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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -62.179130 0.0000000) to (35.897105 62.179130 6.0968202) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226316 5.5798625 6.0968202 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179130 0.0000000) to (35.897105 62.179130 6.0968202) create_atoms CPU = 0.002 seconds 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226316 5.5798625 6.0968202 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179130 0.0000000) to (35.897105 62.179130 6.0968202) create_atoms CPU = 0.002 seconds 1250 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 32 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2472 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.541 | 6.541 | 6.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10915.399 0 -10915.399 -2565.725 79 0 -10957.2 0 -10957.2 -10470.231 Loop time of 2.98749 on 1 procs for 79 steps with 2472 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 = -10915.3992739818 -10957.1905151538 -10957.2001548217 Force two-norm initial, final = 26.429942 0.41992866 Force max component initial, final = 4.4539317 0.082455398 Final line search alpha, max atom move = 1.0000000 0.082455398 Iterations, force evaluations = 79 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8796 | 2.8796 | 2.8796 | 0.0 | 96.39 Neigh | 0.07537 | 0.07537 | 0.07537 | 0.0 | 2.52 Comm | 0.017277 | 0.017277 | 0.017277 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01527 | | | 0.51 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11988.0 ave 11988 max 11988 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: 434358.0 ave 434358 max 434358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434358 Ave neighs/atom = 175.71117 Neighbor list builds = 3 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.538 | 6.538 | 6.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -10957.2 0 -10957.2 -10470.231 27216.824 82 0 -10957.517 0 -10957.517 -2812.3789 27104.588 Loop time of 0.103724 on 1 procs for 3 steps with 2472 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 = -10957.2001548216 -10957.5141935407 -10957.5168953776 Force two-norm initial, final = 217.26984 4.0139215 Force max component initial, final = 159.54845 3.7367840 Final line search alpha, max atom move = 5.5488433e-05 0.00020734829 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10129 | 0.10129 | 0.10129 | 0.0 | 97.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042246 | 0.00042246 | 0.00042246 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002014 | | | 1.94 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11812.0 ave 11812 max 11812 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: 434426.0 ave 434426 max 434426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434426 Ave neighs/atom = 175.73867 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.677 | 6.677 | 6.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10957.517 0 -10957.517 -2812.3789 Loop time of 1.783e-06 on 1 procs for 0 steps with 2472 atoms 112.2% 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 | | 1.783e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11874.0 ave 11874 max 11874 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: 434704.0 ave 434704 max 434704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434704 Ave neighs/atom = 175.85113 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.677 | 6.677 | 6.677 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 -10957.517 -10957.517 35.815788 124.35826 6.0854635 -2812.3789 -2812.3789 -81.357185 -8576.2528 220.4732 2.2795864 1000.1909 Loop time of 2.066e-06 on 1 procs for 0 steps with 2472 atoms 242.0% 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 | | 2.066e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11874.0 ave 11874 max 11874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217352.0 ave 217352 max 217352 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 434704.0 ave 434704 max 434704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434704 Ave neighs/atom = 175.85113 Neighbor list builds = 0 Dangerous builds = 0 2472 -10957.5168953776 eV 2.27958644769778 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03