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Fixing broken links/references in documentation

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This commit is contained in:
Joel Thomas Clemmer
2022-04-12 13:36:39 -06:00
parent 929e46b5c7
commit ca37c01476
6 changed files with 15 additions and 11 deletions
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1
doc/src/Commands_pair.rst
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@ -53,6 +53,7 @@ OPT.
* :doc:`born/coul/msm (o) <pair_born>` * :doc:`born/coul/msm (o) <pair_born>`
* :doc:`born/coul/wolf (go) <pair_born>` * :doc:`born/coul/wolf (go) <pair_born>`
* :doc:`born/coul/wolf/cs (g) <pair_cs>` * :doc:`born/coul/wolf/cs (g) <pair_cs>`
* :doc:`bpm/spring <pair_bpm_spring>`
* :doc:`brownian (o) <pair_brownian>` * :doc:`brownian (o) <pair_brownian>`
* :doc:`brownian/poly (o) <pair_brownian>` * :doc:`brownian/poly (o) <pair_brownian>`
* :doc:`buck (giko) <pair_buck>` * :doc:`buck (giko) <pair_buck>`

8
doc/src/bond_bpm_rotational.rst
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@ -98,7 +98,7 @@ added or removed using the *smooth* keyword.
Finally, additional damping forces and torques are applied to the two Finally, additional damping forces and torques are applied to the two
particles. A force is applied proportional to the difference in the particles. A force is applied proportional to the difference in the
normal velocity of particles using a similar construction as normal velocity of particles using a similar construction as
dissipative particle dynamics (:ref:`(Groot) <Groot1>`): dissipative particle dynamics (:ref:`(Groot) <Groot3>`):
.. math:: .. 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 between the two particles. Similarly, tangential forces are applied to
each atom proportional to the relative differences in sliding each atom proportional to the relative differences in sliding
velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et
al.) <Wang2015>`) along with their associated torques. The rolling and al.) <Wang20152>`) along with their associated torques. The rolling and
twisting components of the relative angular velocities of the two twisting components of the relative angular velocities of the two
atoms are also damped by applying torques with prefactors of atoms are also damped by applying torques with prefactors of
:math:`\gamma_r` and :math:`\gamma_t`, respectively. :math:`\gamma_r` and :math:`\gamma_t`, respectively.
@ -247,11 +247,11 @@ p 117-127 (2009).
**(Wang and Mora)** Wang, Mora, Advances in Geocomputing, **(Wang and Mora)** Wang, Mora, Advances in Geocomputing,
119, p 183-228 (2009). 119, p 183-228 (2009).
.. _Groot1: .. _Groot3:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
.. _Wang2015: .. _Wang20152:
**(Wang et al, 2015)** Wang, Y., Alonso-Marroquin, F., & Guo, **(Wang et al, 2015)** Wang, Y., Alonso-Marroquin, F., & Guo,
W. W. (2015). Rolling and sliding in 3-D discrete element W. W. (2015). Rolling and sliding in 3-D discrete element

4
doc/src/bond_bpm_spring.rst
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@ -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 An additional damping force is applied to the bonded
particles. This forces is proportional to the difference in the particles. This forces is proportional to the difference in the
normal velocity of particles using a similar construction as normal velocity of particles using a similar construction as
dissipative particle dynamics (:ref:`(Groot) <Groot1>`): dissipative particle dynamics (:ref:`(Groot) <Groot4>`):
.. math:: .. math::
@ -197,6 +197,6 @@ The option defaults are *smooth* = *yes*
---------- ----------
.. _Groot1: .. _Groot4:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).

2
doc/src/bond_style.rst
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@ -84,6 +84,8 @@ accelerated styles exist.
* :doc:`zero <bond_zero>` - topology but no interactions * :doc:`zero <bond_zero>` - topology but no interactions
* :doc:`hybrid <bond_hybrid>` - define multiple styles of bond interactions * :doc:`hybrid <bond_hybrid>` - define multiple styles of bond interactions
* :doc:`bpm/rotational <bond_bpm_rotational>` - breakable bond with forces and torques based on deviation from reference state
* :doc:`bpm/spring <bond_bpm_spring>` - breakable bond with forces based on deviation from reference length
* :doc:`class2 <bond_class2>` - COMPASS (class 2) bond * :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
* :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond * :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
* :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles * :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles

10
doc/src/compute_nbonds_atom.rst → doc/src/compute_nbond_atom.rst
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@ -1,6 +1,6 @@
.. index:: compute nbonds/atom .. index:: compute nbond/atom
compute nbonds/atom command compute nbond/atom command
======================= =======================
Syntax Syntax
@ -8,17 +8,17 @@ Syntax
.. parsed-literal:: .. parsed-literal::
compute ID group-ID nbonds/atom compute ID group-ID nbond/atom
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* nbonds/atom = style name of this compute command * nbond/atom = style name of this compute command
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS .. code-block:: LAMMPS
compute 1 all nbonds/atom compute 1 all nbond/atom
Description Description
""""""""""" """""""""""

1
doc/src/pair_style.rst
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@ -131,6 +131,7 @@ accelerated styles exist.
* :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb * :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb
* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb * :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb
* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulomb and core/shell model * :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulomb and core/shell model
* :doc:`bpm/spring <pair_bpm_spring>` - repulsive harmonic force with damping
* :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics * :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics
* :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity * :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity
* :doc:`buck <pair_buck>` - Buckingham potential * :doc:`buck <pair_buck>` - Buckingham potential