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Moved brownian dynamics files to be in USER-BROWNIAN package

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This commit is contained in:
Sam Cameron
2020-12-19 17:42:47 +00:00
parent d9440a582c
commit 4c1f449350
21 changed files with 160 additions and 162 deletions
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4
doc/src/Commands_fix.rst
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@ -39,8 +39,8 @@ OPT.
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
* :doc:`bd/sphere <fix_bd_sphere>`
* :doc:`bd/asphere <fix_bd_asphere>`
* :doc:`brownian/asphere <fix_brownian_asphere>`
* :doc:`brownian/sphere <fix_brownian_sphere>`
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`

4
doc/src/fix.rst
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@ -182,8 +182,8 @@ accelerated styles exist.
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`balance <fix_balance>` - perform dynamic load-balancing
* :doc:`bd/asphere <fix_bd_asphere>` - integrate positions and orientations in overdamped motion
* :doc:`bd/sphere <fix_bd_sphere>` - overdamped translational and rotational brownian dynamics
* :doc:`brownian/asphere <fix_brownian_asphere>` - overdamped translational and rotational brownian for ellipsoids
* :doc:`brownian/sphere <fix_brownian_sphere>` - overdamped translational and rotational brownian for spheres
* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
* :doc:`bond/break <fix_bond_break>` - break bonds on the fly
* :doc:`bond/create <fix_bond_create>` - create bonds on the fly

22
doc/src/fix_bd_asphere.rst → doc/src/fix_brownian_asphere.rst
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@ -1,17 +1,17 @@
.. index:: fix bd/asphere
.. index:: fix brownian/asphere
fix bd/asphere command
======================
fix brownian/asphere command
============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID bd/asphere gamma_t gamma_r diff_t diff_r seed keyword args
fix ID group-ID brownian/asphere gamma_t gamma_r diff_t diff_r seed keyword args
* ID, group-ID are documented in :doc:`fix <fix>` command
* bd/asphere = style name of this fix command
* brownian/asphere = style name of this fix command
* gamma_t = translational friction coefficient
* gamma_r = rotational friction coefficient
* diff_t = translational diffusion coefficient
@ -32,10 +32,10 @@ Examples
.. code-block:: LAMMPS
fix 1 all bd/asphere 1.0 1.0 1.0 1.0 1294019
fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng none dipole
fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng uniform
fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian
fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 1294019
fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 rng none dipole
fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 rng uniform
fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian
Description
@ -59,7 +59,7 @@ Chapter 4 of :ref:`(Goldstein) <GoldsteinCM1>`), :math:`dW_t` and
The quaternions :math:`q` of the ellipsoid are updated each timestep from
the angular velocity vector.
See :doc:`fix bd/sphere <fix_bd_sphere>` for discussion on the
See :doc:`fix brownian/sphere <fix_brownian_sphere>` for discussion on the
values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`,
:math:`D_r`, and temperature when simulating equilibrium systems.
@ -124,7 +124,7 @@ be point particles.
Related commands
""""""""""""""""
:doc:`fix bd/sphere <fix_bd_sphere>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix brownian/sphere <fix_brownian_sphere>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix nve/asphere <fix_nve_asphere>`, :doc:`atom style <atom_style>`
Default

18
doc/src/fix_bd_sphere.rst → doc/src/fix_brownian_sphere.rst
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@ -1,17 +1,17 @@
.. index:: fix bd/sphere
.. index:: fix brownian/sphere
fix bd/sphere command
======================
fix brownian/sphere command
===========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID bd/sphere gamma_t gamma_r diff_t diff_r seed keyword args
fix ID group-ID brownian/sphere gamma_t gamma_r diff_t diff_r seed keyword args
* ID, group-ID are documented in :doc:`fix <fix>` command
* bd/sphere = style name of this fix command
* brownian/sphere = style name of this fix command
* gamma_t = translational friction coefficient
* gamma_r = rotational friction coefficient
* diff_t = translational diffusion coefficient
@ -32,10 +32,10 @@ Examples
.. code-block:: LAMMPS
fix 1 all bd/sphere 1.0 1.0 1.0 1.0 1294019
fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng none dipole
fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform
fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian
fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 1294019
fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 rng none dipole
fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform
fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian
Description