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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -32.056519 0.0000000) to (15.703018 32.056519 7.0226033) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1874716 3.8464382 4.6817355 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -32.056519 0.0000000) to (15.703018 32.056519 7.0226033) create_atoms CPU = 0.001 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1874716 3.8464382 4.6817355 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -32.056519 0.0000000) to (15.703018 32.056519 7.0226033) create_atoms CPU = 0.000 seconds 306 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 588 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.546 | 4.546 | 4.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2335.4141 0 -2335.4141 -2308.4571 135 0 -2356.849 0 -2356.849 -59011.95 Loop time of 1.11778 on 1 procs for 135 steps with 588 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 = -2335.41413133171 -2356.84693317431 -2356.84900965691 Force two-norm initial, final = 4.4707303 0.11375182 Force max component initial, final = 0.73704183 0.053959495 Final line search alpha, max atom move = 1.0000000 0.053959495 Iterations, force evaluations = 135 265 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0981 | 1.0981 | 1.0981 | 0.0 | 98.24 Neigh | 0.0054606 | 0.0054606 | 0.0054606 | 0.0 | 0.49 Comm | 0.0076433 | 0.0076433 | 0.0076433 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006543 | | | 0.59 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3925.00 ave 3925 max 3925 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: 93478.0 ave 93478 max 93478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93478 Ave neighs/atom = 158.97619 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 135 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.546 | 4.546 | 4.546 Mbytes Step Temp E_pair E_mol TotEng Press Volume 135 0 -2356.849 0 -2356.849 -59011.95 7070.1337 719 0 -2390.7301 0 -2390.7301 -4185.9684 6223.0356 Loop time of 2.98203 on 1 procs for 584 steps with 588 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 = -2356.84900965691 -2390.729412864 -2390.73010465105 Force two-norm initial, final = 364.91930 3.7698090 Force max component initial, final = 284.95747 2.0251620 Final line search alpha, max atom move = 0.00037467314 0.00075877380 Iterations, force evaluations = 584 653 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8643 | 2.8643 | 2.8643 | 0.0 | 96.05 Neigh | 0.0062545 | 0.0062545 | 0.0062545 | 0.0 | 0.21 Comm | 0.019516 | 0.019516 | 0.019516 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09194 | | | 3.08 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4130.00 ave 4130 max 4130 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: 96280.0 ave 96280 max 96280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96280 Ave neighs/atom = 163.74150 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2390.7301 0 -2390.7301 -4185.9684 Loop time of 1.551e-06 on 1 procs for 0 steps with 588 atoms 128.9% 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 | | 1.551e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4240.00 ave 4240 max 4240 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: 98006.0 ave 98006 max 98006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98006 Ave neighs/atom = 166.67687 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.686 | 4.686 | 4.686 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 -2390.7301 -2390.7301 14.417718 64.113038 6.7322372 -4185.9684 -4185.9684 -478.71961 -11676.855 -402.33085 2.2959041 1879.7734 Loop time of 1.538e-06 on 1 procs for 0 steps with 588 atoms 195.1% 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 | | 1.538e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4240.00 ave 4240 max 4240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49003.0 ave 49003 max 49003 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98006.0 ave 98006 max 98006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98006 Ave neighs/atom = 166.67687 Neighbor list builds = 0 Dangerous builds = 0 588 -2390.73010465105 eV 2.29590409541411 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04