LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52 3.52 3.52 Created orthogonal box = (0 -44.8058 0) to (10.56 44.8058 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.86667 4.97803 4.97803 Created 218 atoms create_atoms CPU = 0.000189781 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.86667 4.97803 4.97803 Created 218 atoms create_atoms CPU = 8.91685e-05 secs 218 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 22 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.541 | 4.541 | 4.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1886.228 0 -1886.228 6039.8445 43 0 -1898.0501 0 -1898.0501 -8662.3403 Loop time of 0.15976 on 1 procs for 43 steps with 428 atoms 93.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1886.22795056 -1898.04878363 -1898.05013798 Force two-norm initial, final = 27.6038 0.12636 Force max component initial, final = 10.9723 0.0205398 Final line search alpha, max atom move = 1 0.0205398 Iterations, force evaluations = 43 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1561 | 0.1561 | 0.1561 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024478 | 0.0024478 | 0.0024478 | 0.0 | 1.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001213 | | | 0.76 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5557 ave 5557 max 5557 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95284 ave 95284 max 95284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95284 Ave neighs/atom = 222.626 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.541 | 4.541 | 4.541 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -1898.0501 0 -1898.0501 -8662.3403 4710.7045 46 0 -1898.0853 0 -1898.0853 -2679.0698 4694.8593 Loop time of 0.0133519 on 1 procs for 3 steps with 428 atoms 74.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1898.05013798 -1898.0850796 -1898.08530111 Force two-norm initial, final = 28.538 0.340542 Force max component initial, final = 23.5125 0.27982 Final line search alpha, max atom move = 0.00060512 0.000169324 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012687 | 0.012687 | 0.012687 | 0.0 | 95.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001781 | 0.0001781 | 0.0001781 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004869 | | | 3.65 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5431 ave 5431 max 5431 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95688 ave 95688 max 95688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95688 Ave neighs/atom = 223.57 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.678 | 4.678 | 4.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1898.0853 0 -1898.0853 -2679.0698 Loop time of 9.53674e-07 on 1 procs for 0 steps with 428 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5440 ave 5440 max 5440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95716 ave 95716 max 95716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95716 Ave neighs/atom = 223.636 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.678 | 4.678 | 4.678 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1898.0853 -1898.0853 10.547824 89.611611 4.9670143 -2679.0698 -2679.0698 95.381644 -8180.5844 47.993376 2.3352349 168.43738 Loop time of 2.14577e-06 on 1 procs for 0 steps with 428 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.146e-06 | | |100.00 Nlocal: 428 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5440 ave 5440 max 5440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47858 ave 47858 max 47858 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95716 ave 95716 max 95716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95716 Ave neighs/atom = 223.636 Neighbor list builds = 0 Dangerous builds = 0 428 -1898.08530111129 eV 2.33523492949566 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00