diff --git a/doc/src/fix_brownian.rst b/doc/src/fix_brownian.rst index ac8863bdd5..d032346617 100644 --- a/doc/src/fix_brownian.rst +++ b/doc/src/fix_brownian.rst @@ -21,7 +21,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style_name = *brownian* or *brownian/sphere* or *brownian/asphere* -* temp = temperature +* temp = temperature * seed = random number generator seed * 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* @@ -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 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/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 @@ -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 :math:`\sigma` is the spherical diameter). A similar (though more complex) relationship holds for ellipsoids and rod-like particles. - + --------- .. note:: @@ -141,7 +141,7 @@ The units of *gamma_t* are mass/time. The *gamma_r* keyword sets the (isotropic) rotational viscous damping. 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 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:: 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 - *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 ` doc page for more info. - Related commands """""""""""""""" diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index 85dd53cd62..ddc96817f9 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -28,8 +28,8 @@ Examples .. code-block:: LAMMPS - fix active all propel/self dipole 40.0 - fix active all propel/self velocity 10.0 + fix active all propel/self dipole 40.0 + fix active all propel/self velocity 10.0 fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0 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*. .. note:: - + In using keyword *quatvec*, the three arguments *sx*, *sy*, and *sz* will be automatically normalized to components of a unit vector internally to avoid users having to explicitly 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 @@ -117,14 +117,13 @@ in pressure computations. to turn off the virial contribution of this fix). Again, see :ref:`(Winkler) ` for discussion of why this is the case. - + Furthermore, when dealing with active systems, the temperature is no longer well defined. Therefore, one should ensure that the *virial* flag is used in the :doc:`compute pressure ` command (turning off temperature contributions). - ---------- Restart, fix_modify, output, run start/stop, minimize info