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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -35.599251 0.0000000) to (15.414928 35.599251 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1383093 4.4499063 5.4500000 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -35.599251 0.0000000) to (15.414928 35.599251 5.4500000) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1383093 4.4499063 5.4500000 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -35.599251 0.0000000) to (15.414928 35.599251 5.4500000) create_atoms CPU = 0.000 seconds 204 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 25 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 392 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2472.2824 0 -2472.2824 125133.56 24 0 -6244.1078 0 -6244.1078 80839.316 Loop time of 1.65539 on 1 procs for 24 steps with 392 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 = -2472.28242780702 -6244.10565965908 -6244.10779004773 Force two-norm initial, final = 61.034132 360.87732 Force max component initial, final = 15.855881 82.813689 Final line search alpha, max atom move = 4.1498395e-08 3.4366352e-06 Iterations, force evaluations = 24 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6493 | 1.6493 | 1.6493 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032754 | 0.0032754 | 0.0032754 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002835 | | | 0.17 Nlocal: 392.000 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2104.00 ave 2104 max 2104 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: 23160.0 ave 23160 max 23160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23160 Ave neighs/atom = 59.081633 Neighbor list builds = 0 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -6244.1078 0 -6244.1078 80839.316 5981.4827 25 0 -6244.1093 0 -6244.1093 79441.942 5981.5348 Loop time of 0.0314492 on 1 procs for 1 steps with 392 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 = -6244.10779004765 -6244.10779004765 -6244.10931230918 Force two-norm initial, final = 635.97071 1121.2761 Force max component initial, final = 326.59927 320.70408 Final line search alpha, max atom move = 3.0618562e-06 0.00098194977 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.03111 | 0.03111 | 0.03111 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.8389e-05 | 5.8389e-05 | 5.8389e-05 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002805 | | | 0.89 Nlocal: 392.000 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2098.00 ave 2098 max 2098 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: 23112.0 ave 23112 max 23112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23112 Ave neighs/atom = 58.959184 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.573 | 4.573 | 4.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6244.1093 0 -6244.1093 79441.942 Loop time of 2.098e-06 on 1 procs for 0 steps with 392 atoms 143.0% 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 | | 2.098e-06 | | |100.00 Nlocal: 392.000 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2098.00 ave 2098 max 2098 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: 23112.0 ave 23112 max 23112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23112 Ave neighs/atom = 58.959184 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.573 | 4.573 | 4.573 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 -6244.1093 -6244.1093 15.414971 71.198696 5.4500171 79441.942 79441.942 76486.027 75937.742 85902.058 0.0056896045 201.04754 Loop time of 2.313e-06 on 1 procs for 0 steps with 392 atoms 172.9% 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 | | 2.313e-06 | | |100.00 Nlocal: 392.000 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2098.00 ave 2098 max 2098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11556.0 ave 11556 max 11556 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23112.0 ave 23112 max 23112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23112 Ave neighs/atom = 58.959184 Neighbor list builds = 0 Dangerous builds = 0 392 -6244.10931230918 eV 0.00568960448903845 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01