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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -53.129434 0.0000000) to (18.784091 53.129434 5.1123821) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8699496 5.9032704 5.1123821 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.129434 0.0000000) to (18.784091 53.129434 5.1123821) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8699496 5.9032704 5.1123821 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.129434 0.0000000) to (18.784091 53.129434 5.1123821) create_atoms CPU = 0.001 seconds 434 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 29 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 862 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_346334655118_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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.000 | 5.000 | 5.000 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2472.069 0 -2472.069 148808.15 98 0 -3041.0838 0 -3041.0838 2827.0522 Loop time of 1.18209 on 1 procs for 98 steps with 862 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 = -2472.06900052805 -3041.08084726322 -3041.08382513586 Force two-norm initial, final = 1699.3388 0.17309478 Force max component initial, final = 454.95820 0.041362743 Final line search alpha, max atom move = 1.0000000 0.041362743 Iterations, force evaluations = 98 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1446 | 1.1446 | 1.1446 | 0.0 | 96.83 Neigh | 0.016341 | 0.016341 | 0.016341 | 0.0 | 1.38 Comm | 0.01197 | 0.01197 | 0.01197 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00915 | | | 0.77 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6161.00 ave 6161 max 6161 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: 121000.0 ave 121000 max 121000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121000 Ave neighs/atom = 140.37123 Neighbor list builds = 2 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -3041.0838 0 -3041.0838 2827.0522 10204.194 100 0 -3041.1063 0 -3041.1063 2.7683857 10224.965 Loop time of 0.0332737 on 1 procs for 2 steps with 862 atoms 93.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3041.08382513586 -3041.10454180542 -3041.10632577727 Force two-norm initial, final = 32.376553 1.0949601 Force max component initial, final = 23.229011 0.86128579 Final line search alpha, max atom move = 0.00020126457 0.00017334631 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.03207 | 0.03207 | 0.03207 | 0.0 | 96.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023567 | 0.00023567 | 0.00023567 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009679 | | | 2.91 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5808.00 ave 5808 max 5808 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: 121016.0 ave 121016 max 121016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121016 Ave neighs/atom = 140.38979 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.135 | 5.135 | 5.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3041.1063 0 -3041.1063 2.7683857 Loop time of 2.501e-06 on 1 procs for 0 steps with 862 atoms 159.9% 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 | | 2.501e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5808.00 ave 5808 max 5808 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: 120960.0 ave 120960 max 120960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120960 Ave neighs/atom = 140.32483 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.135 | 5.135 | 5.135 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 -3041.1063 -3041.1063 18.800824 106.38959 5.1119409 2.7683857 2.7683857 135.07733 -98.305988 -28.466188 2.3401251 489.03466 Loop time of 2.365e-06 on 1 procs for 0 steps with 862 atoms 211.4% 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 | | 2.365e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5808.00 ave 5808 max 5808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60480.0 ave 60480 max 60480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120960.0 ave 120960 max 120960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120960 Ave neighs/atom = 140.32483 Neighbor list builds = 0 Dangerous builds = 0 862 -3041.10615259394 eV 2.34012512648493 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01