Hello, I want to create a square shape molecule in LAMMPS. The shape of the molecule is defined in a different file. For calling it in the script I have written the following code: Pour 2d granular particles into container dimension 2 lattice sq 0.95 atom_style sphere boundary f fm p newton off comm_modify vel yes cutoff 2.5 fix prop all property/atom mol gh…

Dear LAMMPS users, I use the 3Mar20 version of the package. I am performing the Np_zAT simulations for the rough estimation of melting pressure of the TIP4P/Ice model. I have arranged the simulation box so that there are approximately 50% of ice and water molecules in the cell that is elongated in “z” direction. The unit cell of ice is congruent with the desired pressure and …

hi all, I tried to compute aggregate/atom during rerun, in order to include all pairs in the neighbor list. The dump file was obtained in the original run using “dump custom” command, including wrapped and unscaled coordinates, velocity, image flags. And in the rerun process, simulation box was first defined by reading a restart file, and the x,y,z,vx,vy,vz,ix,iy,iz information w…

Hi, I’m performing a simulation in which I use LAMMPS to calculate the mean square displacement of some particles at certain times calculated through the logfreq3 function. This is the relevant part of the code I’m using. group A type 1 group B type 2 # B is smaller compute msdA A msd # default com=no and average=no so rvec(t=0) used compute msdB B msd # default com…

Dear LAMMPS users, I am trying to run some simulations in LAMMPS and I want to look at per-atom forces at each timestep. To do so, I included the following line in my input file: dump 1 all custom 1 dump x y z fx fy fz The values I got out from the dump command looked weird, so I tried to modify the compute function of the potential I’m using in a way such that before it return…