forked from lijiext/lammps
Axel Kohlmeyer
GitHub
commit
795a872bf3
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@ -156,6 +156,7 @@ OPT.
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* :doc:`precession/spin <fix_precession_spin>`
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* :doc:`press/berendsen <fix_press_berendsen>`
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* :doc:`print <fix_print>`
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* :doc:`propel/self <fix_propel_self>`
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* :doc:`property/atom (k) <fix_property_atom>`
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* :doc:`python/invoke <fix_python_invoke>`
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* :doc:`python/move <fix_python_move>`
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@ -243,4 +244,3 @@ OPT.
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*
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*
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*
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*
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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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@ -0,0 +1,113 @@
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.. index:: fix propel/self
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fix propel/self command
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=======================
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Syntax
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""""""
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fix ID group-ID propel/self mode magnitude keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* propel/self = style name of this fix command
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* mode = velocity or quat
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* magnitude = magnitude of the active force
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* one or more keyword/value pairs may be appended to args
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* keyword = *types*
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*types* values = one or more atom types
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Examples
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""""""""
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.. parsed-literal::
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fix active_group all propel/self velocity 1.0
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fix constant_velocity all viscous 1.0
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fix active_group all propel/self quat 1.0
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fix active all propel/self quat 1.0 types 1 2 4
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Description
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"""""""""""
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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
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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* = *quat* 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
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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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**Restart, fix\_modify, output, run start/stop, minimize info:**
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No information about this fix is written to :doc:`binary restart files <restart>`.
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This fix is not imposed during minimization.
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Restrictions
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""""""""""""
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In quat 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 quat 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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:doc:`fix setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`
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.. _Erdmann:
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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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**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
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.. _Bialke:
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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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**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.
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**Default:** types
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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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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@ -2327,6 +2336,7 @@ quadratically
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quadrupolar
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Quant
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quartic
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quat
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quaternion
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quaternions
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quati
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@ -2529,6 +2539,7 @@ 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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@ -0,0 +1,54 @@
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dimension 2
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boundary p p p
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variable L equal 20
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region total block -$L $L -$L $L -0.5 0.5
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lattice hex 0.3
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create_box 2 total
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create_atoms 1 box
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# Set random fraction to passive:
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set type 1 type/fraction 2 0.5 1337
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# Purely repulsive particles:
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variable rc equal "2^(1.0/6.0)"
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pair_style lj/cut ${rc}
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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mass * 1.0
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fix step all nve
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fix temp all langevin 1.0 1.0 1.0 13
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fix twod all enforce2d
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neighbor 0.6 bin
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dump traj all custom 250 2d_active.dump.bin id type x y z
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thermo_style custom time step pe ke etotal temp
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thermo 1000
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run 5000
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group one type 1
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group two type 2
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compute ke1 one ke
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compute ke2 two ke
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thermo_style custom step pe ke etotal temp c_ke1 c_ke2
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fix active all propel/self velocity 1.0
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# With active force there is more motion so increase bin size:
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neighbor 1.0 bin
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run 10000
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# Only make type 1 active:
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fix active all propel/self velocity 1.0 types 1
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# With active force there is more motion so increase bin size:
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neighbor 1.0 bin
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run 10000
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@ -0,0 +1,37 @@
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dimension 2
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boundary p p p
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variable L equal 20
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region total block -$L $L -$L $L -0.5 0.5
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lattice hex 0.3
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create_box 2 total
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create_atoms 1 box
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# Set random fraction to passive:
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set type 1 type/fraction 2 0.5 1337
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# Purely repulsive particles:
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variable rc equal "2^(1.0/6.0)"
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pair_style lj/cut ${rc}
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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mass * 1.0
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fix step all nve
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fix twod all enforce2d
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neighbor 0.6 bin
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dump traj all custom 250 2d_active.dump.bin id type x y z
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thermo_style custom step pe ke etotal temp
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thermo 1000
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run 10000
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fix active all propel/self velocity 1.0
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fix fric all viscous 1.0
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# With active force there is more motion so increase bin size:
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neighbor 1.0 bin
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run 10000
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@ -0,0 +1,40 @@
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dimension 3
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boundary p p p
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atom_style ellipsoid
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variable L equal 20
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region total block -$L $L -$L $L -$L $L
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lattice sc 0.1
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create_box 2 total
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create_atoms 1 box
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# Set random fraction to passive:
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set type 1 type/fraction 2 0.5 1337
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# Purely repulsive particles:
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variable rc equal "2^(1.0/6.0)"
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pair_style lj/cut ${rc}
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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# mass * 1.0
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set type * shape 1.0 1.0 1.0
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set type * density 1.9098593171027443
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set type * quat 0 0 1 0
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fix step all nve/asphere
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fix temp all langevin 1.0 1.0 1.0 13 angmom 3.333333333
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neighbor 0.6 bin
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dump traj all custom 100 3d_active.dump.bin id type x y z fx fy fz
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thermo_style custom step pe ke etotal temp
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thermo 100
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run 500
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fix active all propel/self quat 1.0
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# With active force there is more motion so increase bin size:
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neighbor 1.0 bin
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run 500
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@ -6,7 +6,7 @@ SHELL = /bin/sh
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# compiler/linker settings
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# specify flags and libraries needed for your compiler
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KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
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KOKKOS_ABSOLUTE_PATH = /home/stefan/projects/lammps-mine/lib/kokkos
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export MPICH_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
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export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
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CC = mpicxx
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@ -33,7 +33,7 @@ KOKKOS_ARCH = Kepler35
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# LAMMPS ifdef settings
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# see possible settings in Section 2.2 (step 4) of manual
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LMP_INC = -DLAMMPS_GZIP
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LMP_INC = -DLAMMPS_GZIP -DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG
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# MPI library
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# see discussion in Section 2.2 (step 5) of manual
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@ -55,9 +55,9 @@ MPI_LIB =
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# PATH = path for FFT library
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# LIB = name of FFT library
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FFT_INC =
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FFT_PATH =
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FFT_LIB =
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FFT_INC = -I/usr/include/
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FFT_PATH = -L/usr/lib/
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FFT_LIB = -lfftw3
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# JPEG and/or PNG library
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# see discussion in Section 2.2 (step 7) of manual
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@ -68,7 +68,7 @@ FFT_LIB =
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JPG_INC =
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JPG_PATH =
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JPG_LIB =
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JPG_LIB = -ljpeg -lpng
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# ---------------------------------------------------------------------
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# build rules and dependencies
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|
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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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|
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|
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|
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@ -0,0 +1,268 @@
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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
|
||||
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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|
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/* -----------------------------------------------------------------------
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Contributed by Stefan Paquay @ Brandeis University
|
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|
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Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions!
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----------------------------------------------------------------------- */
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|
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#include "fix_propel_self.h"
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|
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#include <cstdio>
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#include <cstring>
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#include <string>
|
||||
|
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#include "atom.h"
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#include "atom_vec_ellipsoid.h"
|
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#include "citeme.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "group.h"
|
||||
#include "math.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
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||||
#include "math_vector.h"
|
||||
#include "modify.h"
|
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#include "random_mars.h"
|
||||
#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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||||
|
||||
#define PRINT_DEBUG_OUTPUT 0
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||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv )
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: Fix(lmp, narg, argv), magnitude(0.0),
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mode(VELOCITY), n_types_filter(0), apply_to_type(NULL)
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{
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||||
if (narg < 5) error->all(FLERR, "Illegal fix propel/self command");
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|
||||
// The fix is to support the following cases:
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// 1. Simple atoms, in which case the force points along the velocity
|
||||
// 2. Aspherical particles with an orientation.
|
||||
// The first argument (mode) is used to differentiate between these.
|
||||
|
||||
// args: fix ID all propel/self mode magnitude
|
||||
// Optional args are
|
||||
|
||||
const char *mode_str = argv[3];
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||||
|
||||
if (strcmp(mode_str, "velocity") == 0) {
|
||||
mode = VELOCITY;
|
||||
|
||||
} else if (strcmp(mode_str, "quat") == 0) {
|
||||
|
||||
// This mode should only be supported if the atom style has
|
||||
// a quaternion (and if all atoms in the group have it)
|
||||
|
||||
if (!atoms_have_quaternion()) {
|
||||
error->all(FLERR, "All fix atoms need to be extended particles");
|
||||
}
|
||||
mode = QUATERNION;
|
||||
|
||||
} else {
|
||||
char msg[2048];
|
||||
sprintf(msg, "Illegal mode \"%s\" for fix propel/self", mode_str);
|
||||
error->all(FLERR, msg);
|
||||
}
|
||||
|
||||
magnitude = force->numeric( FLERR, argv[4] );
|
||||
|
||||
// Handle rest of args:
|
||||
|
||||
int iarg = 5;
|
||||
while (iarg < narg) {
|
||||
|
||||
if (strcmp(argv[iarg],"types") == 0) {
|
||||
|
||||
apply_to_type = new int[atom->ntypes+1];
|
||||
memset(apply_to_type, 0, atom->ntypes * sizeof(int));
|
||||
|
||||
// consume all following numerical arguments as types
|
||||
|
||||
iarg++;
|
||||
int flag=0;
|
||||
while (iarg < narg) {
|
||||
if (isdigit(argv[iarg][0])) {
|
||||
int thistype = force->inumeric(FLERR,argv[iarg]);
|
||||
if ((thistype < 1) || (thistype > atom->ntypes))
|
||||
error->all(FLERR,"Illegal atom type to types keyword");
|
||||
apply_to_type[thistype] = 1;
|
||||
flag = 1;
|
||||
iarg++;
|
||||
} else break;
|
||||
}
|
||||
if (!flag)
|
||||
error->all(FLERR,"'types' keyword requires at least one type");
|
||||
else
|
||||
n_types_filter = 1;
|
||||
|
||||
} else {
|
||||
error->all(FLERR,"Illegal fix propel/self command.");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixPropelSelf::~FixPropelSelf()
|
||||
{
|
||||
delete[] apply_to_type;
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPropelSelf::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixPropelSelf::memory_usage()
|
||||
{
|
||||
// magnitude + thermostat_orient + mode + n_types_filter + apply_to_type
|
||||
double bytes = sizeof(double) + 3*sizeof(int) + sizeof(int*);
|
||||
bytes += sizeof(int)*atom->ntypes*n_types_filter;
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPropelSelf::post_force(int vflag )
|
||||
{
|
||||
switch(mode) {
|
||||
case QUATERNION:
|
||||
if (n_types_filter) post_force_quaternion<1>(vflag);
|
||||
else post_force_quaternion<0>(vflag);
|
||||
break;
|
||||
case VELOCITY:
|
||||
if (n_types_filter) post_force_velocity<1>(vflag);
|
||||
else post_force_velocity<0>(vflag);
|
||||
break;
|
||||
default:
|
||||
;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int filter_by_type>
|
||||
void FixPropelSelf::post_force_quaternion(int /* vflag */ )
|
||||
{
|
||||
double **f = atom->f;
|
||||
AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->avec);
|
||||
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int *type = atom->type;
|
||||
int* ellipsoid = atom->ellipsoid;
|
||||
|
||||
AtomVecEllipsoid::Bonus *bonus = av->bonus;
|
||||
|
||||
// Add the active force to the atom force:
|
||||
|
||||
for( int i = 0; i < nlocal; ++i ){
|
||||
if( mask[i] & groupbit ){
|
||||
if (filter_by_type && !apply_to_type[type[i]]) {
|
||||
continue;
|
||||
}
|
||||
|
||||
double f_act[3] = { 1.0, 0.0, 0.0 };
|
||||
double f_rot[3];
|
||||
|
||||
double *quat = bonus[ellipsoid[i]].quat;
|
||||
|
||||
double Q[3][3];
|
||||
MathExtra::quat_to_mat( quat, Q );
|
||||
MathExtra::matvec( Q, f_act, f_rot );
|
||||
|
||||
f[i][0] += magnitude * f_rot[0];
|
||||
f[i][1] += magnitude * f_rot[1];
|
||||
f[i][2] += magnitude * f_rot[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int filter_by_type>
|
||||
void FixPropelSelf::post_force_velocity(int /*vflag*/)
|
||||
{
|
||||
double **f = atom->f;
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int *type = atom->type;
|
||||
|
||||
// Add the active force to the atom force:
|
||||
|
||||
for(int i = 0; i < nlocal; ++i) {
|
||||
if( mask[i] & groupbit ){
|
||||
if (filter_by_type && !apply_to_type[type[i]]) {
|
||||
continue;
|
||||
}
|
||||
|
||||
const double *vi = v[i];
|
||||
double f_act[3] = { vi[0], vi[1], vi[2] };
|
||||
double nv2 = vi[0]*vi[0] + vi[1]*vi[1] + vi[2]*vi[2];
|
||||
double fnorm = 0.0;
|
||||
const double TOL = 1e-14;
|
||||
|
||||
if (nv2 > TOL) {
|
||||
|
||||
// Without this check you can run into numerical
|
||||
// issues because fnorm will blow up.
|
||||
|
||||
fnorm = magnitude / sqrt(nv2);
|
||||
}
|
||||
|
||||
f[i][0] += fnorm * f_act[0];
|
||||
f[i][1] += fnorm * f_act[1];
|
||||
f[i][2] += fnorm * f_act[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPropelSelf::atoms_have_quaternion()
|
||||
{
|
||||
if (!atom->ellipsoid_flag) {
|
||||
error->all(FLERR, "Mode 'quat' requires atom style ellipsoid");
|
||||
return 0;
|
||||
}
|
||||
|
||||
int *mask = atom->mask;
|
||||
int flag=0,flagall=0;
|
||||
|
||||
// Make sure all atoms have ellipsoid data:
|
||||
|
||||
for (int i = 0; i < atom->nlocal; ++i)
|
||||
if (mask[i] & groupbit)
|
||||
if (atom->ellipsoid[i] < 0) ++flag;
|
||||
|
||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
|
||||
if (flagall > 0) return 0;
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(propel/self,FixPropelSelf)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_PROPEL_SELF_H
|
||||
#define LMP_FIX_PROPEL_SELF_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixPropelSelf : public Fix {
|
||||
public:
|
||||
|
||||
FixPropelSelf(class LAMMPS *, int, char **);
|
||||
virtual ~FixPropelSelf();
|
||||
virtual int setmask();
|
||||
virtual void post_force(int);
|
||||
|
||||
double memory_usage();
|
||||
|
||||
protected:
|
||||
enum operation_modes {
|
||||
VELOCITY = 0,
|
||||
QUATERNION = 1
|
||||
};
|
||||
|
||||
private:
|
||||
double magnitude;
|
||||
int mode;
|
||||
|
||||
// If 0, apply fix to everything in group. If > 0, apply only to those
|
||||
// types i for which i <= n_types_filter _and_ apply_to_type[i] == 1:
|
||||
int n_types_filter;
|
||||
int *apply_to_type; //< Specifies, per type, if the fix applies to it or not.
|
||||
|
||||
|
||||
int atoms_have_quaternion();
|
||||
|
||||
template <int filter_by_type> void post_force_velocity(int);
|
||||
template <int filter_by_type> void post_force_quaternion(int);
|
||||
};
|
||||
}
|
||||
|
||||
#endif
|
||||
#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