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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -48.993630 0.0000000) to (40.003131 48.993630 9.8982079) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7147330 5.6659300 6.5988053 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -48.993630 0.0000000) to (40.003131 48.993630 9.8982079) create_atoms CPU = 0.002 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7147330 5.6659300 6.5988053 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -48.993630 0.0000000) to (40.003131 48.993630 9.8982079) create_atoms CPU = 0.001 seconds 1183 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2336 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.930 | 6.930 | 6.930 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8870.1842 0 -8870.1842 15032.774 81 0 -9095.4246 0 -9095.4246 976.51867 Loop time of 4.70277 on 1 procs for 81 steps with 2336 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8870.18419907677 -9095.41709320891 -9095.42458854797 Force two-norm initial, final = 243.59298 0.20221912 Force max component initial, final = 40.314268 0.017853782 Final line search alpha, max atom move = 1.0000000 0.017853782 Iterations, force evaluations = 81 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5993 | 4.5993 | 4.5993 | 0.0 | 97.80 Neigh | 0.070348 | 0.070348 | 0.070348 | 0.0 | 1.50 Comm | 0.015816 | 0.015816 | 0.015816 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01729 | | | 0.37 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10600.0 ave 10600 max 10600 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: 574658.0 ave 574658 max 574658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574658 Ave neighs/atom = 246.00086 Neighbor list builds = 2 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.929 | 6.929 | 6.929 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -9095.4246 0 -9095.4246 976.51867 38798.968 84 0 -9095.5236 0 -9095.5236 117.71573 38840.47 Loop time of 0.155409 on 1 procs for 3 steps with 2336 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 = -9095.42458854788 -9095.51495097868 -9095.52358988789 Force two-norm initial, final = 67.739065 5.2045203 Force max component initial, final = 62.999815 3.6702870 Final line search alpha, max atom move = 8.1749611e-05 0.00030004453 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15317 | 0.15317 | 0.15317 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036967 | 0.00036967 | 0.00036967 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00187 | | | 1.20 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10264.0 ave 10264 max 10264 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: 574238.0 ave 574238 max 574238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574238 Ave neighs/atom = 245.82106 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 7.067 | 7.067 | 7.067 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9095.5236 0 -9095.5236 117.71573 Loop time of 1.93e-06 on 1 procs for 0 steps with 2336 atoms 155.4% 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 | | 1.93e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10264.0 ave 10264 max 10264 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: 573940.0 ave 573940 max 573940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 573940 Ave neighs/atom = 245.69349 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 7.067 | 7.067 | 7.067 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 -9095.5236 -9095.5236 40.006093 98.252231 9.8813417 117.71573 117.71573 63.645949 151.80942 137.69182 2.5715833 1845.2228 Loop time of 2.205e-06 on 1 procs for 0 steps with 2336 atoms 226.8% 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 | | 2.205e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10264.0 ave 10264 max 10264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 286970.0 ave 286970 max 286970 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 573940.0 ave 573940 max 573940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 573940 Ave neighs/atom = 245.69349 Neighbor list builds = 0 Dangerous builds = 0 2336 -9095.52358988789 eV 2.57158332999374 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05