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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -53.177161 0.0000000) to (18.799952 53.177161 4.0545019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8092900 4.9464459 4.0545019 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.177161 0.0000000) to (18.799952 53.177161 4.0545019) create_atoms CPU = 0.004 seconds 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8092900 4.9464459 4.0545019 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.177161 0.0000000) to (18.799952 53.177161 4.0545019) create_atoms CPU = 0.003 seconds 346 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 688 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2669.5118 0 -2669.5118 51893.678 619 0 -2797.6145 0 -2797.6145 -86000.311 Loop time of 14.6412 on 1 procs for 619 steps with 688 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 = -2669.5117893201 -2797.61192387318 -2797.61447337875 Force two-norm initial, final = 195.17351 0.14454904 Force max component initial, final = 53.805381 0.024161052 Final line search alpha, max atom move = 1.0000000 0.024161052 Iterations, force evaluations = 619 1219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.224 | 14.224 | 14.224 | 0.0 | 97.15 Neigh | 0.11818 | 0.11818 | 0.11818 | 0.0 | 0.81 Comm | 0.17535 | 0.17535 | 0.17535 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.124 | | | 0.85 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6397.00 ave 6397 max 6397 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: 101764.0 ave 101764 max 101764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101764 Ave neighs/atom = 147.91279 Neighbor list builds = 7 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 619 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press Volume 619 0 -2797.6145 0 -2797.6145 -86000.311 8106.7987 686 0 -2817.2314 0 -2817.2314 -20614.926 7541.231 Loop time of 0.93055 on 1 procs for 67 steps with 688 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 = -2797.61447337875 -2817.22970324221 -2817.23141068486 Force two-norm initial, final = 669.35592 5.7825377 Force max component initial, final = 629.93101 5.0993688 Final line search alpha, max atom move = 0.0010556200 0.0053829958 Iterations, force evaluations = 67 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86857 | 0.86857 | 0.86857 | 0.0 | 93.34 Neigh | 0.016748 | 0.016748 | 0.016748 | 0.0 | 1.80 Comm | 0.010471 | 0.010471 | 0.010471 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03476 | | | 3.74 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6572.00 ave 6572 max 6572 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: 106276.0 ave 106276 max 106276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106276 Ave neighs/atom = 154.47093 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2817.2314 0 -2817.2314 -20614.926 Loop time of 6.555e-06 on 1 procs for 0 steps with 688 atoms 167.8% 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 | | 6.555e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6597.00 ave 6597 max 6597 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: 106324.0 ave 106324 max 106324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106324 Ave neighs/atom = 154.54070 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.087 | 5.087 | 5.087 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 -2817.2314 -2817.2314 17.686559 106.35432 4.0090711 -20614.926 -20614.926 -1019.2275 -61201.035 375.48473 2.3126508 4179.0464 Loop time of 7.167e-06 on 1 procs for 0 steps with 688 atoms 279.1% 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 | | 7.167e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6597.00 ave 6597 max 6597 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53162.0 ave 53162 max 53162 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106324.0 ave 106324 max 106324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106324 Ave neighs/atom = 154.54070 Neighbor list builds = 0 Dangerous builds = 0 688 -2817.23141068486 eV 2.31265084439695 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16