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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -52.712637 0.0000000) to (24.848975 52.712637 5.7007459) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2313632 6.4734818 5.7007459 Created 450 atoms using lattice units in orthogonal box = (0.0000000 -52.712637 0.0000000) to (24.848975 52.712637 5.7007459) create_atoms CPU = 0.005 seconds 450 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2313632 6.4734818 5.7007459 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -52.712637 0.0000000) to (24.848975 52.712637 5.7007459) create_atoms CPU = 0.004 seconds 458 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 898 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2996.6809 0 -2996.6809 -1206.5583 41 0 -3008.8742 0 -3008.8742 -6884.4324 Loop time of 0.873146 on 1 procs for 41 steps with 898 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 = -2996.68093126392 -3008.87124170676 -3008.87419280528 Force two-norm initial, final = 18.884572 0.14226107 Force max component initial, final = 8.9587938 0.039043419 Final line search alpha, max atom move = 1.0000000 0.039043419 Iterations, force evaluations = 41 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8378 | 0.8378 | 0.8378 | 0.0 | 95.95 Neigh | 0.015872 | 0.015872 | 0.015872 | 0.0 | 1.82 Comm | 0.010252 | 0.010252 | 0.010252 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009224 | | | 1.06 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5331.00 ave 5331 max 5331 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: 117488.0 ave 117488 max 117488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117488 Ave neighs/atom = 130.83296 Neighbor list builds = 1 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3008.8742 0 -3008.8742 -6884.4324 14934.301 47 0 -3009.1863 0 -3009.1863 28.713591 14794.85 Loop time of 0.106279 on 1 procs for 6 steps with 898 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 = -3008.87419280528 -3009.18629998211 -3009.18633554116 Force two-norm initial, final = 111.73322 0.60968388 Force max component initial, final = 73.460511 0.48226083 Final line search alpha, max atom move = 0.0014377348 0.00069336318 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10153 | 0.10153 | 0.10153 | 0.0 | 95.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010764 | 0.0010764 | 0.0010764 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00367 | | | 3.45 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5331.00 ave 5331 max 5331 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: 117500.0 ave 117500 max 117500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117500 Ave neighs/atom = 130.84633 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.117 | 5.117 | 5.117 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3009.1863 0 -3009.1863 28.713591 Loop time of 6.305e-06 on 1 procs for 0 steps with 898 atoms 158.6% 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 | | 6.305e-06 | | |100.00 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5331.00 ave 5331 max 5331 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: 117800.0 ave 117800 max 117800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117800 Ave neighs/atom = 131.18040 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.117 | 5.117 | 5.117 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 -3009.1863 -3009.1863 24.795925 104.91838 5.6869405 28.713591 28.713591 52.113904 35.658062 -1.631193 2.6166021 674.5498 Loop time of 6.896e-06 on 1 procs for 0 steps with 898 atoms 232.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5331.00 ave 5331 max 5331 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58900.0 ave 58900 max 58900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117800.0 ave 117800 max 117800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117800 Ave neighs/atom = 131.18040 Neighbor list builds = 0 Dangerous builds = 0 898 -3009.18633554116 eV 2.61660212350239 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01