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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -71.446821 0.0000000) to (41.247506 71.446821 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3457702 6.4115312 7.0055406 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.446821 0.0000000) to (41.247506 71.446821 7.0055406) create_atoms CPU = 0.008 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3457702 6.4115312 7.0055406 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.446821 0.0000000) to (41.247506 71.446821 7.0055406) create_atoms CPU = 0.008 seconds 1251 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2488 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_876687166519_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.307 | 5.307 | 5.307 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8302.0157 0 -8302.0157 3939.9524 39 0 -8337.9319 0 -8337.9319 938.21978 Loop time of 15.2381 on 1 procs for 39 steps with 2488 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 = -8302.01574048028 -8337.92491855168 -8337.93187462511 Force two-norm initial, final = 41.002022 0.20286799 Force max component initial, final = 4.8591242 0.029598811 Final line search alpha, max atom move = 1.0000000 0.029598811 Iterations, force evaluations = 39 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.204 | 15.204 | 15.204 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014904 | 0.014904 | 0.014904 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01963 | | | 0.13 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8234.00 ave 8234 max 8234 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: 192656.0 ave 192656 max 192656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192656 Ave neighs/atom = 77.434084 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.307 | 5.307 | 5.307 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -8337.9319 0 -8337.9319 938.21978 41290.701 40 0 -8337.9339 0 -8337.9339 719.93772 41302.139 Loop time of 0.571712 on 1 procs for 1 steps with 2488 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8337.9318746251 -8337.9318746251 -8337.93392106831 Force two-norm initial, final = 9.4581243 5.1237168 Force max component initial, final = 8.9835781 4.8532255 Final line search alpha, max atom move = 0.00011131422 0.00054023302 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56932 | 0.56932 | 0.56932 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053908 | 0.00053908 | 0.00053908 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001854 | | | 0.32 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8225.00 ave 8225 max 8225 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: 191232.0 ave 191232 max 191232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191232 Ave neighs/atom = 76.861736 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.445 | 5.445 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8337.9339 0 -8337.9339 719.93772 Loop time of 7.006e-06 on 1 procs for 0 steps with 2488 atoms 185.6% 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 | | 7.006e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8225.00 ave 8225 max 8225 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: 191232.0 ave 191232 max 191232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191232 Ave neighs/atom = 76.861736 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.445 | 5.445 | 5.445 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 -8337.9339 -8337.9339 41.264526 142.89364 7.004591 719.93772 719.93772 -63.262871 2411.3149 -188.23891 2.5491782 1076.1217 Loop time of 8.549e-06 on 1 procs for 0 steps with 2488 atoms 222.2% 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 | | 8.549e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8225.00 ave 8225 max 8225 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95616.0 ave 95616 max 95616 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191232.0 ave 191232 max 191232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191232 Ave neighs/atom = 76.861736 Neighbor list builds = 0 Dangerous builds = 0 2488 -8337.93392106831 eV 2.54917822389295 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17