# GayBerne ellipsoids units lj atom_style hybrid molecular ellipsoid dipole #molecular #template # ellipsoid full dimension 3 boundary p p p read_data ellipse_dipole.dat #mass 1 1.0 #set type 1 mass 1.0 #set type 2 mass 0.00001 #read_restart restart.gblammps group spheroid type 1 # Spherical particles without dipole group pointdip type 2 # point particles with dipole #velocity spheroid create 0.5 87287 mom yes rot yes loop geom variable nom equal count(spheroid) variable dof equal ${nom}*6 #compute_modify rot extra/dof ${dof} #group lip molecule 1:${nom} #compute caltemp lip temp/asphere compute q spheroid property/atom quatw quati quatj quatk compute shape spheroid property/atom shapex shapey shapez compute dipmom pointdip property/atom mux muy muz mu # Commenting out -Andrew #dump 1 spheroid custom 1000 dump.soft.spheroid & # x y z c_q[1] c_q[2] c_q[3] c_q[4] & # c_shape[1] c_shape[2] c_shape[3] #dump 2 pointdip custom 1000 dump.soft.pointdip x y z mux muy muz #dump 3 spheroid custom 1000 dump.vel.all & # vx vy vz angmomx angmomy angmomz ##dump 2 all image 50000 image_t3.0.*.jpg type type & ## center d 0.5 0.5 0.5 # There's no way to store ellipse or dipole direction information in an XYZ file #dump traj all xyz 100 traj.xyz # # ########### Using this instead: ######## # This combines all the information into a single file: dump 1 all custom 100 traj.lammpstrj & id type x y z c_q[1] c_q[2] c_q[3] c_q[4] & c_shape[1] c_shape[2] c_shape[3] mux muy muz ix iy iz & pair_style hybrid/overlay lj/cut/dipole/long 10.0 gayberne 1.0 2.0 1.0 10.0 pair_coeff 1 1 gayberne 1.0 1.0 1.0 1.0 0.2 1.0 1.0 0.2 pair_coeff * * lj/cut/dipole/long 0.0 0.0 #pair_modify tail yes kspace_style ewald/dipole 0.0001 neigh_modify exclude type 1 2 timestep 0.001 #variable dofmod equal -${nom} fix fixrigid all rigid/nvt/small molecule temp 2.0 2.0 0.1 #compute_modify thermo_temp extra/dof 3 #fix fixnvtdip pointdip nvt temp 2.0 2.0 0.1 #compute_modify thermo_temp extra/dof ${dofmod} fix 2 all ave/time 1 5000 5000 c_thermo_temp ave running file avetemp.dat thermo_style custom step temp pe etotal vol press temp thermo 100 run 1000000 #thermo_style custom f_2 #thermo 50000 write_restart restart.gblammps