LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -51.584363 0.0000000) to (25.790358 51.584363 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1264573 4.1264573 3.6473074 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -51.584363 0.0000000) to (25.790358 51.584363 3.6473074) create_atoms CPU = 0.002 seconds 402 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1264573 4.1264573 3.6473074 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -51.584363 0.0000000) to (25.790358 51.584363 3.6473074) create_atoms CPU = 0.001 seconds 402 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 800 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_608695023236_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.293 | 5.293 | 5.293 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3254.889 0 -3254.889 25095.956 25 0 -3306.8281 0 -3306.8281 6382.6457 Loop time of 6.42423 on 1 procs for 25 steps with 800 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3254.88898270897 -3306.82534384591 -3306.8281072294 Force two-norm initial, final = 57.695649 0.20862662 Force max component initial, final = 12.617020 0.043222292 Final line search alpha, max atom move = 1.0000000 0.043222292 Iterations, force evaluations = 25 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4134 | 6.4134 | 6.4134 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0052292 | 0.0052292 | 0.0052292 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005588 | | | 0.09 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4180.00 ave 4180 max 4180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43032.0 ave 43032 max 43032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43032 Ave neighs/atom = 53.790000 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.293 | 5.293 | 5.293 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -3306.8281 0 -3306.8281 6382.6457 9704.6037 30 0 -3306.9111 0 -3306.9111 603.4306 9738.9654 Loop time of 0.838691 on 1 procs for 5 steps with 800 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3306.8281072294 -3306.91064233132 -3306.9110888287 Force two-norm initial, final = 53.821414 0.53400859 Force max component initial, final = 45.878635 0.44466480 Final line search alpha, max atom move = 0.00024370758 0.00010836818 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83571 | 0.83571 | 0.83571 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061671 | 0.00061671 | 0.00061671 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002361 | | | 0.28 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4188.00 ave 4188 max 4188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42956.0 ave 42956 max 42956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42956 Ave neighs/atom = 53.695000 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.431 | 5.431 | 5.431 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3306.9111 0 -3306.9111 603.4306 Loop time of 6.084e-06 on 1 procs for 0 steps with 800 atoms 180.8% 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 | | 6.084e-06 | | |100.00 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4188.00 ave 4188 max 4188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42940.0 ave 42940 max 42940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42940 Ave neighs/atom = 53.675000 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.431 | 5.431 | 5.431 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 -3306.9111 -3306.9111 25.784169 103.16873 3.6611002 603.4306 603.4306 -73.135133 1908.3995 -24.972592 2.3282391 92.778806 Loop time of 6.545e-06 on 1 procs for 0 steps with 800 atoms 259.7% 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 | | 6.545e-06 | | |100.00 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4188.00 ave 4188 max 4188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21470.0 ave 21470 max 21470 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42940.0 ave 42940 max 42940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42940 Ave neighs/atom = 53.675000 Neighbor list builds = 0 Dangerous builds = 0 800 -3306.9110888287 eV 2.3282390995627 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08