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 -44.437331 0.0000000) to (15.710969 44.437331 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7882518 4.6776138 5.0973115 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -44.437331 0.0000000) to (15.710969 44.437331 5.0973115) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7882518 4.6776138 5.0973115 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -44.437331 0.0000000) to (15.710969 44.437331 5.0973115) create_atoms CPU = 0.001 seconds 306 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 = 6 30 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 610 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 = 6 30 2 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) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2387.6769 0 -2387.6769 109754.04 177 0 -2585.2762 0 -2585.2762 5737.0366 Loop time of 8.23353 on 1 procs for 177 steps with 610 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 = -2387.6769449529 -2585.27369350399 -2585.27621033362 Force two-norm initial, final = 589.45352 0.15482402 Force max component initial, final = 170.38920 0.032918356 Final line search alpha, max atom move = 1.0000000 0.032918356 Iterations, force evaluations = 177 334 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.1878 | 8.1878 | 8.1878 | 0.0 | 99.44 Neigh | 0.011337 | 0.011337 | 0.011337 | 0.0 | 0.14 Comm | 0.018572 | 0.018572 | 0.018572 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01583 | | | 0.19 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3511.00 ave 3511 max 3511 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: 44660.0 ave 44660 max 44660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44660 Ave neighs/atom = 73.213115 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 = 6 30 2 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 : 177 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 177 0 -2585.2762 0 -2585.2762 5737.0366 7117.412 197 0 -2586.4886 0 -2586.4886 -4.8189095 7140.1858 Loop time of 0.530405 on 1 procs for 20 steps with 610 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 = -2585.27621033362 -2586.48781398136 -2586.48862805674 Force two-norm initial, final = 112.81023 1.2623156 Force max component initial, final = 100.86105 0.48966658 Final line search alpha, max atom move = 0.00061406575 0.00030068748 Iterations, force evaluations = 20 21 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52204 | 0.52204 | 0.52204 | 0.0 | 98.42 Neigh | 0.0036682 | 0.0036682 | 0.0036682 | 0.0 | 0.69 Comm | 0.00084013 | 0.00084013 | 0.00084013 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003856 | | | 0.73 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3501.00 ave 3501 max 3501 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: 43916.0 ave 43916 max 43916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43916 Ave neighs/atom = 71.993443 Neighbor list builds = 1 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 = 6 31 2 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) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2586.4886 0 -2586.4886 -4.8189095 Loop time of 1.948e-06 on 1 procs for 0 steps with 610 atoms 205.3% 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 | | 1.948e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3518.00 ave 3518 max 3518 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: 43804.0 ave 43804 max 43804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43804 Ave neighs/atom = 71.809836 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 = 6 31 2 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) = 4.647 | 4.647 | 4.647 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 -2586.4886 -2586.4886 15.642431 90.609064 5.0377152 -4.8189095 -4.8189095 76.941195 -112.01985 20.621928 2.342261 1121.359 Loop time of 1.848e-06 on 1 procs for 0 steps with 610 atoms 216.5% 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 | | 1.848e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3518.00 ave 3518 max 3518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21902.0 ave 21902 max 21902 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43804.0 ave 43804 max 43804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43804 Ave neighs/atom = 71.809836 Neighbor list builds = 0 Dangerous builds = 0 610 -2586.48862805674 eV 2.34226096127105 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09