#number of particles variable npart equal 350 #temperature at start and stop (in reduced units) variable tempstart equal 1.0 variable tempstop equal 1.0 units lj dimension 2 atom_style molecular boundary p p p comm_modify cutoff 5 neighbor 0.5 bin neigh_modify every 1 delay 0 check yes # create 2D box region box block -20 20 -20 20 -0.1 0.1 create_box 2 box bond/types 2 angle/types 1 extra/bond/per/atom 10 extra/angle/per/atom 10 extra/special/per/atom 1000 #put z=0 all the time fix 2d all enforce2d #put the particles randomly into the box region box2 block -20 20 -20 20 -0.1 0.1 create_atoms 1 random ${npart} 324523 box2 #all particles has mass 1 mass * 1 #Lennard-Jones pair interaction between particles pair_style lj/cut 1.1225 pair_coeff * * 1.0 1.0 #minimize energy first to avoid overlapping particles minimize 1e-4 1e-4 1000 1000 ##pair_style lj/cut 2.5 ##pair_coeff * * 1.0 1.0 bond_style harmonic bond_coeff * 100 1.0 angle_style cosine angle_coeff * 20 special_bonds lj 1 1 1 extra 100 reset_timestep 0 #save images shell "mkdir img" shell "rm img/*" dump img all image 10 img/t*.jpg type type adiam 0.9 zoom 1.7 dump_modify img backcolor white boxcolor black dump_modify img pad 6 #save video dump video all movie 100 movie.avi type type adiam 0.9 zoom 1.7 dump_modify video backcolor white boxcolor black #integrate Newtons equation of motion with stochastic kicks and friction #the kicks and friction model the effect of temperature variable rmin equal 1.05 variable maxfunc equal 3 ## iparam ${maxfunc} 2 jparam ${maxfunc} 2 fix integrator all nve fix dynamics all langevin ${tempstart} ${tempstop} 0.5 2352325 fix bondcreate all bond/create 1 1 1 ${rmin} 1 prob 1.0 235825 atype 1 ##fix bondbreak all bond/break 1 1 ${rmax} #output time step, temperature, average kinetic and potential energy thermo_style custom step temp ke pe f_bondcreate[2] thermo 100 #time step of integrator timestep 0.01 #number of steps to run run 100000