forked from lijiext/lammps
Commit before merging latest changes in master.
This commit is contained in:
Stefan Paquay
Pierre de Buyl
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8c7890b6df
commit
074dfd8651
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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 active command :pre
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[Syntax:]
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fix ID group-ID magnitude
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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addforce = style name of this fix command :l
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magnitude = magnitude of the active force :l
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:ule
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[Examples:]
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fix active_group all active 1.0
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fix constant_velocity all viscous 1.0
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[Description:]
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Adds a force of a constant magnitude to each atom in the group. The direction
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of the force is along the axis obtained by rotating the z-axis along the atom's
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quaternion. In other words, the force is along the z-axis in the atom's body
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frame.
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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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This fix makes use of per-atom quaternions to take into
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account the fact that the orientation can rotate and hence the direction
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of the active force can change. Therefore, this fix only works with
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ellipsoidal particles.
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[Related commands:]
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"fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html
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@ -6,28 +6,33 @@
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:line
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fix active command :pre
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fix propel/self command :pre
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[Syntax:]
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fix ID group-ID magnitude
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fix ID group-ID propel/self mode magnitude
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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addforce = style name of this fix command :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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:ule
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[Examples:]
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fix active_group all active 1.0
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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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[Description:]
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Adds a force of a constant magnitude to each atom in the group. The direction
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of the force is along the axis obtained by rotating the z-axis along the atom's
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quaternion. In other words, the force is along the z-axis in the atom's body
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frame.
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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
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atom.
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For mode = quaternion the force is along the axis obtained by rotating the
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z-axis along the atom's quaternion. In other words, the force is along the
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z-axis in the atom's body frame. This mode requires all atoms in the group
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to have a quaternion, so atom_style should either be ellipsoid or body.
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:line
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@ -1,61 +0,0 @@
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# Uses a combnation of fix active and fix langevin to achieve
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# self-propelled particles.
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dimension 3
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boundary p p p
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units lj
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# Fix active uses quaternions to orient the active force so you need
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# ellipsoidal particles, even if you do not care about asymmetric shape
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atom_style ellipsoid
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# Set up box and particles:
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variable L equal 10
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region total block -$L $L -$L $L -$L $L
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create_box 1 total
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variable N equal 1000
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create_atoms 1 random $N 123456 total
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# Set particle shape:
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set group all shape 1 1 1
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set group all quat/random 18238
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variable V equal "4.0*PI"
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variable rho equal "1.0 / v_V"
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# Density so that mass = 1
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set group all density ${rho}
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# Simple repulsive LJ
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pair_style lj/cut 1.1225
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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# Remove initial overlap:
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minimize 1e-4 1e-6 1000 10000
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reset_timestep 0
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# Fixes for time integration
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fix step all nve/asphere
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fix active all active 1.0
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fix temp all langevin 1.0 1.0 1.0 12341 angmom 3.333333333333
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variable DUMP_OUT string "active_langevin.dump"
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variable MSD_OUT string "active_langevin_msd.dat"
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# Compute temperature and orientation
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compute T all temp/asphere
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compute quat all property/atom quatw quati quatj quatk
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compute msd all msd
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compute vacf all vacf
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# Some output:
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thermo_style custom time step pe ke etotal temp c_T
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thermo 1000
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dump traj all custom 100 ${DUMP_OUT} id type x y z &
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c_quat[1] c_quat[2] c_quat[3] c_quat[4]
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fix msd all ave/time 1 10 50 c_msd[4] c_vacf[1] c_vacf[2] c_vacf[3] c_vacf[4] file ${MSD_OUT}
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timestep 0.001
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run 10000
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@ -1,66 +0,0 @@
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# Uses a combnation of fix active and fix langevin to achieve
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# self-propelled particles.
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dimension 3
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boundary p p p
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units lj
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# Fix active uses quaternions to orient the active force so you need
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# ellipsoidal particles, even if you do not care about asymmetric shape
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atom_style ellipsoid
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# Set up box and particles:
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variable L equal 10
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region total block -$L $L -$L $L -$L $L
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create_box 1 total
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variable N equal 1000
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create_atoms 1 random $N 123456 total
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# Set particle shape:
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set group all shape 1 1 1
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set group all quat/random 18238
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variable V equal "4.0*PI"
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variable rho equal "1.0 / v_V"
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# Density so that mass = 1
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set group all density ${rho}
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# Simple repulsive LJ
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pair_style lj/cut 1.1225
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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# Remove initial overlap:
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minimize 1e-4 1e-6 1000 10000
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reset_timestep 0
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# Fixes for time integration
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fix step all nve/asphere
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# Should lead to constant velocity of 10 per particle
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fix active all active 1.0
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fix visc all viscous 0.1
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# Initial velocities:
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velocity all create 1.0 1234
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variable DUMP_OUT string "active_viscous.dump"
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variable MSD_OUT string "active_viscous_msd.dat"
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# Compute temperature and orientation
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compute T all temp/asphere
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compute quat all property/atom quatw quati quatj quatk
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compute msd all msd
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compute vacf all vacf
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# Some output:
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thermo_style custom time step pe ke etotal temp c_T
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thermo 1000
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dump traj all custom 100 ${DUMP_OUT} id type x y z &
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c_quat[1] c_quat[2] c_quat[3] c_quat[4]
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fix msd all ave/time 1 10 50 c_msd[4] c_vacf[1] c_vacf[2] c_vacf[3] c_vacf[4] file ${MSD_OUT}
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timestep 0.001
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run 100000
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@ -58,7 +58,7 @@ FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv )
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// 2. Cases where the atoms have an internal ellipsoid. Currently those
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// styles are only body and aspherical particles.
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// The first argument (mode) is used to differentiate between these.
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// args: fix ID all propel/self mode magnitude
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// Optional args are
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const char *mode_str = argv[3];
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@ -77,7 +77,6 @@ FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv )
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error->all(FLERR, msg);
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}
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magnitude = force->numeric( FLERR, argv[4] );
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}
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@ -217,12 +216,12 @@ int FixPropelSelf::verify_atoms_have_quaternion()
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if (mask[i] & groupbit) {
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if (ellipsoid_flag && atom->ellipsoid[i] < 0) {
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error->all(FLERR, "Got atom without ellipsoid set");
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// Kind-of pointless but silences some compiler warnings:
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// Kind-of pointless return but silences compiler warnings:
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return 1;
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}
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if (body_flag && atom->body[i] < 0) {
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error->all(FLERR, "Got atom without body set");
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// Kind-of pointless but silences some compiler warnings:
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// Kind-of pointless return silences compiler warnings:
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return 1;
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}
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}
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