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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -41.108664 0.0000000) to (35.601147 41.108664 6.9819593) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3899495 6.3244098 6.9819593 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -41.108664 0.0000000) to (35.601147 41.108664 6.9819593) create_atoms CPU = 0.001 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3899495 6.3244098 6.9819593 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.108664 0.0000000) to (35.601147 41.108664 6.9819593) create_atoms CPU = 0.001 seconds 629 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 22 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1253 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4051.6313 0 -4051.6313 16723.026 103 0 -4193.2072 0 -4193.2072 7205.0906 Loop time of 1.4119 on 1 procs for 103 steps with 1253 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 = -4051.6313133153 -4193.20371953529 -4193.20724002224 Force two-norm initial, final = 56.618809 0.18565938 Force max component initial, final = 8.4493518 0.056778188 Final line search alpha, max atom move = 1.0000000 0.056778188 Iterations, force evaluations = 103 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3406 | 1.3406 | 1.3406 | 0.0 | 94.95 Neigh | 0.049331 | 0.049331 | 0.049331 | 0.0 | 3.49 Comm | 0.010287 | 0.010287 | 0.010287 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01169 | | | 0.83 Nlocal: 1253.00 ave 1253 max 1253 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 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: 163308.0 ave 163308 max 163308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163308 Ave neighs/atom = 130.33360 Neighbor list builds = 5 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -4193.2072 0 -4193.2072 7205.0906 20436.412 114 0 -4193.9144 0 -4193.9144 12.802353 20628.3 Loop time of 0.107108 on 1 procs for 11 steps with 1253 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 = -4193.20724002225 -4193.91440315794 -4193.91443655718 Force two-norm initial, final = 173.25776 0.61227692 Force max component initial, final = 146.92778 0.32908644 Final line search alpha, max atom move = 0.0010653021 0.00035057647 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10263 | 0.10263 | 0.10263 | 0.0 | 95.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060778 | 0.00060778 | 0.00060778 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003875 | | | 3.62 Nlocal: 1253.00 ave 1253 max 1253 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5199.00 ave 5199 max 5199 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: 163290.0 ave 163290 max 163290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163290 Ave neighs/atom = 130.31923 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.181 | 5.181 | 5.181 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4193.9144 0 -4193.9144 12.802353 Loop time of 2.096e-06 on 1 procs for 0 steps with 1253 atoms 190.8% 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 | | 2.096e-06 | | |100.00 Nlocal: 1253.00 ave 1253 max 1253 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5193.00 ave 5193 max 5193 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: 162826.0 ave 162826 max 162826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162826 Ave neighs/atom = 129.94892 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.181 | 5.181 | 5.181 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 -4193.9144 -4193.9144 35.618228 83.02797 6.9753613 12.802353 12.802353 2.705517 10.165927 25.535614 2.5344142 1365.1595 Loop time of 2.888e-06 on 1 procs for 0 steps with 1253 atoms 242.4% 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 | | 2.888e-06 | | |100.00 Nlocal: 1253.00 ave 1253 max 1253 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5193.00 ave 5193 max 5193 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81413.0 ave 81413 max 81413 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162826.0 ave 162826 max 162826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162826 Ave neighs/atom = 129.94892 Neighbor list builds = 0 Dangerous builds = 0 1253 -4193.91443655718 eV 2.5344141774778 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01