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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -63.945568 0.0000000) to (36.916901 63.945568 6.2700239) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6795232 5.7383800 6.2700239 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.945568 0.0000000) to (36.916901 63.945568 6.2700239) create_atoms CPU = 0.008 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6795232 5.7383800 6.2700239 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.945568 0.0000000) to (36.916901 63.945568 6.2700239) create_atoms CPU = 0.008 seconds 1249 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2476 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_313717476091_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.202 | 5.202 | 5.202 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8688.0886 0 -8688.0886 3137.458 20 0 -8724.2802 0 -8724.2802 -2316.3313 Loop time of 3.23864 on 1 procs for 20 steps with 2476 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 = -8688.08861689471 -8724.27218678419 -8724.28023788625 Force two-norm initial, final = 48.777554 0.36479611 Force max component initial, final = 8.9543269 0.064542240 Final line search alpha, max atom move = 1.0000000 0.064542240 Iterations, force evaluations = 20 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2232 | 3.2232 | 3.2232 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0059264 | 0.0059264 | 0.0059264 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00949 | | | 0.29 Nlocal: 2476.00 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7016.00 ave 7016 max 7016 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: 191354.0 ave 191354 max 191354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191354 Ave neighs/atom = 77.283522 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -8724.2802 0 -8724.2802 -2316.3313 29602.942 22 0 -8724.3143 0 -8724.3143 -239.15449 29557.926 Loop time of 0.435342 on 1 procs for 2 steps with 2476 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8724.28023788624 -8724.31423986603 -8724.31425261872 Force two-norm initial, final = 63.310198 0.50956364 Force max component initial, final = 45.936229 0.29476187 Final line search alpha, max atom move = 0.0023842668 0.00070279095 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43128 | 0.43128 | 0.43128 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087596 | 0.00087596 | 0.00087596 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003185 | | | 0.73 Nlocal: 2476.00 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7174.00 ave 7174 max 7174 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: 191320.0 ave 191320 max 191320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191320 Ave neighs/atom = 77.269790 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.342 | 5.342 | 5.342 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8724.3143 0 -8724.3143 -239.15449 Loop time of 6.946e-06 on 1 procs for 0 steps with 2476 atoms 187.2% 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 | | 6.946e-06 | | |100.00 Nlocal: 2476.00 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7212.00 ave 7212 max 7212 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: 191322.0 ave 191322 max 191322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191322 Ave neighs/atom = 77.270598 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.342 | 5.342 | 5.342 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 -8724.3143 -8724.3143 36.888773 127.89114 6.2652629 -239.15449 -239.15449 15.965285 -727.47346 -5.9552937 2.2705098 1217.984 Loop time of 8.851e-06 on 1 procs for 0 steps with 2476 atoms 248.6% 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 | | 8.851e-06 | | |100.00 Nlocal: 2476.00 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7212.00 ave 7212 max 7212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95661.0 ave 95661 max 95661 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191322.0 ave 191322 max 191322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191322 Ave neighs/atom = 77.270598 Neighbor list builds = 0 Dangerous builds = 0 2476 -8724.31425261872 eV 2.27050975237972 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04