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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -67.048293 0.0000000) to (23.705151 67.048293 5.1123844) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0641085 6.2370505 5.1123844 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -67.048293 0.0000000) to (23.705151 67.048293 5.1123844) create_atoms CPU = 0.007 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0641085 6.2370505 5.1123844 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -67.048293 0.0000000) to (23.705151 67.048293 5.1123844) create_atoms CPU = 0.006 seconds 690 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 32 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1376 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.554 | 5.554 | 5.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4748.5043 0 -4748.5043 17765.707 87 0 -4863.461 0 -4863.461 2781.233 Loop time of 5.50262 on 1 procs for 87 steps with 1376 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 = -4748.50427568409 -4863.45675543876 -4863.46097963132 Force two-norm initial, final = 167.36970 0.19042959 Force max component initial, final = 53.050338 0.036654761 Final line search alpha, max atom move = 1.0000000 0.036654761 Iterations, force evaluations = 87 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3966 | 5.3966 | 5.3966 | 0.0 | 98.07 Neigh | 0.038662 | 0.038662 | 0.038662 | 0.0 | 0.70 Comm | 0.039075 | 0.039075 | 0.039075 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02827 | | | 0.51 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9889.00 ave 9889 max 9889 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: 282332.0 ave 282332 max 282332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 282332 Ave neighs/atom = 205.18314 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -4863.461 0 -4863.461 2781.233 16251.145 90 0 -4863.5287 0 -4863.5287 274.07182 16280.238 Loop time of 0.163343 on 1 procs for 3 steps with 1376 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4863.46097963132 -4863.52587155834 -4863.52866618537 Force two-norm initial, final = 60.403718 6.2033471 Force max component initial, final = 54.129439 5.8917296 Final line search alpha, max atom move = 9.8578961e-05 0.00058080058 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15922 | 0.15922 | 0.15922 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010767 | 0.0010767 | 0.0010767 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003042 | | | 1.86 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9869.00 ave 9869 max 9869 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: 280980.0 ave 280980 max 280980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280980 Ave neighs/atom = 204.20058 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.691 | 5.691 | 5.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4863.5287 0 -4863.5287 274.07182 Loop time of 6.576e-06 on 1 procs for 0 steps with 1376 atoms 167.3% 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 | | 6.576e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9869.00 ave 9869 max 9869 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: 280568.0 ave 280568 max 280568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280568 Ave neighs/atom = 203.90116 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.691 | 5.691 | 5.691 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 -4863.5287 -4863.5287 23.755215 133.99454 5.1146352 274.07182 274.07182 581.04351 61.250991 179.92095 2.3899504 540.86257 Loop time of 6.836e-06 on 1 procs for 0 steps with 1376 atoms 307.2% 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 | | 6.836e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9869.00 ave 9869 max 9869 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140284.0 ave 140284 max 140284 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280568.0 ave 280568 max 280568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280568 Ave neighs/atom = 203.90116 Neighbor list builds = 0 Dangerous builds = 0 1376 -4863.52866618537 eV 2.38995035965505 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06