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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -68.958756 0.0000000) to (39.811275 68.958756 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8737947 5.2752575 6.2429061 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -68.958756 0.0000000) to (39.811275 68.958756 6.2429061) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8737947 5.2752575 6.2429061 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -68.958756 0.0000000) to (39.811275 68.958756 6.2429061) create_atoms CPU = 0.002 seconds 1466 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 46 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2902 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.782 | 5.782 | 5.782 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12246.646 0 -12246.646 -2147.9273 566 0 -12351.02 0 -12351.02 -21489.446 Loop time of 264.092 on 1 procs for 566 steps with 2902 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 = -12246.6456022632 -12351.0084371955 -12351.0195882245 Force two-norm initial, final = 29.971344 0.32193725 Force max component initial, final = 5.4124911 0.063681286 Final line search alpha, max atom move = 1.0000000 0.063681286 Iterations, force evaluations = 566 1069 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 262.97 | 262.97 | 262.97 | 0.0 | 99.57 Neigh | 0.69839 | 0.69839 | 0.69839 | 0.0 | 0.26 Comm | 0.18496 | 0.18496 | 0.18496 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2431 | | | 0.09 Nlocal: 2902.00 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9281.00 ave 9281 max 9281 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: 194948.0 ave 194948 max 194948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194948 Ave neighs/atom = 67.177119 Neighbor list builds = 20 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 566 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.399 | 5.399 | 5.399 Mbytes Step Temp E_pair E_mol TotEng Press Volume 566 0 -12351.02 0 -12351.02 -21489.446 34277.75 579 0 -12354.656 0 -12354.656 -5709.1966 33937.206 Loop time of 4.72689 on 1 procs for 13 steps with 2902 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 = -12351.0195882246 -12354.6561766232 -12354.6562073065 Force two-norm initial, final = 645.71931 1.2770813 Force max component initial, final = 631.38386 0.55158928 Final line search alpha, max atom move = 0.00090091290 0.00049693390 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7104 | 4.7104 | 4.7104 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021867 | 0.0021867 | 0.0021867 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01427 | | | 0.30 Nlocal: 2902.00 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9288.00 ave 9288 max 9288 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: 194892.0 ave 194892 max 194892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194892 Ave neighs/atom = 67.157822 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.917 | 5.917 | 5.917 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12354.656 0 -12354.656 -5709.1966 Loop time of 3.583e-06 on 1 procs for 0 steps with 2902 atoms 139.5% 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 | | 3.583e-06 | | |100.00 Nlocal: 2902.00 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9286.00 ave 9286 max 9286 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: 198384.0 ave 198384 max 198384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198384 Ave neighs/atom = 68.361130 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.917 | 5.917 | 5.917 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 -12354.656 -12354.656 39.342028 137.91751 6.2546056 -5709.1966 -5709.1966 25.733612 -17176.201 22.878106 2.2560124 3713.1655 Loop time of 3.638e-06 on 1 procs for 0 steps with 2902 atoms 192.4% 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 | | 3.638e-06 | | |100.00 Nlocal: 2902.00 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9286.00 ave 9286 max 9286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99192.0 ave 99192 max 99192 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 198384.0 ave 198384 max 198384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198384 Ave neighs/atom = 68.361130 Neighbor list builds = 0 Dangerous builds = 0 2902 -12354.6562073065 eV 2.25601237001537 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:04:30