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 = 2.8675702 2.8675702 2.8675702 Created orthogonal box = (0.0000000 -34.413710 0.0000000) to (12.166070 34.413710 4.0553566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0553566 4.7792836 4.0553566 Created 146 atoms using lattice units in orthogonal box = (0.0000000 -34.413710 0.0000000) to (12.166070 34.413710 4.0553566) create_atoms CPU = 0.001 seconds 146 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0553566 4.7792836 4.0553566 Created 146 atoms using lattice units in orthogonal box = (0.0000000 -34.413710 0.0000000) to (12.166070 34.413710 4.0553566) create_atoms CPU = 0.000 seconds 146 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 286 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_427873955970_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.431 | 4.431 | 4.431 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1188.2337 0 -1188.2337 31922.1 53 0 -1216.5616 0 -1216.5616 -3576.1425 Loop time of 2.93569 on 1 procs for 53 steps with 286 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 = -1188.23365356684 -1216.5605907917 -1216.56155951045 Force two-norm initial, final = 133.98388 0.092515951 Force max component initial, final = 66.738733 0.014246677 Final line search alpha, max atom move = 1.0000000 0.014246677 Iterations, force evaluations = 53 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9294 | 2.9294 | 2.9294 | 0.0 | 99.78 Neigh | 0.0022647 | 0.0022647 | 0.0022647 | 0.0 | 0.08 Comm | 0.002314 | 0.002314 | 0.002314 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00174 | | | 0.06 Nlocal: 286.000 ave 286 max 286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2989.00 ave 2989 max 2989 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: 32952.0 ave 32952 max 32952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32952 Ave neighs/atom = 115.21678 Neighbor list builds = 1 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.432 | 4.432 | 4.432 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1216.5616 0 -1216.5616 -3576.1425 3395.7901 56 0 -1216.5723 0 -1216.5723 -408.83926 3389.288 Loop time of 0.17885 on 1 procs for 3 steps with 286 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 = -1216.56155951045 -1216.57186713367 -1216.57228483363 Force two-norm initial, final = 11.679965 0.10449673 Force max component initial, final = 10.723451 0.021840172 Final line search alpha, max atom move = 0.00041557118 9.0761459e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17821 | 0.17821 | 0.17821 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013211 | 0.00013211 | 0.00013211 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005037 | | | 0.28 Nlocal: 286.000 ave 286 max 286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3066.00 ave 3066 max 3066 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: 32828.0 ave 32828 max 32828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32828 Ave neighs/atom = 114.78322 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.570 | 4.570 | 4.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1216.5723 0 -1216.5723 -408.83926 Loop time of 1.812e-06 on 1 procs for 0 steps with 286 atoms 110.4% 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 | | 1.812e-06 | | |100.00 Nlocal: 286.000 ave 286 max 286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3066.00 ave 3066 max 3066 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: 32948.0 ave 32948 max 32948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32948 Ave neighs/atom = 115.20280 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.570 | 4.570 | 4.570 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 -1216.5723 -1216.5723 12.141045 68.827419 4.0559344 -408.83926 -408.83926 -0.37166979 -1221.3024 -4.843746 2.2442752 247.75192 Loop time of 1.433e-06 on 1 procs for 0 steps with 286 atoms 139.6% 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 | | 1.433e-06 | | |100.00 Nlocal: 286.000 ave 286 max 286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3066.00 ave 3066 max 3066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16474.0 ave 16474 max 16474 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32948.0 ave 32948 max 32948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32948 Ave neighs/atom = 115.20280 Neighbor list builds = 0 Dangerous builds = 0 286 -1216.57228483363 eV 2.24427517727911 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03