forked from lijiext/lammps
Added a fix to add active force to particles.
This commit is contained in:
Stefan Paquay
Pierre de Buyl
parent
5139f3af33
commit
c93ca5b4a4
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@ -0,0 +1,50 @@
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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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@ -0,0 +1,61 @@
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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 ${MSD_OUT}
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timestep 0.001
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run 10000
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@ -0,0 +1,66 @@
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# Uses a combnation of fix active and fix langevin to achieve
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# self-propelled particles.
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dimension 3
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boundary p p p
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units lj
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# Fix active uses quaternions to orient the active force so you need
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# ellipsoidal particles, even if you do not care about asymmetric shape
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atom_style ellipsoid
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# Set up box and particles:
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variable L equal 10
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region total block -$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 * * 0.0 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 10000
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@ -121,13 +121,12 @@ void FixMomentumKokkos<DeviceType>::end_of_step()
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auto xflag2 = xflag;
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auto yflag2 = yflag;
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auto zflag2 = zflag;
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const Few<double,3> &vcm_ref = vcm;
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Kokkos::parallel_for(nlocal, LAMMPS_LAMBDA(int i) {
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if (mask(i) & groupbit2) {
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if (xflag2) v(i,0) -= vcm_ref[0];
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if (yflag2) v(i,1) -= vcm_ref[1];
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if (zflag2) v(i,2) -= vcm_ref[2];
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if (xflag2) v(i,0) -= vcm[0];
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if (yflag2) v(i,1) -= vcm[1];
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if (zflag2) v(i,2) -= vcm[2];
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}
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});
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atomKK->modified(execution_space, V_MASK);
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@ -161,10 +160,6 @@ void FixMomentumKokkos<DeviceType>::end_of_step()
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auto prd = Few<double,3>(domain->prd);
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auto h = Few<double,6>(domain->h);
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auto triclinic = domain->triclinic;
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const Few<double,3> &xcm_ref = xcm;
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const Few<double,3> &omega_ref = omega;
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Kokkos::parallel_for(nlocal, LAMMPS_LAMBDA(int i) {
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if (mask[i] & groupbit2) {
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Few<double,3> x_i;
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@ -172,12 +167,12 @@ void FixMomentumKokkos<DeviceType>::end_of_step()
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x_i[1] = x(i,1);
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x_i[2] = x(i,2);
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auto unwrap = DomainKokkos::unmap(prd,h,triclinic,x_i,image(i));
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auto dx = unwrap[0] - xcm_ref[0];
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auto dy = unwrap[1] - xcm_ref[1];
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auto dz = unwrap[2] - xcm_ref[2];
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v(i,0) -= omega_ref[1]*dz - omega_ref[2]*dy;
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v(i,1) -= omega_ref[2]*dx - omega_ref[0]*dz;
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v(i,2) -= omega_ref[0]*dy - omega_ref[1]*dx;
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auto dx = unwrap[0] - xcm[0];
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auto dy = unwrap[1] - xcm[1];
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auto dz = unwrap[2] - xcm[2];
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v(i,0) -= omega[1]*dz - omega[2]*dy;
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v(i,1) -= omega[2]*dx - omega[0]*dz;
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v(i,2) -= omega[0]*dy - omega[1]*dx;
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}
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});
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atomKK->modified(execution_space, V_MASK);
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@ -208,3 +203,4 @@ template class FixMomentumKokkos<LMPDeviceType>;
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template class FixMomentumKokkos<LMPHostType>;
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#endif
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}
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@ -0,0 +1,163 @@
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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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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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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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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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@ -0,0 +1,55 @@
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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
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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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#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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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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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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*/
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