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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1197 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) create_atoms CPU = 0.004 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) create_atoms CPU = 0.004 seconds 1205 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 = 9 44 4 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 = 2402 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 9 44 4 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) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8168.8511 0 -8168.8511 37112.102 129 0 -8480.2965 0 -8480.2965 4540.4081 Loop time of 17.4063 on 1 procs for 129 steps with 2402 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8168.85112608398 -8480.28863005835 -8480.29652836814 Force two-norm initial, final = 331.22694 0.27301468 Force max component initial, final = 61.141148 0.047080854 Final line search alpha, max atom move = 1.0000000 0.047080854 Iterations, force evaluations = 129 224 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.212 | 17.212 | 17.212 | 0.0 | 98.88 Neigh | 0.10911 | 0.10911 | 0.10911 | 0.0 | 0.63 Comm | 0.032484 | 0.032484 | 0.032484 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05281 | | | 0.30 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6179.00 ave 6179 max 6179 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: 149152.0 ave 149152 max 149152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149152 Ave neighs/atom = 62.094921 Neighbor list builds = 4 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 = 9 44 4 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 : 129 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press Volume 129 0 -8480.2965 0 -8480.2965 4540.4081 28305.378 134 0 -8480.6015 0 -8480.6015 -65.423701 28396.572 Loop time of 0.541238 on 1 procs for 5 steps with 2402 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 = -8480.29652836816 -8480.60054756043 -8480.60147225515 Force two-norm initial, final = 167.23904 3.9674347 Force max component initial, final = 155.90282 3.6220292 Final line search alpha, max atom move = 0.00011185102 0.00040512766 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5353 | 0.5353 | 0.5353 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072587 | 0.00072587 | 0.00072587 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005217 | | | 0.96 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301.00 ave 6301 max 6301 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: 149630.0 ave 149630 max 149630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149630 Ave neighs/atom = 62.293922 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 = 9 45 4 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) = 5.245 | 5.245 | 5.245 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8480.6015 0 -8480.6015 -65.423701 Loop time of 4.329e-06 on 1 procs for 0 steps with 2402 atoms 161.7% 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 | | 4.329e-06 | | |100.00 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6315.00 ave 6315 max 6315 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: 143412.0 ave 143412 max 143412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143412 Ave neighs/atom = 59.705246 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 = 9 45 4 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) = 5.245 | 5.245 | 5.245 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 -8480.6015 -8480.6015 25.536902 125.68782 8.8471731 -65.423701 -65.423701 -59.267278 67.273139 -204.27696 2.3442616 918.01072 Loop time of 4.794e-06 on 1 procs for 0 steps with 2402 atoms 208.6% 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 | | 4.794e-06 | | |100.00 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6315.00 ave 6315 max 6315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71706.0 ave 71706 max 71706 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 143412.0 ave 143412 max 143412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143412 Ave neighs/atom = 59.705246 Neighbor list builds = 0 Dangerous builds = 0 2402 -8480.60147225515 eV 2.34426155561068 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18