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 = 3.6284422 3.6284422 3.6284422 Created orthogonal box = (0.0000000 -37.002995 0.0000000) to (18.501497 37.002995 3.6284422) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2695763 4.2695763 3.6284422 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -37.002995 0.0000000) to (18.501497 37.002995 3.6284422) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2695763 4.2695763 3.6284422 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -37.002995 0.0000000) to (18.501497 37.002995 3.6284422) create_atoms CPU = 0.000 seconds 210 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 20 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 418 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1112.8182 0 -1112.8182 312459.5 61 0 -1746.6541 0 -1746.6541 9548.0833 Loop time of 0.392738 on 1 procs for 61 steps with 418 atoms 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1112.81823168028 -1746.6525226408 -1746.6540923819 Force two-norm initial, final = 1567.1479 0.15224646 Force max component initial, final = 504.62521 0.037508183 Final line search alpha, max atom move = 1.0000000 0.037508183 Iterations, force evaluations = 61 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38578 | 0.38578 | 0.38578 | 0.0 | 98.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039915 | 0.0039915 | 0.0039915 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002963 | | | 0.75 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4142.00 ave 4142 max 4142 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: 59240.0 ave 59240 max 59240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59240 Ave neighs/atom = 141.72249 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -1746.6541 0 -1746.6541 9548.0833 4968.1415 464 0 -1758.5117 0 -1758.5117 -769.84267 4993.9419 Loop time of 1.76329 on 1 procs for 403 steps with 418 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 = -1746.6540923819 -1758.51013089764 -1758.5116917151 Force two-norm initial, final = 82.104803 5.4362319 Force max component initial, final = 81.866105 4.1549645 Final line search alpha, max atom move = 0.00054686524 0.0022722057 Iterations, force evaluations = 403 471 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6312 | 1.6312 | 1.6312 | 0.0 | 92.51 Neigh | 0.044284 | 0.044284 | 0.044284 | 0.0 | 2.51 Comm | 0.016005 | 0.016005 | 0.016005 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07184 | | | 4.07 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3674.00 ave 3674 max 3674 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: 64704.0 ave 64704 max 64704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64704 Ave neighs/atom = 154.79426 Neighbor list builds = 11 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1758.5117 0 -1758.5117 -769.84267 Loop time of 1.896e-06 on 1 procs for 0 steps with 418 atoms 158.2% 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 | | 1.896e-06 | | |100.00 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3674.00 ave 3674 max 3674 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: 64700.0 ave 64700 max 64700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64700 Ave neighs/atom = 154.78469 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.599 | 4.599 | 4.599 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 -1758.5117 -1758.5117 20.155018 62.665933 3.9539283 -769.84267 -769.84267 -548.38672 -1128.7527 -632.38854 2.2674195 369.63019 Loop time of 1.804e-06 on 1 procs for 0 steps with 418 atoms 166.3% 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 | | 1.804e-06 | | |100.00 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3674.00 ave 3674 max 3674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32350.0 ave 32350 max 32350 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64700.0 ave 64700 max 64700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64700 Ave neighs/atom = 154.78469 Neighbor list builds = 0 Dangerous builds = 0 418 -1758.5116917151 eV 2.26741953151602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02