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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -76.075623 0.0000000) to (38.037812 76.075623 4.0320000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5560849 5.5560849 4.0320000 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -76.075623 0.0000000) to (38.037812 76.075623 4.0320000) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5560849 5.5560849 4.0320000 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.075623 0.0000000) to (38.037812 76.075623 4.0320000) create_atoms CPU = 0.003 seconds 714 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 35 1 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1420 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.537 | 5.537 | 5.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4603.8601 0 -4603.8601 12620.556 139 0 -4762.7654 0 -4762.7654 567.79149 Loop time of 7.73619 on 1 procs for 139 steps with 1420 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 = -4603.86010172916 -4762.76168893904 -4762.7653578222 Force two-norm initial, final = 259.68520 0.13938966 Force max component initial, final = 86.299845 0.025856319 Final line search alpha, max atom move = 1.0000000 0.025856319 Iterations, force evaluations = 139 254 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.567 | 7.567 | 7.567 | 0.0 | 97.81 Neigh | 0.064908 | 0.064908 | 0.064908 | 0.0 | 0.84 Comm | 0.059545 | 0.059545 | 0.059545 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0447 | | | 0.58 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 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: 249604.0 ave 249604 max 249604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249604 Ave neighs/atom = 175.77746 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 139 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.537 | 5.537 | 5.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 139 0 -4762.7654 0 -4762.7654 567.79149 23335.202 142 0 -4762.7995 0 -4762.7995 -17.301496 23352.028 Loop time of 0.149678 on 1 procs for 3 steps with 1420 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 = -4762.76535782219 -4762.79841436158 -4762.79948576608 Force two-norm initial, final = 30.217408 0.67136246 Force max component initial, final = 26.890327 0.64864185 Final line search alpha, max atom move = 0.00013090985 8.4913607e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14537 | 0.14537 | 0.14537 | 0.0 | 97.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010059 | 0.0010059 | 0.0010059 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0033 | | | 2.21 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 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: 249240.0 ave 249240 max 249240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249240 Ave neighs/atom = 175.52113 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.675 | 5.675 | 5.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4762.7995 0 -4762.7995 -17.301496 Loop time of 6.836e-06 on 1 procs for 0 steps with 1420 atoms 175.5% 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 | | 6.836e-06 | | |100.00 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 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: 249160.0 ave 249160 max 249160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249160 Ave neighs/atom = 175.46479 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.675 | 5.675 | 5.675 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 -4762.7995 -4762.7995 37.983784 152.43281 4.033183 -17.301496 -17.301496 -44.439936 -3.6247439 -3.8398071 2.5602961 577.36799 Loop time of 7.447e-06 on 1 procs for 0 steps with 1420 atoms 241.7% 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 | | 7.447e-06 | | |100.00 Nlocal: 1420.00 ave 1420 max 1420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124580.0 ave 124580 max 124580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249160.0 ave 249160 max 249160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249160 Ave neighs/atom = 175.46479 Neighbor list builds = 0 Dangerous builds = 0 1420 -4762.79948576608 eV 2.56029610785947 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08