From 7b32b1e595e2bfbb5350f28e615958cf384d56c5 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 14 Feb 2020 09:52:06 +0100 Subject: [PATCH] Update pair_body_rounded_polyhedron docs --- doc/src/pair_body_rounded_polygon.rst | 2 +- doc/src/pair_body_rounded_polyhedron.rst | 55 +++++++++++++++--------- 2 files changed, 35 insertions(+), 22 deletions(-) diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index 3cfa73813d..652c618d4a 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -115,7 +115,7 @@ or in the data file read by the :doc:`read_data ` command: * :math:`k_n` (energy/distance\^2 units) * :math:`k_{na}` (energy/distance\^2 units) -Effectively, :math:`k_n` and :math:`k_na` are the slopes of the red lines in the plot +Effectively, :math:`k_n` and :math:`k_{na}` are the slopes of the red lines in the plot above for force versus surface separation, for :math:`\delta_n < 0` and :math:`0 < \delta_n < r_c` respectively. diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index 23623a640e..20dbbafb13 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -1,16 +1,18 @@ -.. index:: pair\_style body/rounded/polyhedron +.. index:: pair_style body/rounded/polyhedron -pair\_style body/rounded/polyhedron command -=========================================== +pair_style body/rounded/polyhedron command +========================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff +.. parsed-literal:: + c_n = normal damping coefficient c_t = tangential damping coefficient mu = normal friction coefficient during gross sliding @@ -21,10 +23,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5 - pair_coeff \* \* 100.0 1.0 + pair_coeff * * 100.0 1.0 pair_coeff 1 1 100.0 1.0 Description @@ -33,7 +35,8 @@ Description Style *body/rounded/polygon* is for use with 3d models of body particles of style *rounded/polyhedron*\ . It calculates pairwise body/body interactions which can include body particles modeled as -1-vertex spheres with a specified diameter. See the :doc:`Howto body ` doc page for more details on using body +1-vertex spheres with a specified diameter. See the +:doc:`Howto body ` doc page for more details on using body rounded/polyhedron particles. This pairwise interaction between the rounded polyhedra is described @@ -54,26 +57,35 @@ separation of their respective rounded surfaces, not by the separation of the vertices, edges, and faces themselves. This means that the specified cutoff in the pair\_style command is the -cutoff distance, r\_c, for the surface separation, \delta\_n (see figure +cutoff distance, :math:`r_c`, for the surface separation, :math:`\delta_n` (see figure below). This is the distance at which two particles no longer -interact. If r\_c is specified as 0.0, then it is a contact-only +interact. If :math:`r_c` is specified as 0.0, then it is a contact-only interaction. I.e. the two particles must overlap in order to exert a -repulsive force on each other. If r\_c > 0.0, then the force between +repulsive force on each other. If :math:`r_c > 0.0`, then the force between two particles will be attractive for surface separations from 0 to -r\_c, and repulsive once the particles overlap. +:math:`r_c`, and repulsive once the particles overlap. Note that unlike for other pair styles, the specified cutoff is not the distance between the centers of two particles at which they stop interacting. This center-to-center distance depends on the shape and size of the two particles and their relative orientation. LAMMPS takes that into account when computing the surface separation distance -and applying the r\_c cutoff. +and applying the :math:`r_c` cutoff. The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge, and edge-face overlaps are given by: -.. image:: Eqs/pair_body_rounded.jpg - :align: center +.. math:: + + F_n &= \begin{cases} + k_n \delta_n - c_n v_n, & \delta_n \le 0 \\ + -k_{na} \delta_n - c_n v_n & 0 < \delta_n \le r_c \\ + 0 & \delta_n > r_c \\ + \end{cases} \\ + F_t &= \begin{cases} + \mu k_n \delta_n - c_t v_t & \delta_n \le 0 \\ + 0 & \delta_n > 0 + \end{cases} .. image:: JPG/pair_body_rounded.jpg :align: center @@ -93,20 +105,21 @@ The following coefficients must be defined for each pair of atom types via the :doc:`pair_coeff ` command as in the examples above, or in the data file read by the :doc:`read_data ` command: -* k\_n (energy/distance\^2 units) -* k\_na (energy/distance\^2 units) +* :math:`k_n` (energy/distance\^2 units) +* :math:`k_{na}` (energy/distance\^2 units) -Effectively, k\_n and k\_na are the slopes of the red lines in the plot -above for force versus surface separation, for \delta\_n < 0 and 0 < -\delta\_n < r\_c respectively. +Effectively, :math:`k_n` and :math:`k_{na}` are the slopes of the red lines in the plot +above for force versus surface separation, for :math:`\delta_n` < 0 and +:math:`0 < \delta_n < r_c` respectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This pair style does not write its information to :doc:`binary restart files `. +Thus, you need to re-specify the pair\_style and pair\_coeff +commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the