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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -62.515886 0.0000000) to (31.257943 62.515886 3.6336621) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0688556 5.0688556 3.6336621 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.515886 0.0000000) to (31.257943 62.515886 3.6336621) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0688556 5.0688556 3.6336621 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.515886 0.0000000) to (31.257943 62.515886 3.6336621) create_atoms CPU = 0.001 seconds 594 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4789.9794 0 -4789.9794 9582.3818 29 0 -4853.3493 0 -4853.3493 8115.8057 Loop time of 16.8152 on 1 procs for 29 steps with 1186 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4789.97943909766 -4853.34632201849 -4853.34930065537 Force two-norm initial, final = 44.016401 0.17317912 Force max component initial, final = 8.9681513 0.040690377 Final line search alpha, max atom move = 1.0000000 0.040690377 Iterations, force evaluations = 29 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.807 | 16.807 | 16.807 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039534 | 0.0039534 | 0.0039534 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004105 | | | 0.02 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6750.00 ave 6750 max 6750 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: 64756.0 ave 64756 max 64756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64756 Ave neighs/atom = 54.600337 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -4853.3493 0 -4853.3493 8115.8057 14201.209 35 0 -4853.7169 0 -4853.7169 -199.9939 14281.782 Loop time of 2.32155 on 1 procs for 6 steps with 1186 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 = -4853.34930065537 -4853.71462752221 -4853.71687566715 Force two-norm initial, final = 142.76328 4.1767134 Force max component initial, final = 119.18911 3.4874140 Final line search alpha, max atom move = 0.00019824944 0.00069137787 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3192 | 2.3192 | 2.3192 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040549 | 0.00040549 | 0.00040549 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001943 | | | 0.08 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 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: 66328.0 ave 66328 max 66328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66328 Ave neighs/atom = 55.925801 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.775 | 4.775 | 4.775 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4853.7169 0 -4853.7169 -199.9939 Loop time of 1.848e-06 on 1 procs for 0 steps with 1186 atoms 162.3% 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 | | 1.848e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 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: 65896.0 ave 65896 max 65896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65896 Ave neighs/atom = 55.561551 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.775 | 4.775 | 4.775 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 -4853.7169 -4853.7169 31.197274 125.65913 3.643105 -199.9939 -199.9939 -252.03164 -393.19244 45.242375 2.3316211 312.29074 Loop time of 1.924e-06 on 1 procs for 0 steps with 1186 atoms 207.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32948.0 ave 32948 max 32948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65896.0 ave 65896 max 65896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65896 Ave neighs/atom = 55.561551 Neighbor list builds = 0 Dangerous builds = 0 1186 -3032.92814238813 eV 2.33162108016416 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20