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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -43.551448 0.0000000) to (53.339413 43.551448 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1147382 5.3693566 5.8858683 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.551448 0.0000000) to (53.339413 43.551448 8.8288024) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1147382 5.3693566 5.8858683 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.551448 0.0000000) to (53.339413 43.551448 8.8288024) create_atoms CPU = 0.002 seconds 1756 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 30 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_492310898779_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14569.147 0 -14569.147 28554.364 98 0 -14854.998 0 -14854.998 3738.245 Loop time of 22.6262 on 1 procs for 98 steps with 3506 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14569.1465933716 -14854.9871821291 -14854.9983831386 Force two-norm initial, final = 257.13699 0.31445168 Force max component initial, final = 68.076085 0.053395323 Final line search alpha, max atom move = 1.0000000 0.053395323 Iterations, force evaluations = 98 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.495 | 22.495 | 22.495 | 0.0 | 99.42 Neigh | 0.067355 | 0.067355 | 0.067355 | 0.0 | 0.30 Comm | 0.024547 | 0.024547 | 0.024547 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03916 | | | 0.17 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7961.00 ave 7961 max 7961 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: 270664.0 ave 270664 max 270664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270664 Ave neighs/atom = 77.200228 Neighbor list builds = 3 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.633 | 5.633 | 5.633 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -14854.998 0 -14854.998 3738.245 41018.769 103 0 -14855.396 0 -14855.396 -93.555991 41115.31 Loop time of 0.865601 on 1 procs for 5 steps with 3506 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 = -14854.9983831386 -14855.3949316852 -14855.3962520601 Force two-norm initial, final = 214.49865 4.2131225 Force max component initial, final = 202.62200 2.7565611 Final line search alpha, max atom move = 0.00013279896 0.00036606845 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86102 | 0.86102 | 0.86102 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052816 | 0.00052816 | 0.00052816 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004049 | | | 0.47 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7961.00 ave 7961 max 7961 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: 270562.0 ave 270562 max 270562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270562 Ave neighs/atom = 77.171135 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.770 | 5.770 | 5.770 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14855.396 0 -14855.396 -93.555991 Loop time of 2.181e-06 on 1 procs for 0 steps with 3506 atoms 183.4% 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 | | 2.181e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7951.00 ave 7951 max 7951 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: 270426.0 ave 270426 max 270426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270426 Ave neighs/atom = 77.132345 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.770 | 5.770 | 5.770 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 -14855.396 -14855.396 53.369231 86.916484 8.8636067 -93.555991 -93.555991 -77.946483 -107.18746 -95.534033 2.3205142 1618.8001 Loop time of 2.725e-06 on 1 procs for 0 steps with 3506 atoms 256.9% 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 | | 2.725e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7951.00 ave 7951 max 7951 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135213.0 ave 135213 max 135213 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270426.0 ave 270426 max 270426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270426 Ave neighs/atom = 77.132345 Neighbor list builds = 0 Dangerous builds = 0 3506 -14855.3962520602 eV 2.32051424482017 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24