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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -48.936338 0.0000000) to (59.934529 48.936338 9.9204338) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7471466 6.0332471 6.6136225 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -48.936338 0.0000000) to (59.934529 48.936338 9.9204338) create_atoms CPU = 0.006 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7471466 6.0332471 6.6136225 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -48.936338 0.0000000) to (59.934529 48.936338 9.9204338) create_atoms CPU = 0.004 seconds 1757 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 15 24 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 3503 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_678952612413_000#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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.013 | 7.013 | 7.013 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11630.117 0 -11630.117 4510.0376 22 0 -11742.583 0 -11742.583 3147.7374 Loop time of 1.06808 on 1 procs for 22 steps with 3503 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 = -11630.1166752897 -11742.572989069 -11742.583393856 Force two-norm initial, final = 41.240504 0.25366323 Force max component initial, final = 5.1960297 0.040494833 Final line search alpha, max atom move = 1.0000000 0.040494833 Iterations, force evaluations = 22 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0559 | 1.0559 | 1.0559 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0048454 | 0.0048454 | 0.0048454 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007333 | | | 0.69 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10988.0 ave 10988 max 10988 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: 494244.0 ave 494244 max 494244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 494244 Ave neighs/atom = 141.09164 Neighbor list builds = 0 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.013 | 7.013 | 7.013 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -11742.583 0 -11742.583 3147.7374 58192.796 29 0 -11743.304 0 -11743.304 -30.227249 58425.399 Loop time of 0.26216 on 1 procs for 7 steps with 3503 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 = -11742.5833938561 -11743.2932621835 -11743.3038921111 Force two-norm initial, final = 246.36561 2.1071187 Force max component initial, final = 232.30753 1.7087964 Final line search alpha, max atom move = 5.6634614e-05 9.6777026e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25585 | 0.25585 | 0.25585 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083149 | 0.00083149 | 0.00083149 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005482 | | | 2.09 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10988.0 ave 10988 max 10988 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: 500082.0 ave 500082 max 500082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 500082 Ave neighs/atom = 142.75821 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.151 | 7.151 | 7.151 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11743.304 0 -11743.304 -30.227249 Loop time of 1.986e-06 on 1 procs for 0 steps with 3503 atoms 151.1% 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 | | 1.986e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10966.0 ave 10966 max 10966 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: 498252.0 ave 498252 max 498252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498252 Ave neighs/atom = 142.23580 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.151 | 7.151 | 7.151 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 -11743.304 -11743.304 59.890056 98.541574 9.899824 -30.227249 -30.227249 -46.824875 -27.860625 -15.996249 2.5318738 2095.7277 Loop time of 2.705e-06 on 1 procs for 0 steps with 3503 atoms 221.8% 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 | | 2.705e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10966.0 ave 10966 max 10966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 249126.0 ave 249126 max 249126 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 498252.0 ave 498252 max 498252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498252 Ave neighs/atom = 142.23580 Neighbor list builds = 0 Dangerous builds = 0 3503 -11743.3038921111 eV 2.53187384222376 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02