Commit before merging latest changes in master.

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

fix active command  :pre

[Syntax:]

fix ID group-ID magnitude

ID, group-ID are documented in "fix"_fix.html command :ulb,l

addforce = style name of this fix command :l

magnitude = magnitude of the active force :l

:ule

[Examples:]

fix active_group all active 1.0

fix constant_velocity all viscous 1.0

[Description:]

Adds a force of a constant magnitude to each atom in the group. The direction

of 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.

:line

[Restart, fix_modify, output, run start/stop, minimize info:]

No information about this fix is written to "binary restart

files"_restart.html.

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

ellipsoidal particles.

[Related commands:]

"fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html

:line

fix active command  :pre

fix propel/self command  :pre

[Syntax:]

fix ID group-ID magnitude

fix ID group-ID propel/self mode magnitude

ID, group-ID are documented in "fix"_fix.html command :ulb,l

addforce = style name of this fix command :l

propel/self = style name of this fix command :l

mode = velocity or quaternion :l

magnitude = magnitude of the active force :l

:ule

[Examples:]

fix active_group all active 1.0

fix active_group all propel/self velocity 1.0

fix constant_velocity all viscous 1.0

[Description:]

Adds a force of a constant magnitude to each atom in the group. The direction

of 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.

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.

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.

:line

# Uses a combnation of fix active and fix langevin to achieve

# self-propelled particles.

dimension 3

boundary p p p

units lj

# Fix active uses quaternions to orient the active force so you need 

# ellipsoidal particles, even if you do not care about asymmetric shape

atom_style ellipsoid

# Set up box and particles:

variable L equal 10

region total block -$L $L -$L $L -$L $L

create_box 1 total

variable N equal 1000

create_atoms 1 random $N 123456 total

# Set particle shape:

set group all shape 1 1 1

set group all quat/random 18238

variable V   equal "4.0*PI"

variable rho equal "1.0 / v_V"

# Density so that mass = 1

set group all density ${rho}

# Simple repulsive LJ

pair_style lj/cut 1.1225

pair_coeff * * 1.0 1.0

pair_modify shift yes

# Remove initial overlap:

minimize 1e-4 1e-6 1000 10000

reset_timestep 0

# Fixes for time integration

fix step all nve/asphere

fix active all active 1.0

fix temp all langevin 1.0 1.0 1.0 12341 angmom 3.333333333333

variable DUMP_OUT string "active_langevin.dump"

variable MSD_OUT string "active_langevin_msd.dat"

# Compute temperature and orientation

compute T    all temp/asphere

compute quat all property/atom quatw quati quatj quatk

compute msd  all msd

compute vacf all vacf

# Some output:

thermo_style custom time step pe ke etotal temp c_T

thermo 1000

dump traj all custom 100 ${DUMP_OUT} id type x y z &

	c_quat[1] c_quat[2] c_quat[3] c_quat[4] 

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}

timestep 0.001

run 10000

# Uses a combnation of fix active and fix langevin to achieve

# self-propelled particles.

dimension 3

boundary p p p

units lj

# Fix active uses quaternions to orient the active force so you need 

# ellipsoidal particles, even if you do not care about asymmetric shape

atom_style ellipsoid

# Set up box and particles:

variable L equal 10

region total block -$L $L -$L $L -$L $L

create_box 1 total

variable N equal 1000

create_atoms 1 random $N 123456 total

# Set particle shape:

set group all shape 1 1 1

set group all quat/random 18238

variable V   equal "4.0*PI"

variable rho equal "1.0 / v_V"

# Density so that mass = 1

set group all density ${rho}

# Simple repulsive LJ

pair_style lj/cut 1.1225

pair_coeff * * 1.0 1.0

pair_modify shift yes

# Remove initial overlap:

minimize 1e-4 1e-6 1000 10000

reset_timestep 0

# Fixes for time integration

fix step all nve/asphere

# Should lead to constant velocity of 10 per particle

fix active all active 1.0

fix visc all viscous 0.1

# Initial velocities:

velocity all create 1.0 1234

variable DUMP_OUT string "active_viscous.dump"

variable MSD_OUT string "active_viscous_msd.dat"

# Compute temperature and orientation

compute T    all temp/asphere

compute quat all property/atom quatw quati quatj quatk

compute msd  all msd

compute vacf all vacf

# Some output:

thermo_style custom time step pe ke etotal temp c_T

thermo 1000

dump traj all custom 100 ${DUMP_OUT} id type x y z &

	c_quat[1] c_quat[2] c_quat[3] c_quat[4] 

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}

timestep 0.001

run 100000

    error->all(FLERR, msg);

  }

  magnitude = force->numeric( FLERR, argv[4] );

}

    if (mask[i] & groupbit) {

	    if (ellipsoid_flag && atom->ellipsoid[i] < 0) {

		    error->all(FLERR, "Got atom without ellipsoid set");

		    // Kind-of pointless but silences some compiler warnings:

		    // Kind-of pointless return but silences compiler warnings:

		    return 1;

	    }

	    if (body_flag && atom->body[i] < 0) {

		    error->all(FLERR, "Got atom without body set");

		    // Kind-of pointless but silences some compiler warnings:

		    // Kind-of pointless return silences compiler warnings:

		    return 1;

	    }

    }