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This commit is contained in:
Stefan Paquay
2019-08-29 09:00:36 -04:00
committed by Pierre de Buyl
parent 8c7890b6df
commit 074dfd8651
5 changed files with 16 additions and 189 deletions
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50
doc/src/fix_active.txt
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@ -1,50 +0,0 @@
"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

21
doc/src/fix_propel_self.txt
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@ -6,28 +6,33 @@
:line :line
fix active command :pre fix propel/self command :pre
[Syntax:] [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 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 magnitude = magnitude of the active force :l
:ule :ule
[Examples:] [Examples:]
fix active_group all active 1.0 fix active_group all propel/self velocity 1.0
fix constant_velocity all viscous 1.0 fix constant_velocity all viscous 1.0
[Description:] [Description:]
Adds a force of a constant magnitude to each atom in the group. The direction Adds a force of a constant magnitude to each atom in the group. The nature in
of the force is along the axis obtained by rotating the z-axis along the atom's which the force is added depends on the mode.
quaternion. In other words, the force is along the z-axis in the atom's body For mode = velocity, the active force acts along the velocity vector of each
frame. 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 :line

61
examples/USER/misc/active/active_langevin.in
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@ -1,61 +0,0 @@
# 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

66
examples/USER/misc/active/active_viscous.in
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@ -1,66 +0,0 @@
# 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

7
src/USER-MISC/fix_propel_self.cpp
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@ -58,7 +58,7 @@ FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv )
// 2. Cases where the atoms have an internal ellipsoid. Currently those // 2. Cases where the atoms have an internal ellipsoid. Currently those
// styles are only body and aspherical particles. // styles are only body and aspherical particles.
// The first argument (mode) is used to differentiate between these. // The first argument (mode) is used to differentiate between these.
// args: fix ID all propel/self mode magnitude // args: fix ID all propel/self mode magnitude
// Optional args are // Optional args are
const char *mode_str = argv[3]; const char *mode_str = argv[3];
@ -77,7 +77,6 @@ FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv )
error->all(FLERR, msg); error->all(FLERR, msg);
} }
magnitude = force->numeric( FLERR, argv[4] ); magnitude = force->numeric( FLERR, argv[4] );
} }
@ -217,12 +216,12 @@ int FixPropelSelf::verify_atoms_have_quaternion()
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (ellipsoid_flag && atom->ellipsoid[i] < 0) { if (ellipsoid_flag && atom->ellipsoid[i] < 0) {
error->all(FLERR, "Got atom without ellipsoid set"); 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; return 1;
} }
if (body_flag && atom->body[i] < 0) { if (body_flag && atom->body[i] < 0) {
error->all(FLERR, "Got atom without body set"); 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; return 1;
} }
} }