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 = 4.0499992 4.0499992 4.0499992 Created orthogonal box = (0.0000000 -41.302050 0.0000000) to (35.768624 41.302050 7.0148043) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4200095 6.3541615 7.0148043 Created 620 atoms using lattice units in orthogonal box = (0.0000000 -41.302050 0.0000000) to (35.768624 41.302050 7.0148043) create_atoms CPU = 0.001 seconds 620 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4200095 6.3541615 7.0148043 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.302050 0.0000000) to (35.768624 41.302050 7.0148043) create_atoms CPU = 0.001 seconds 629 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1247 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_262519520678_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3696.3154 0 -3696.3154 35622.881 109 0 -4160.5571 0 -4160.5571 4250.8009 Loop time of 12.2701 on 1 procs for 109 steps with 1247 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3696.31544984983 -4160.55351352706 -4160.557112214 Force two-norm initial, final = 444.94306 0.16643436 Force max component initial, final = 106.11604 0.027116511 Final line search alpha, max atom move = 1.0000000 0.027116511 Iterations, force evaluations = 109 202 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.218 | 12.218 | 12.218 | 0.0 | 99.58 Neigh | 0.023716 | 0.023716 | 0.023716 | 0.0 | 0.19 Comm | 0.011487 | 0.011487 | 0.011487 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01642 | | | 0.13 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4505.00 ave 4505 max 4505 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: 100864.0 ave 100864 max 100864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100864 Ave neighs/atom = 80.885325 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -4160.5571 0 -4160.5571 4250.8009 20726.186 117 0 -4160.8829 0 -4160.8829 79.812583 20837.073 Loop time of 0.551416 on 1 procs for 8 steps with 1247 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4160.557112214 -4160.8813764756 -4160.88291897191 Force two-norm initial, final = 107.94263 1.8311294 Force max component initial, final = 96.159319 1.1944868 Final line search alpha, max atom move = 0.00028307684 0.00033813156 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54878 | 0.54878 | 0.54878 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036961 | 0.00036961 | 0.00036961 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002264 | | | 0.41 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4619.00 ave 4619 max 4619 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: 100798.0 ave 100798 max 100798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100798 Ave neighs/atom = 80.832398 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.150 | 5.150 | 5.150 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4160.8829 0 -4160.8829 79.812583 Loop time of 1.853e-06 on 1 procs for 0 steps with 1247 atoms 161.9% 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 | | 1.853e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4796.00 ave 4796 max 4796 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: 98790.0 ave 98790 max 98790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98790 Ave neighs/atom = 79.222133 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.150 | 5.150 | 5.150 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 -4160.8829 -4160.8829 35.74999 83.221943 7.0036258 79.812583 79.812583 69.872003 92.531854 77.033893 2.4254587 1020.0811 Loop time of 2.01e-06 on 1 procs for 0 steps with 1247 atoms 199.0% 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 | | 2.01e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4796.00 ave 4796 max 4796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49395.0 ave 49395 max 49395 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98790.0 ave 98790 max 98790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98790 Ave neighs/atom = 79.222133 Neighbor list builds = 0 Dangerous builds = 0 1247 -4160.88291897191 eV 2.42545868381877 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13