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 = 2.8147787 2.8147787 2.8147787 Created orthogonal box = (0.0000000 -30.053613 0.0000000) to (21.251113 30.053613 3.9806983) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8467452 4.7453073 3.9806983 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.053613 0.0000000) to (21.251113 30.053613 3.9806983) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8467452 4.7453073 3.9806983 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.053613 0.0000000) to (21.251113 30.053613 3.9806983) create_atoms CPU = 0.000 seconds 230 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 17 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 454 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1421.5915 0 -1421.5915 192759.76 99 0 -1860.5312 0 -1860.5312 -235.67301 Loop time of 0.739142 on 1 procs for 99 steps with 454 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 = -1421.59153750664 -1860.52946491032 -1860.53115987585 Force two-norm initial, final = 1058.2619 0.17038944 Force max component initial, final = 369.24171 0.039212485 Final line search alpha, max atom move = 1.0000000 0.039212485 Iterations, force evaluations = 99 190 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71964 | 0.71964 | 0.71964 | 0.0 | 97.36 Neigh | 0.0087492 | 0.0087492 | 0.0087492 | 0.0 | 1.18 Comm | 0.0060838 | 0.0060838 | 0.0060838 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004664 | | | 0.63 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3919.00 ave 3919 max 3919 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: 74700.0 ave 74700 max 74700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74700 Ave neighs/atom = 164.53744 Neighbor list builds = 2 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -1860.5312 0 -1860.5312 -235.67301 5084.7269 101 0 -1860.5437 0 -1860.5437 -253.34278 5084.8324 Loop time of 0.0161223 on 1 procs for 2 steps with 454 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1860.53115987584 -1860.54263135622 -1860.54372639385 Force two-norm initial, final = 13.575131 1.4645022 Force max component initial, final = 10.317050 1.1230040 Final line search alpha, max atom move = 0.00030834151 0.00034626873 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015519 | 0.015519 | 0.015519 | 0.0 | 96.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011764 | 0.00011764 | 0.00011764 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004856 | | | 3.01 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3888.00 ave 3888 max 3888 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: 75064.0 ave 75064 max 75064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75064 Ave neighs/atom = 165.33921 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1860.5437 0 -1860.5437 -253.34278 Loop time of 1.843e-06 on 1 procs for 0 steps with 454 atoms 162.8% 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 | | 1.843e-06 | | |100.00 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3888.00 ave 3888 max 3888 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: 75072.0 ave 75072 max 75072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75072 Ave neighs/atom = 165.35683 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.610 | 4.610 | 4.610 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 -1860.5437 -1860.5437 21.252415 60.183134 3.9755165 -253.34278 -253.34278 -207.67361 -198.96876 -353.38597 2.2680593 412.79884 Loop time of 2.149e-06 on 1 procs for 0 steps with 454 atoms 232.7% 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 | | 2.149e-06 | | |100.00 Nlocal: 454.000 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3888.00 ave 3888 max 3888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37536.0 ave 37536 max 37536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75072.0 ave 75072 max 75072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75072 Ave neighs/atom = 165.35683 Neighbor list builds = 0 Dangerous builds = 0 454 -1860.54372639385 eV 2.26805929670765 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01