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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -39.059916 0.0000000) to (27.619532 39.059916 5.1736123) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3300851 6.1673552 5.1736123 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -39.059916 0.0000000) to (27.619532 39.059916 5.1736123) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3300851 6.1673552 5.1736123 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.059916 0.0000000) to (27.619532 39.059916 5.1736123) create_atoms CPU = 0.001 seconds 458 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 ghost atom cutoff = 8 binsize = 4, bins = 7 20 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_942420706858_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 ghost atom cutoff = 8 binsize = 4, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2854.7537 0 -2854.7537 184871.67 676 0 -3720.53 0 -3720.53 -63194.997 Loop time of 9.6595 on 1 procs for 676 steps with 914 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 = -2854.75366589995 -3720.52685253733 -3720.53002737116 Force two-norm initial, final = 643.34332 0.17778263 Force max component initial, final = 137.12780 0.016656309 Final line search alpha, max atom move = 1.0000000 0.016656309 Iterations, force evaluations = 676 1233 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3927 | 9.3927 | 9.3927 | 0.0 | 97.24 Neigh | 0.15587 | 0.15587 | 0.15587 | 0.0 | 1.61 Comm | 0.062631 | 0.062631 | 0.062631 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04833 | | | 0.50 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6098.00 ave 6098 max 6098 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: 154284.0 ave 154284 max 154284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154284 Ave neighs/atom = 168.80088 Neighbor list builds = 17 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 ghost atom cutoff = 8 binsize = 4, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 676 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.990 | 4.990 | 4.990 Mbytes Step Temp E_pair E_mol TotEng Press Volume 676 0 -3720.53 0 -3720.53 -63194.997 11162.758 718 0 -3738.8822 0 -3738.8822 8.7013615 10694.892 Loop time of 0.338376 on 1 procs for 42 steps with 914 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 = -3720.53002737115 -3738.8801546066 -3738.88216292199 Force two-norm initial, final = 871.25743 2.3892332 Force max component initial, final = 767.64148 1.0864577 Final line search alpha, max atom move = 0.00019081527 0.00020731273 Iterations, force evaluations = 42 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32681 | 0.32681 | 0.32681 | 0.0 | 96.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019859 | 0.0019859 | 0.0019859 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009577 | | | 2.83 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6095.00 ave 6095 max 6095 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: 154236.0 ave 154236 max 154236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154236 Ave neighs/atom = 168.74836 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 ghost atom cutoff = 8 binsize = 4, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.135 | 5.135 | 5.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3738.8822 0 -3738.8822 8.7013615 Loop time of 1.713e-06 on 1 procs for 0 steps with 914 atoms 116.8% 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 | | 1.713e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6544.00 ave 6544 max 6544 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: 156928.0 ave 156928 max 156928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156928 Ave neighs/atom = 171.69365 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 ghost atom cutoff = 8 binsize = 4, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 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 -3738.8822 -3738.8822 27.835162 77.439607 4.9615746 8.7013615 8.7013615 -73.030522 -56.954438 156.08904 2.2767007 2773.8869 Loop time of 1.747e-06 on 1 procs for 0 steps with 914 atoms 229.0% 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 | | 1.747e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6544.00 ave 6544 max 6544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78464.0 ave 78464 max 78464 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156928.0 ave 156928 max 156928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156928 Ave neighs/atom = 171.69365 Neighbor list builds = 0 Dangerous builds = 0 914 -3738.88216292199 eV 2.27670073290053 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10