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 -71.573350 0.0000000) to (43.829547 71.573350 8.8549056) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0687231 5.1123821 5.9032704 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.573350 0.0000000) to (43.829547 71.573350 8.8549056) create_atoms CPU = 0.012 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0687231 5.1123821 5.9032704 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.573350 0.0000000) to (43.829547 71.573350 8.8549056) create_atoms CPU = 0.010 seconds 2358 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 = 12 39 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 4680 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 = 12 39 3 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) = 11.54 | 11.54 | 11.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15870.432 0 -15870.432 34431.374 93 0 -16520.629 0 -16520.629 -2205.6896 Loop time of 11.396 on 1 procs for 93 steps with 4680 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 = -15870.4320287718 -16520.6149702599 -16520.6288732995 Force two-norm initial, final = 1012.4085 0.40865177 Force max component initial, final = 187.97878 0.061793112 Final line search alpha, max atom move = 1.0000000 0.061793112 Iterations, force evaluations = 93 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.148 | 11.148 | 11.148 | 0.0 | 97.82 Neigh | 0.10376 | 0.10376 | 0.10376 | 0.0 | 0.91 Comm | 0.058537 | 0.058537 | 0.058537 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08573 | | | 0.75 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14329.0 ave 14329 max 14329 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: 656028.0 ave 656028 max 656028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 656028 Ave neighs/atom = 140.17692 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 12 39 3 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 : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.53 | 11.53 | 11.53 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -16520.629 0 -16520.629 -2205.6896 55556.165 95 0 -16520.713 0 -16520.713 -2.1952086 55467.24 Loop time of 0.319385 on 1 procs for 2 steps with 4680 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16520.6288732994 -16520.7005874177 -16520.7127538274 Force two-norm initial, final = 138.62887 5.9219701 Force max component initial, final = 102.52124 4.7777739 Final line search alpha, max atom move = 3.8344016e-05 0.00018319904 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31197 | 0.31197 | 0.31197 | 0.0 | 97.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014823 | 0.0014823 | 0.0014823 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005927 | | | 1.86 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13793.0 ave 13793 max 13793 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: 655368.0 ave 655368 max 655368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 655368 Ave neighs/atom = 140.03590 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 = 12 39 3 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) = 11.05 | 11.05 | 11.05 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16520.713 0 -16520.713 -2.1952086 Loop time of 6.385e-06 on 1 procs for 0 steps with 4680 atoms 203.6% 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 | | 6.385e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13793.0 ave 13793 max 13793 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: 655500.0 ave 655500 max 655500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 655500 Ave neighs/atom = 140.06410 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 = 12 39 3 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) = 11.05 | 11.05 | 11.05 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 -16520.713 -16520.713 43.798263 143.19302 8.8441853 -2.1952086 -2.1952086 -137.90795 39.123571 92.198755 2.2744281 1753.7898 Loop time of 7.027e-06 on 1 procs for 0 steps with 4680 atoms 298.8% 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 | | 7.027e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13793.0 ave 13793 max 13793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327750.0 ave 327750 max 327750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 655500.0 ave 655500 max 655500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 655500 Ave neighs/atom = 140.06410 Neighbor list builds = 0 Dangerous builds = 0 4680 -16520.7118135745 eV 2.2744281385725 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13