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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -41.389674 0.0000000) to (6.3364738 41.389674 8.9611272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3364738 5.1737092 5.9740848 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -41.389674 0.0000000) to (6.3364738 41.389674 8.9611272) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3364738 5.1737092 5.9740848 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -41.389674 0.0000000) to (6.3364738 41.389674 8.9611272) create_atoms CPU = 0.001 seconds 198 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 2 22 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 387 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 2 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1051.3015 0 -1051.3015 235074.99 237 0 -1562.793 0 -1562.793 -50559.909 Loop time of 1.80655 on 1 procs for 237 steps with 387 atoms 86.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1051.30146799998 -1562.79151899274 -1562.79299982598 Force two-norm initial, final = 1669.9255 0.10643409 Force max component initial, final = 681.95401 0.013177712 Final line search alpha, max atom move = 1.0000000 0.013177712 Iterations, force evaluations = 237 456 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7549 | 1.7549 | 1.7549 | 0.0 | 97.14 Neigh | 0.021237 | 0.021237 | 0.021237 | 0.0 | 1.18 Comm | 0.017037 | 0.017037 | 0.017037 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01334 | | | 0.74 Nlocal: 387.000 ave 387 max 387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3767.00 ave 3767 max 3767 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: 59946.0 ave 59946 max 59946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59946 Ave neighs/atom = 154.89922 Neighbor list builds = 5 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 2 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 237 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press Volume 237 0 -1562.793 0 -1562.793 -50559.909 4700.3725 262 0 -1566.0938 0 -1566.0938 -418.40098 4525.8656 Loop time of 0.114925 on 1 procs for 25 steps with 387 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1562.79299982598 -1566.09280521626 -1566.09376229827 Force two-norm initial, final = 262.93531 2.4671807 Force max component initial, final = 181.17695 1.5461107 Final line search alpha, max atom move = 0.00033901198 0.00052415005 Iterations, force evaluations = 25 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10505 | 0.10505 | 0.10505 | 0.0 | 91.41 Neigh | 0.0043241 | 0.0043241 | 0.0043241 | 0.0 | 3.76 Comm | 0.0010532 | 0.0010532 | 0.0010532 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004498 | | | 3.91 Nlocal: 387.000 ave 387 max 387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3868.00 ave 3868 max 3868 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: 61228.0 ave 61228 max 61228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61228 Ave neighs/atom = 158.21189 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 2 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.654 | 4.654 | 4.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1566.0938 0 -1566.0938 -418.40098 Loop time of 2.511e-06 on 1 procs for 0 steps with 387 atoms 159.3% 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 | | 2.511e-06 | | |100.00 Nlocal: 387.000 ave 387 max 387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3895.00 ave 3895 max 3895 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: 61378.0 ave 61378 max 61378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61378 Ave neighs/atom = 158.59948 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 2 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.654 | 4.654 | 4.654 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 -1566.0938 -1566.0938 6.3361821 81.452118 8.7694353 -418.40098 -418.40098 -485.76163 -233.81947 -535.62184 2.3011185 1311.4535 Loop time of 3.083e-06 on 1 procs for 0 steps with 387 atoms 227.1% 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 | | 3.083e-06 | | |100.00 Nlocal: 387.000 ave 387 max 387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3895.00 ave 3895 max 3895 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30689.0 ave 30689 max 30689 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61378.0 ave 61378 max 61378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61378 Ave neighs/atom = 158.59948 Neighbor list builds = 0 Dangerous builds = 0 387 -1566.09376229827 eV 2.30111851537922 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02