From ca37c014769b446dfa6ddc9b105c4bc7a594abfe Mon Sep 17 00:00:00 2001 From: Joel Thomas Clemmer <=> Date: Tue, 12 Apr 2022 13:36:39 -0600 Subject: [PATCH] Fixing broken links/references in documentation --- doc/src/Commands_pair.rst | 1 + doc/src/bond_bpm_rotational.rst | 8 ++++---- doc/src/bond_bpm_spring.rst | 4 ++-- doc/src/bond_style.rst | 2 ++ ...{compute_nbonds_atom.rst => compute_nbond_atom.rst} | 10 +++++----- doc/src/pair_style.rst | 1 + 6 files changed, 15 insertions(+), 11 deletions(-) rename doc/src/{compute_nbonds_atom.rst => compute_nbond_atom.rst} (85%) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 7a1ed4ee72..d9ee22ce86 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -53,6 +53,7 @@ OPT. * :doc:`born/coul/msm (o) ` * :doc:`born/coul/wolf (go) ` * :doc:`born/coul/wolf/cs (g) ` + * :doc:`bpm/spring ` * :doc:`brownian (o) ` * :doc:`brownian/poly (o) ` * :doc:`buck (giko) ` diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst index 40b1752285..2a752217e3 100644 --- a/doc/src/bond_bpm_rotational.rst +++ b/doc/src/bond_bpm_rotational.rst @@ -98,7 +98,7 @@ added or removed using the *smooth* keyword. Finally, additional damping forces and torques are applied to the two particles. A force is applied proportional to the difference in the normal velocity of particles using a similar construction as -dissipative particle dynamics (:ref:`(Groot) `): +dissipative particle dynamics (:ref:`(Groot) `): .. math:: @@ -109,7 +109,7 @@ radial normal vector, and :math:`\vec{v}` is the velocity difference between the two particles. Similarly, tangential forces are applied to each atom proportional to the relative differences in sliding velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et -al.) `) along with their associated torques. The rolling and +al.) `) along with their associated torques. The rolling and twisting components of the relative angular velocities of the two atoms are also damped by applying torques with prefactors of :math:`\gamma_r` and :math:`\gamma_t`, respectively. @@ -247,11 +247,11 @@ p 117-127 (2009). **(Wang and Mora)** Wang, Mora, Advances in Geocomputing, 119, p 183-228 (2009). -.. _Groot1: +.. _Groot3: **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). -.. _Wang2015: +.. _Wang20152: **(Wang et al, 2015)** Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015). Rolling and sliding in 3-D discrete element diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 2881bab5f7..4084aa760a 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -69,7 +69,7 @@ setting its type to 0 such that forces are no longer computed. An additional damping force is applied to the bonded particles. This forces is proportional to the difference in the normal velocity of particles using a similar construction as -dissipative particle dynamics (:ref:`(Groot) `): +dissipative particle dynamics (:ref:`(Groot) `): .. math:: @@ -197,6 +197,6 @@ The option defaults are *smooth* = *yes* ---------- -.. _Groot1: +.. _Groot4: **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index 4dee48a78d..95ba1572c1 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -84,6 +84,8 @@ accelerated styles exist. * :doc:`zero ` - topology but no interactions * :doc:`hybrid ` - define multiple styles of bond interactions +* :doc:`bpm/rotational ` - breakable bond with forces and torques based on deviation from reference state +* :doc:`bpm/spring ` - breakable bond with forces based on deviation from reference length * :doc:`class2 ` - COMPASS (class 2) bond * :doc:`fene ` - FENE (finite-extensible non-linear elastic) bond * :doc:`fene/expand ` - FENE bonds with variable size particles diff --git a/doc/src/compute_nbonds_atom.rst b/doc/src/compute_nbond_atom.rst similarity index 85% rename from doc/src/compute_nbonds_atom.rst rename to doc/src/compute_nbond_atom.rst index 3a8ea0577f..8322f16330 100644 --- a/doc/src/compute_nbonds_atom.rst +++ b/doc/src/compute_nbond_atom.rst @@ -1,6 +1,6 @@ -.. index:: compute nbonds/atom +.. index:: compute nbond/atom -compute nbonds/atom command +compute nbond/atom command ======================= Syntax @@ -8,17 +8,17 @@ Syntax .. parsed-literal:: - compute ID group-ID nbonds/atom + compute ID group-ID nbond/atom * ID, group-ID are documented in :doc:`compute ` command -* nbonds/atom = style name of this compute command +* nbond/atom = style name of this compute command Examples """""""" .. code-block:: LAMMPS - compute 1 all nbonds/atom + compute 1 all nbond/atom Description """"""""""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index f90a718d95..b42e3c9a50 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -131,6 +131,7 @@ accelerated styles exist. * :doc:`born/coul/msm ` - Born with long-range MSM Coulomb * :doc:`born/coul/wolf ` - Born with Wolf potential for Coulomb * :doc:`born/coul/wolf/cs ` - Born with Wolf potential for Coulomb and core/shell model +* :doc:`bpm/spring ` - repulsive harmonic force with damping * :doc:`brownian ` - Brownian potential for Fast Lubrication Dynamics * :doc:`brownian/poly ` - Brownian potential for Fast Lubrication Dynamics with polydispersity * :doc:`buck ` - Buckingham potential