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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -54.214664 0.0000000) to (38.335556 54.214664 4.6834336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7217248 5.2596315 4.6834336 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -54.214664 0.0000000) to (38.335556 54.214664 4.6834336) create_atoms CPU = 0.002 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7217248 5.2596315 4.6834336 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -54.214664 0.0000000) to (38.335556 54.214664 4.6834336) create_atoms CPU = 0.002 seconds 1080 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 = 11 29 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 24 atoms, new total = 2128 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 = 11 29 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) = 6.443 | 6.443 | 6.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8082.7777 0 -8082.7777 33123.455 203 0 -8296.073 0 -8296.073 159210.68 Loop time of 7.93943 on 1 procs for 203 steps with 2128 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8082.77774697531 -8296.06528337773 -8296.07303155136 Force two-norm initial, final = 258.78864 0.57505448 Force max component initial, final = 45.632442 0.056384057 Final line search alpha, max atom move = 0.99887229 0.056320472 Iterations, force evaluations = 203 403 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8079 | 7.8079 | 7.8079 | 0.0 | 98.34 Neigh | 0.045286 | 0.045286 | 0.045286 | 0.0 | 0.57 Comm | 0.047608 | 0.047608 | 0.047608 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03859 | | | 0.49 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12002.0 ave 12002 max 12002 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: 409168.0 ave 409168 max 409168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409168 Ave neighs/atom = 192.27820 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 = 11 29 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 : 203 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.442 | 6.442 | 6.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 203 0 -8296.073 0 -8296.073 159210.68 19467.622 801 0 -8479.3688 0 -8479.3688 -842.69197 22886.102 Loop time of 11.8879 on 1 procs for 598 steps with 2128 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 = -8296.07303155139 -8479.3629768158 -8479.36884336033 Force two-norm initial, final = 3399.9962 26.547320 Force max component initial, final = 2237.4932 19.978588 Final line search alpha, max atom move = 0.00013794723 0.0027559909 Iterations, force evaluations = 598 672 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.268 | 11.268 | 11.268 | 0.0 | 94.78 Neigh | 0.26167 | 0.26167 | 0.26167 | 0.0 | 2.20 Comm | 0.059257 | 0.059257 | 0.059257 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2994 | | | 2.52 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10320.0 ave 10320 max 10320 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: 355280.0 ave 355280 max 355280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 355280 Ave neighs/atom = 166.95489 Neighbor list builds = 13 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 = 11 28 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) = 6.186 | 6.186 | 6.186 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8479.3688 0 -8479.3688 -842.69197 Loop time of 1.631e-06 on 1 procs for 0 steps with 2128 atoms 122.6% 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 | | 1.631e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10371.0 ave 10371 max 10371 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: 358688.0 ave 358688 max 358688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 358688 Ave neighs/atom = 168.55639 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 = 11 28 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) = 6.186 | 6.186 | 6.186 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 -8479.3688 -8479.3688 38.944591 103.0822 5.7008684 -842.69197 -842.69197 -534.99255 -1329.6588 -663.42456 2.2493273 3095.096 Loop time of 2.205e-06 on 1 procs for 0 steps with 2128 atoms 181.4% 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 | | 2.205e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10371.0 ave 10371 max 10371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 179344.0 ave 179344 max 179344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 358688.0 ave 358688 max 358688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 358688 Ave neighs/atom = 168.55639 Neighbor list builds = 0 Dangerous builds = 0 2128 -8479.36884336033 eV 2.24932727940963 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20