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 -58.563650 0.0000000) to (20.705377 58.563650 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6469210 6.2112962 5.0973115 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.563650 0.0000000) to (20.705377 58.563650 5.0973115) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6469210 6.2112962 5.0973115 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.563650 0.0000000) to (20.705377 58.563650 5.0973115) create_atoms CPU = 0.002 seconds 530 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4353.8179 0 -4353.8179 46185.999 616 0 -4513.8681 0 -4513.8681 -8301.8551 Loop time of 60.5237 on 1 procs for 616 steps with 1058 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4353.81786371663 -4513.86368262895 -4513.86810857138 Force two-norm initial, final = 302.16525 0.19169994 Force max component initial, final = 77.146935 0.023125859 Final line search alpha, max atom move = 1.0000000 0.023125859 Iterations, force evaluations = 616 1134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 60.225 | 60.225 | 60.225 | 0.0 | 99.51 Neigh | 0.15025 | 0.15025 | 0.15025 | 0.0 | 0.25 Comm | 0.077375 | 0.077375 | 0.077375 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07133 | | | 0.12 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5141.00 ave 5141 max 5141 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: 70544.0 ave 70544 max 70544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70544 Ave neighs/atom = 66.676749 Neighbor list builds = 24 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 616 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press Volume 616 0 -4513.8681 0 -4513.8681 -8301.8551 12361.821 648 0 -4524.723 0 -4524.723 -13.431408 12280.209 Loop time of 2.21362 on 1 procs for 32 steps with 1058 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4513.86810857139 -4524.72273153702 -4524.7230383225 Force two-norm initial, final = 587.34545 0.80499348 Force max component initial, final = 534.84255 0.28029828 Final line search alpha, max atom move = 0.00043641541 0.00012232649 Iterations, force evaluations = 32 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1977 | 2.1977 | 2.1977 | 0.0 | 99.28 Neigh | 0.0060526 | 0.0060526 | 0.0060526 | 0.0 | 0.27 Comm | 0.0016546 | 0.0016546 | 0.0016546 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0082 | | | 0.37 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5241.00 ave 5241 max 5241 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: 69092.0 ave 69092 max 69092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69092 Ave neighs/atom = 65.304348 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.763 | 4.763 | 4.763 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4524.723 0 -4524.723 -13.431408 Loop time of 2.149e-06 on 1 procs for 0 steps with 1058 atoms 186.1% 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 | | 2.149e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5244.00 ave 5244 max 5244 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: 68940.0 ave 68940 max 68940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68940 Ave neighs/atom = 65.160681 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.763 | 4.763 | 4.763 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 -4524.723 -4524.723 20.948395 118.70039 4.9385885 -13.431408 -13.431408 -36.999226 -10.540552 7.2455538 2.3653386 2713.686 Loop time of 2.532e-06 on 1 procs for 0 steps with 1058 atoms 197.5% 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 | | 2.532e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5244.00 ave 5244 max 5244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34470.0 ave 34470 max 34470 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68940.0 ave 68940 max 68940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68940 Ave neighs/atom = 65.160681 Neighbor list builds = 0 Dangerous builds = 0 1058 -4524.7230383225 eV 2.36533863757387 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:03