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 = 2.8552583 2.8552583 2.8552583 Created orthogonal box = (0.0000000 -33.783872 0.0000000) to (41.376624 33.783872 6.9939259) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7287570 4.3436407 4.6626173 Created 835 atoms using lattice units in orthogonal box = (0.0000000 -33.783872 0.0000000) to (41.376624 33.783872 6.9939259) create_atoms CPU = 0.004 seconds 835 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7287570 4.3436407 4.6626173 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -33.783872 0.0000000) to (41.376624 33.783872 6.9939259) create_atoms CPU = 0.003 seconds 841 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 17 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1669 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_942420706858_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.557 | 5.557 | 5.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5313.8358 0 -5313.8358 167752.4 108 0 -6850.6806 0 -6850.6806 -3248.2555 Loop time of 6.10196 on 1 procs for 108 steps with 1669 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 = -5313.83578659131 -6850.67483346001 -6850.68057373235 Force two-norm initial, final = 1759.5746 0.24624330 Force max component initial, final = 326.24930 0.053485194 Final line search alpha, max atom move = 1.0000000 0.053485194 Iterations, force evaluations = 108 203 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9816 | 5.9816 | 5.9816 | 0.0 | 98.03 Neigh | 0.041078 | 0.041078 | 0.041078 | 0.0 | 0.67 Comm | 0.041341 | 0.041341 | 0.041341 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03792 | | | 0.62 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7860.00 ave 7860 max 7860 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: 282450.0 ave 282450 max 282450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 282450 Ave neighs/atom = 169.23307 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -6850.6806 0 -6850.6806 -3248.2555 19553.094 110 0 -6850.7321 0 -6850.7321 -0.21061596 19516.107 Loop time of 0.148744 on 1 procs for 2 steps with 1669 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 = -6850.68057373239 -6850.72632671283 -6850.73213701205 Force two-norm initial, final = 72.906956 0.26538844 Force max component initial, final = 53.111095 0.048730823 Final line search alpha, max atom move = 6.9493047e-05 3.3864534e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14495 | 0.14495 | 0.14495 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090527 | 0.00090527 | 0.00090527 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002889 | | | 1.94 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7861.00 ave 7861 max 7861 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: 281770.0 ave 281770 max 281770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281770 Ave neighs/atom = 168.82564 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.695 | 5.695 | 5.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6850.7321 0 -6850.7321 -0.21061596 Loop time of 6.596e-06 on 1 procs for 0 steps with 1669 atoms 181.9% 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 | | 6.596e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7865.00 ave 7865 max 7865 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: 281874.0 ave 281874 max 281874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281874 Ave neighs/atom = 168.88796 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.695 | 5.695 | 5.695 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 -6850.7321 -6850.7321 41.338975 67.586831 6.9850803 -0.21061596 -0.21061596 2.466025 -1.1807429 -1.91713 2.1855604 1451.5368 Loop time of 6.495e-06 on 1 procs for 0 steps with 1669 atoms 261.7% 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 | | 6.495e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7865.00 ave 7865 max 7865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140937.0 ave 140937 max 140937 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 281874.0 ave 281874 max 281874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281874 Ave neighs/atom = 168.88796 Neighbor list builds = 0 Dangerous builds = 0 1669 -6850.73213701205 eV 2.18556037894201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07