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fix whitespace in doc files

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This commit is contained in:
Axel Kohlmeyer
2021-05-11 21:20:29 -04:00
parent 57a2f21757
commit e874446b7c
2 changed files with 10 additions and 12 deletions
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11
doc/src/fix_brownian.rst
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@ -21,7 +21,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* style_name = *brownian* or *brownian/sphere* or *brownian/asphere* * style_name = *brownian* or *brownian/sphere* or *brownian/asphere*
* temp = temperature * temp = temperature
* seed = random number generator seed * seed = random number generator seed
* one or more keyword/value pairs may be appended * one or more keyword/value pairs may be appended
* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t* * keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t*
@ -51,7 +51,7 @@ Examples
fix 1 all brownian 1.0 12908410 gamma_t 1.0 fix 1 all brownian 1.0 12908410 gamma_t 1.0
fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian
fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0 fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0
fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0 fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0
@ -107,7 +107,7 @@ friction tensors can be diagonalized in a certain (body) reference frame.
accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where
:math:`\sigma` is the spherical diameter). A similar (though more complex) :math:`\sigma` is the spherical diameter). A similar (though more complex)
relationship holds for ellipsoids and rod-like particles. relationship holds for ellipsoids and rod-like particles.
--------- ---------
.. note:: .. note::
@ -141,7 +141,7 @@ The units of *gamma_t* are mass/time.
The *gamma_r* keyword sets the (isotropic) rotational viscous damping. The *gamma_r* keyword sets the (isotropic) rotational viscous damping.
Required for (and only compatible with) *brownian/sphere*. Required for (and only compatible with) *brownian/sphere*.
The units of *gamma_r* are mass*length**2/time. The units of *gamma_r* are mass*length**2/time.
The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of
the rotational and viscous damping tensors (having the same units as the rotational and viscous damping tensors (having the same units as
@ -159,7 +159,7 @@ are updated as described above. Only compatible with *brownian/asphere*
.. note:: .. note::
For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and
*gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the *gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the
*brownian/sphere* style with *gamma_t* = x and *gamma_r* = y. *brownian/sphere* style with *gamma_t* = x and *gamma_r* = y.
---------- ----------
@ -189,7 +189,6 @@ This fix is part of the USER-BROWNIAN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
doc page for more info. doc page for more info.
Related commands Related commands
"""""""""""""""" """"""""""""""""

11
doc/src/fix_propel_self.rst
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@ -28,8 +28,8 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix active all propel/self dipole 40.0 fix active all propel/self dipole 40.0
fix active all propel/self velocity 10.0 fix active all propel/self velocity 10.0
fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0 fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0
Description Description
@ -81,12 +81,12 @@ be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal
to zero. This keyword may only be specified for mode *quat*. to zero. This keyword may only be specified for mode *quat*.
.. note:: .. note::
In using keyword *quatvec*, the three arguments *sx*, In using keyword *quatvec*, the three arguments *sx*,
*sy*, and *sz* will be automatically normalized to components *sy*, and *sz* will be automatically normalized to components
of a unit vector internally to avoid users having to explicitly of a unit vector internally to avoid users having to explicitly
do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i` do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i`
will always be of unit length. will always be of unit length.
Along with adding a force contribution, this fix can also Along with adding a force contribution, this fix can also
@ -117,14 +117,13 @@ in pressure computations.
to turn off the virial contribution of this fix). Again, to turn off the virial contribution of this fix). Again,
see :ref:`(Winkler) <Winkler1>` for discussion of why this see :ref:`(Winkler) <Winkler1>` for discussion of why this
is the case. is the case.
Furthermore, when dealing with active systems, the temperature Furthermore, when dealing with active systems, the temperature
is no longer well defined. Therefore, one should ensure that is no longer well defined. Therefore, one should ensure that
the *virial* flag is used in the the *virial* flag is used in the
:doc:`compute pressure <compute_pressure>` command (turning :doc:`compute pressure <compute_pressure>` command (turning
off temperature contributions). off temperature contributions).
---------- ----------
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info