forked from lijiext/lammps
documentation and examples cleanup for fix propel/self
- rename example folder - remove .txt format docs - remove obsolete fix active sources - update readme in src/USER-MISC - replace non-ASCII characters and fix spelling issues
This commit is contained in:
Axel Kohlmeyer
parent
f4d9715cc7
commit
5e740c9cc5
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@ -308,6 +308,7 @@ accelerated styles exist.
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* :doc:`precession/spin <fix_precession_spin>` -
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* :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat
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* :doc:`print <fix_print>` - print text and variables during a simulation
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* :doc:`propel/self <fix_propel_self>` - model self-propelled particles
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* :doc:`property/atom <fix_property_atom>` - add customized per-atom values
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* :doc:`python/invoke <fix_python_invoke>` - call a Python function during a simulation
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* :doc:`python/move <fix_python_move>` - call a Python function during a simulation run
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@ -38,19 +38,23 @@ Description
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Adds a force of a constant magnitude to each atom in the group. The nature in
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which the force is added depends on the mode.
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For mode = velocity, the active force acts along the velocity vector of each atom. This can
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be interpreted as a velocity-dependent friction, such as proposed by :ref:`(Erdmann) <Erdmann>`.
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For *mode* = *velocity*, the active force acts along the velocity vector of
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each atom. This can be interpreted as a velocity-dependent friction,
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such as proposed by :ref:`(Erdmann) <Erdmann>`.
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For mode = quaternion the force is along the axis obtained by rotating the x-axis along the
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atom's quaternion. In other words, the force is along the x-axis in the atom's body
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frame. This mode requires all atoms in the group to have a quaternion, so atom\_style should
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either be ellipsoid or body. In combination with Langevin thermostat for translation and
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rotation in the overdamped regime, the quaternion mode corresponds to the active Brownian
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particle model introduced by :ref:`(Henkes) <Henkes>`, :ref:`(Bialke) <Bialke>` and :ref:`(Fily) <Fily>`.
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For *mode* = *quaternion* the force is applied along the axis obtained
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by rotating the x-axis along the atom's quaternion. In other words, the
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force is along the x-axis in the atom's body frame. This mode requires
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all atoms in the group to have a quaternion, so atom\_style should
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either be ellipsoid or body. In combination with Langevin thermostat
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for translation and rotation in the overdamped regime, the quaternion
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mode corresponds to the active Brownian particle model introduced by
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:ref:`(Henkes) <Henkes>`, :ref:`(Bialke) <Bialke>` and :ref:`(Fily)
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<Fily>`.
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By default, this fix is applied to all atoms in the group. You can override this
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behavior by specifying the atom types the fix should work on through the *types*
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keyword.
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By default, this fix is applied to all atoms in the group. You can
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override this behavior by specifying the atom types the fix should work
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on through the *types* keyword.
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----------
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@ -66,10 +70,10 @@ Restrictions
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""""""""""""
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In quaternion mode, this fix makes use of per-atom quaternions to take into account the fact
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that the orientation can rotate and hence the direction of the active force can
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change. Therefore, the quaternion mode of this fix only works with atom\_styles that have a
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quaternion.
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In quaternion mode, this fix makes use of per-atom quaternions to take
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into account the fact that the orientation can rotate and hence the
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direction of the active force can change. The quaternion mode
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of this fix only works with atom\_style ellipsoid.
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Related commands
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""""""""""""""""
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@ -80,7 +84,7 @@ Related commands
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**(Erdmann)** U. Erdmanna , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
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**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
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Eur. Phys. J. B 15, 105-113, 2000.
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.. _Henkes:
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@ -93,7 +97,7 @@ Eur. Phys. J. B 15, 105-113, 2000.
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**(Bialke)** J. Bialké, T. Speck, and H Löwen, Phys. Rev. Lett. 108, 168301, 2012.
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**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
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.. _Fily:
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@ -1,88 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix propel/self command :h3
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[Syntax:]
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fix ID group-ID propel/self mode magnitude keyword values ...
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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propel/self = style name of this fix command :l
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mode = velocity or quaternion :l
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magnitude = magnitude of the active force :l
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one or more keyword/value pairs may be appended to args :l
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keyword = {types} :l
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{types} values = one or more atom types
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:ule
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[Examples:]
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fix active_group all propel/self velocity 1.0
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fix constant_velocity all viscous 1.0 :pre
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fix active_group all propel/self quaternion 1.0 :pre
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fix active all propel/self quaternion 1.0 types 1 2 4 :pre
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[Description:]
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Adds a force of a constant magnitude to each atom in the group. The nature in
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which the force is added depends on the mode.
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For mode = velocity, the active force acts along the velocity vector of each atom. This can
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be interpreted as a velocity-dependent friction, such as proposed by "(Erdmann)"_#Erdmann.
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For mode = quaternion the force is along the axis obtained by rotating the x-axis along the
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atom's quaternion. In other words, the force is along the x-axis in the atom's body
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frame. This mode requires all atoms in the group to have a quaternion, so atom_style should
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either be ellipsoid or body. In combination with Langevin thermostat for translation and
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rotation in the overdamped regime, the quaternion mode corresponds to the active Brownian
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particle model introduced by "(Henkes)"_#Henkes, "(Bialke)"_#Bialke and "(Fily)"_#Fily.
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By default, this fix is applied to all atoms in the group. You can override this
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behavior by specifying the atom types the fix should work on through the {types}
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keyword.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html.
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This fix is not imposed during minimization.
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[Restrictions:]
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In quaternion mode, this fix makes use of per-atom quaternions to take into account the fact
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that the orientation can rotate and hence the direction of the active force can
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change. Therefore, the quaternion mode of this fix only works with atom_styles that have a
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quaternion.
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[Related commands:]
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"fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html
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:link(Erdmann)
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[(Erdmann)] U. Erdmanna , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
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Eur. Phys. J. B 15, 105-113, 2000.
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:link(Henkes)
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[(Henkes)] Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
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:link(Bialke)
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[(Bialke)] J. Bialké, T. Speck, and H Löwen, Phys. Rev. Lett. 108, 168301, 2012.
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:link(Fily)
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[(Fily)] Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.
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[Default:] types
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@ -220,6 +220,7 @@ Bext
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Bfrac
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bgq
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Bh
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Bialke
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Biersack
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bigbig
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bigint
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@ -691,6 +692,7 @@ eangle
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eatom
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Eb
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Eba
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Ebeling
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ebond
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ebook
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ebt
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@ -789,6 +791,7 @@ equilibration
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Equilibria
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equilization
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Ercolessi
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Erdmann
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eradius
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erate
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erc
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@ -879,6 +882,7 @@ filename
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Filename
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filenames
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Filenames
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Fily
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fileper
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filesystem
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Fincham
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@ -975,6 +979,7 @@ gcc
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gcmc
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gdot
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GeC
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Geier
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gencode
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georg
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Georg
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@ -1087,6 +1092,7 @@ Heenen
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Hendrik
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Henin
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Henkelman
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Henkes
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henrich
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Henrich
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Herrmann
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@ -1534,6 +1540,7 @@ lmptype
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ln
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localTemp
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localvectors
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Loewen
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logfile
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logfreq
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logicals
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@ -1598,6 +1605,7 @@ manpages
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manybody
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MANYBODY
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Maras
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Marchetti
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Marrink
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Marroquin
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Marsaglia
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@ -2093,6 +2101,7 @@ outfile
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outmost
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outputss
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Ouyang
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overdamped
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overlayed
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Ovito
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oxdna
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@ -2529,6 +2538,7 @@ scalexz
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scaleyz
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Schaik
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Schilfgarde
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Schimansky
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Schiotz
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Schlitter
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Schmid
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@ -60,6 +60,7 @@ fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov
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fix npt/cauchy, R. E. Miller (Carleton University), F. Pavia and S. Pattamatta, 12 Jan 2020
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fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310
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fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
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fix propel/self, Stefan Paquay (Brandeis U), stefanpaquay at gmail.com, 20 Jan 2020
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fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017
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fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
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fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
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@ -1,163 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* -----------------------------------------------------------------------
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Contributed by Stefan Paquay @ Brandeis University
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Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions!
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----------------------------------------------------------------------- */
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#include <stdio.h>
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#include <string.h>
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#include "fix_active.h"
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#include "atom.h"
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#include "atom_vec_ellipsoid.h"
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#include "citeme.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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#include "group.h"
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#include "math.h"
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#include "math_const.h"
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#include "math_extra.h"
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#include "math_vector.h"
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#include "modify.h"
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#include "random_mars.h"
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#include "respa.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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using namespace MathConst;
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/*
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Might be used later, who knows...
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static const char* cite_fix_active =
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"fix active command:\n\n"
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"@article{paquay-2018,\n"
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" author = {Paquay, Stefan},\n"
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" doi = {},\n"
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" issn = {},\n"
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" journal = {},\n"
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" month = ,\n"
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" number = ,\n"
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" pages = ,\n"
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" title = ,\n"
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" volume = ,\n"
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" year = \n"
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"}\n\n";
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*/
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static constexpr const bool debug_out = false;
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FixActive::FixActive( LAMMPS *lmp, int narg, char **argv )
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: Fix(lmp, narg, argv)
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{
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// if( lmp->citeme) lmp->citeme->add(cite_fix_active);
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if( narg < 4 ) error->all(FLERR, "Illegal fix active command");
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AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->avec);
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if (!av) error->all(FLERR, "FixActive requires atom_style ellipsoid");
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if( debug_out && comm->me == 0 ){
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fprintf(screen, "This is fix active, narg is %d\n", narg );
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fprintf(screen, "args:");
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for( int i = 0; i < narg; ++i ){
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fprintf(screen, " %s", argv[i]);
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}
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fprintf(screen, "\n");
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}
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// args: fix ID all active magnitude prop1 prop2 prop3
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// Optional args are
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magnitude = force->numeric( FLERR, argv[3] );
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}
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FixActive::~FixActive()
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{}
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int FixActive::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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return mask;
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}
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double FixActive::memory_usage()
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{
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double bytes = 0.0;
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return bytes;
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}
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void FixActive::post_force(int /* vflag */ )
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{
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// Then do the rest:
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double **f = atom->f;
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AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->avec);
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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AtomVecEllipsoid::Bonus *bonus = av->bonus;
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// Add the active force to the atom force:
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for( int i = 0; i < nlocal; ++i ){
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if( mask[i] & groupbit ){
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double f_act[3] = { 0.0, 0.0, 1.0 };
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double f_rot[3];
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|
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int* ellipsoid = atom->ellipsoid;
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double *quat = bonus[ellipsoid[i]].quat;
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tagint *tag = atom->tag;
|
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|
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double Q[3][3];
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MathExtra::quat_to_mat( quat, Q );
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MathExtra::matvec( Q, f_act, f_rot );
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|
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if (debug_out && comm->me == 0) {
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// Magical reference particle:
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if (tag[i] == 12) {
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fprintf(screen, "rotation quaternion: (%f %f %f %f)\n",
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quat[0], quat[1], quat[2], quat[3]);
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fprintf(screen, "rotation matrix: / %f %f %f \\\n",
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Q[0][0] ,Q[0][1], Q[0][2]);
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fprintf(screen, " | %f %f %f |\n",
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Q[1][0] ,Q[1][1], Q[1][2]);
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fprintf(screen, " \\ %f %f %f /\n",
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Q[2][0] ,Q[2][1], Q[2][2]);
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fprintf(screen, "Active force on atom %d: (%f %f %f)\n",
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tag[i], f_rot[0], f_rot[1], f_rot[2]);
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fprintf(screen, " Total force before: (%f %f %f)\n",
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f[i][0], f[i][1], f[i][2]);
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}
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}
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f[i][0] += magnitude * f_rot[0];
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f[i][1] += magnitude * f_rot[1];
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f[i][2] += magnitude * f_rot[2];
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}
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}
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}
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@ -1,55 +0,0 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(active,FixActive)
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#else
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#ifndef LMP_FIX_ACTIVE_H
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#define LMP_FIX_ACTIVE_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixActive : public Fix {
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public:
|
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FixActive(class LAMMPS *, int, char **);
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virtual ~FixActive();
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virtual int setmask();
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virtual void post_force(int);
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// virtual void post_force_respa(int, int, int);
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double memory_usage();
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|
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protected:
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double magnitude;
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int thermostat_orient;
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};
|
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|
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}
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#endif
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#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue