diff --git a/doc/src/fix_propel_self.txt b/doc/src/fix_propel_self.txt index 7c3dfd3f45..3e351ba56a 100644 --- a/doc/src/fix_propel_self.txt +++ b/doc/src/fix_propel_self.txt @@ -6,7 +6,7 @@ :line -fix propel/self command :pre +fix propel/self command :h3 [Syntax:] @@ -36,13 +36,16 @@ fix active all propel/self quaternion 1.0 types 1 2 4 :pre Adds a force of a constant magnitude to each atom in the group. The nature in which the force is added depends on the mode. -For mode = velocity, the active force acts along the velocity vector of each -atom. This can be interpreted as an overdamped form of the model used by -"(Szabo)"_#Szabo and "(Henkes)"_#Henkes. -For mode = quaternion the force is along the axis obtained by rotating the -z-axis along the atom's quaternion. In other words, the force is along the -z-axis in the atom's body frame. This mode requires all atoms in the group -to have a quaternion, so atom_style should either be ellipsoid or body. + +For mode = velocity, the active force acts along the velocity vector of each atom. This can +be interpreted as a velocity-dependent friction, such as proposed by "(Erdmann)"_#Erdmann. + +For mode = quaternion the force is along the axis obtained by rotating the z-axis along the +atom's quaternion. In other words, the force is along the z-axis in the atom's body +frame. This mode requires all atoms in the group to have a quaternion, so atom_style should +either be ellipsoid or body. In combination with Langevin thermostat for translation and +rotation in the overdamped regime, the quaternion mode corresponds to the active Brownian +particle model introduced by "(Henkes)"_#Henkes, "(Bialke)"_#Bialke and "(Fily)"_#Fily. By default, this fix is applied to all atoms in the group. You can override this behavior by specifying the atom types the fix should work on through the {types} @@ -59,22 +62,27 @@ This fix is not imposed during minimization. [Restrictions:] -This fix makes use of per-atom quaternions to take into -account the fact that the orientation can rotate and hence the direction -of the active force can change. Therefore, this fix only works with atom_styles -that have a quaternion. +In quaternion mode, this fix makes use of per-atom quaternions to take into account the fact +that the orientation can rotate and hence the direction of the active force can +change. Therefore, the quaternion mode of this fix only works with atom_styles that have a +quaternion. [Related commands:] "fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html -:link(Szabo) -[(Szabo)] Szabo, B, Szollosi, G. J., Gonci, B., Juranyi, Zs., Selmeczi, D. and Viscek, T., -Phys. Rev. E, 74, 061908, 2006 +:link(Erdmann) +[(Erdmann)] U. Erdmanna , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, +Eur. Phys. J. B 15, 105-113, 2000. :link(Henkes) -[(Henkes)] Henkes, S, Fily, Y., and Marchetti, M. C. -Phys. Rev. E, 84, 040301(R), 2011 +[(Henkes)] Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011 + +:link(Bialke) +[(Bialke)] J. Bialké, T. Speck, and H Löwen, Phys. Rev. Lett. 108, 168301, 2012. + +:link(Fily) +[(Fily)] Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012. [Default:] types diff --git a/doc/txt/fix.txt b/doc/txt/fix.txt index fd281bce83..c272bbb397 100644 --- a/doc/txt/fix.txt +++ b/doc/txt/fix.txt @@ -296,6 +296,7 @@ accelerated styles exist. "precession/spin"_fix_precession_spin.html - "press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat "print"_fix_print.html - print text and variables during a simulation +"propel/self"_fix_propel_self.html - add self-propelling force "property/atom"_fix_property_atom.html - add customized per-atom values "python/invoke"_fix_python_invoke.html - call a Python function during a simulation "python/move"_fix_python_move.html - call a Python function during a simulation run