i create a model but it have some amorphous atoms in the initial state . can you show me how to improve the model ? 1 post - 1 participant Read full topic

i create a model but it have some amorphous atoms in the initial state . can you show me how to improve the model ? 1 post - 1 participant Read full topic

Dear LAMMPS users and developers, I ran into a cuda driver error when trying to run lammps on a gpu compute node with four NVIDIA A100. Specifically, the error message is (test with command mpirun -np 32 /home/sijiachen/software/lammps-29Sep2021/build/lmp_beagle3_a100 -sf gpu -pk gpu 1 -in in.chain, in.chain is the one in lammps bench folder): IPL WARN> IPL_init_numa_nodes: ca…

Dear LAMMPS users and developers, I am running pair style dpd on cpu and gpu and getting different aggregate number. On cpu even at 1250th frame there are two clusters consisting of two well separated aggregates consisting of 38 and 69 molecules. Whereas on gpu at 1067th frame, a single aggregate is found with all 107 molecules in it. The single aggregate is formed by coalescence…

Hello all, I have been trying to incorporate langevin dynamics into my system, however I am really confused about the exact role of the damping parameter in the fix langevin command. I have come across many systems where they claim to have damping in the range of 100-200. However when I set damp to 100 in fix langevin, the temperature of the system starts to blow up. The the…

Hello, everyone, I want to access the list number of each atom by atom vector. I used the compute command to run it, and reported an error “non digit character between brackets in variable”. What should I do? I would appreciate it if it could be solved. The script is the following: units metal dimension 3 atom_modify map yes read_data L4_L5_xyza.data change_box all boundary p f …

I am trying to implement fene potential between bonded pairs in a protein structure. I have the distance between the pairs in native state in crystal structure. How can I use this in lamps fene bond calculation. In fene potential my r=(rij-rij_crystal) where rij is distance between I and j and the other one is the distance in native state. In lamps its just rij. Do I implement it o…

Dear LAMMPS users, I am updating the coefficients (bond/angle) via “include new_data.settings” after the completion of one simulation run. And I only want to update these new data settings on selected group IDs. I think here I need information about how to use a “for loop” in LAMMPS? So I can consider specific group IDs and then implement “include new_data.settings” file on them.…

Hello LAMMPS Community, I am trying to model 3D crystal structure packed with liquid and dissolved gaseous molecules. To rigidify individual molecules, I have tried to use fix rigid/small together with fix nvt, however, it’s showed illegal fix error. I have also tried to use fix rigid/nvt/small but still error is same. Here is below my input script; -------------------- Init Sec…

Hello all, I have a question related to the cutoff arg in the lj/cut off command. My aim is to create a purely repulsive potential and I am confused as to whether the cutoff specification scales with the user specified sigma value Suppose if I were to set sigma(the second arg) to 1,then setting the cutoff to 1.122 (2^1/6) would make it purely repulsive as 2^1/6*sigma corresponds …