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 = 2.8553247 2.8553247 2.8553247 Created orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455674) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4798019 4.5262259 4.9455674 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455674) create_atoms CPU = 0.006 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4798019 4.5262259 4.9455674 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455674) create_atoms CPU = 0.005 seconds 626 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1246 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_769582363439_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4467.887 0 -4467.887 116900.48 79 0 -5115.516 0 -5115.516 717.23507 Loop time of 2.83636 on 1 procs for 79 steps with 1246 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4467.88704687332 -5115.5113502598 -5115.51595658813 Force two-norm initial, final = 1540.9138 0.27258545 Force max component initial, final = 361.42224 0.068566812 Final line search alpha, max atom move = 1.0000000 0.068566812 Iterations, force evaluations = 79 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7371 | 2.7371 | 2.7371 | 0.0 | 96.50 Neigh | 0.051497 | 0.051497 | 0.051497 | 0.0 | 1.82 Comm | 0.025646 | 0.025646 | 0.025646 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02214 | | | 0.78 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7298.00 ave 7298 max 7298 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: 170236.0 ave 170236 max 170236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170236 Ave neighs/atom = 136.62600 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -5115.516 0 -5115.516 717.23507 14526.168 80 0 -5115.5189 0 -5115.5189 -246.33403 14534.158 Loop time of 0.0609151 on 1 procs for 1 steps with 1246 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5115.51595658813 -5115.51595658813 -5115.51891707389 Force two-norm initial, final = 14.497717 6.1487322 Force max component initial, final = 11.702284 5.9246901 Final line search alpha, max atom move = 8.5453403e-05 0.00050628493 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.058946 | 0.058946 | 0.058946 | 0.0 | 96.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049737 | 0.00049737 | 0.00049737 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001471 | | | 2.42 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7292.00 ave 7292 max 7292 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: 170224.0 ave 170224 max 170224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170224 Ave neighs/atom = 136.61637 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.202 | 5.202 | 5.202 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5115.5189 0 -5115.5189 -246.33403 Loop time of 6.184e-06 on 1 procs for 0 steps with 1246 atoms 177.9% 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 | | 6.184e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7292.00 ave 7292 max 7292 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: 170216.0 ave 170216 max 170216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170216 Ave neighs/atom = 136.60995 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.202 | 5.202 | 5.202 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 -5115.5189 -5115.5189 29.118123 100.90345 4.9467557 -246.33403 -246.33403 -653.09646 75.980622 -161.88625 2.2610443 610.29289 Loop time of 6.746e-06 on 1 procs for 0 steps with 1246 atoms 296.5% 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 | | 6.746e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7292.00 ave 7292 max 7292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85108.0 ave 85108 max 85108 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170216.0 ave 170216 max 170216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170216 Ave neighs/atom = 136.60995 Neighbor list builds = 0 Dangerous builds = 0 1246 -5115.51891707389 eV 2.2610442872569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03