 1 and 3. This angle potential is +intended for coarse grained MD simulations with the CMM parameterization +using the :doc:`pair_style lj/sdk `. Relative to the +pair\_style *lj/sdk*\ , however, the energy is shifted by +:math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor +is included in :math:`K`. The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above: diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index 3840158fbc..8320d1701c 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -28,13 +28,13 @@ Description """"""""""" Style *line/lj* treats particles which are line segments as a set of -small spherical particles that tile the line segment length as -explained below. Interactions between two line segments, each with N1 -and N2 spherical particles, are calculated as the pairwise sum of -N1\*N2 Lennard-Jones interactions. Interactions between a line segment -with N spherical particles and a point particle are treated as the -pairwise sum of N Lennard-Jones interactions. See the :doc:`pair_style lj/cut ` doc page for the definition of Lennard-Jones -interactions. +small spherical particles that tile the line segment length as explained +below. Interactions between two line segments, each with N1 and N2 +spherical particles, are calculated as the pairwise sum of N1\*N2 +Lennard-Jones interactions. Interactions between a line segment with N +spherical particles and a point particle are treated as the pairwise sum +of N Lennard-Jones interactions. See the :doc:`pair_style lj/cut +` doc page for the definition of Lennard-Jones interactions. The set of non-overlapping spherical sub-particles that represent a line segment are generated in the following manner. Their size is a @@ -50,10 +50,10 @@ each pair of points. The LJ interaction between 2 spheres on different line segments (or a sphere on a line segment and a point particles) is computed with -sub-particle epsilon, sigma, and cutoff values that are set by the -pair\_coeff command, as described below. If the distance between the 2 -spheres is greater than the sub-particle cutoff, there is no -interaction. This means that some pairs of sub-particles on 2 line +sub-particle :math:`\epsilon`, :math:`\sigma`, and *cutoff* values that +are set by the pair\_coeff command, as described below. If the distance +between the 2 spheres is greater than the sub-particle cutoff, there is +no interaction. This means that some pairs of sub-particles on 2 line segments may interact, but others may not. For purposes of creating the neighbor list for pairs of interacting @@ -86,8 +86,8 @@ commands: * sizeI (distance units) * sizeJ (distance units) -* epsilon (energy units) -* sigma (distance units) +* :math:`\epsilon` (energy units) +* :math:`\sigma` (distance units) * subcutoff (distance units) * cutoff (distance units) @@ -102,11 +102,11 @@ sizeI will apply to all segments of type I. If typeI or typeJ refers to point particles, the corresponding sizeI or sizeJ is ignored; it can be set to 0.0. -The *epsilon*\ , *sigma*\ , and *subcutoff* coefficients are used to -compute an LJ interactions between a pair of sub-particles on 2 line -segments (of type I and J), or between a sub particle/point particle -pair. As discussed above, the *subcutoff* and *cutoff* params are -different. The latter is only used for building the neighbor list +The :math:`\epsilon`, :math:`\sigma`, and *subcutoff* coefficients are +used to compute an LJ interactions between a pair of sub-particles on 2 +line segments (of type I and J), or between a sub particle/point +particle pair. As discussed above, the *subcutoff* and *cutoff* params +are different. The latter is only used for building the neighbor list when the distance between centers of two line segments or one segment and a point particle is calculated.