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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -59.180102 0.0000000) to (41.846651 59.180102 5.1123821) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2457689 5.7413532 5.1123821 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.180102 0.0000000) to (41.846651 59.180102 5.1123821) create_atoms CPU = 0.008 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2457689 5.7413532 5.1123821 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.180102 0.0000000) to (41.846651 59.180102 5.1123821) create_atoms CPU = 0.007 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 14 37 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 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2144 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_179025990738_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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 14 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 5.232 | 5.232 | 5.232 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7366.6992 0 -7366.6992 10170.043 109 0 -7525.9952 0 -7525.9952 9001.8359 Loop time of 4.1173 on 1 procs for 109 steps with 2144 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 = -7366.69918482669 -7525.98853504104 -7525.9952226424 Force two-norm initial, final = 90.024736 0.23177377 Force max component initial, final = 13.204410 0.028100273 Final line search alpha, max atom move = 1.0000000 0.028100273 Iterations, force evaluations = 109 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9607 | 3.9607 | 3.9607 | 0.0 | 96.20 Neigh | 0.062435 | 0.062435 | 0.062435 | 0.0 | 1.52 Comm | 0.047431 | 0.047431 | 0.047431 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04673 | | | 1.13 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8734.00 ave 8734 max 8734 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: 184064.0 ave 184064 max 184064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184064 Ave neighs/atom = 85.850746 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 14 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.237 | 5.237 | 5.237 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -7525.9952 0 -7525.9952 9001.8359 25321.517 115 0 -7526.6666 0 -7526.6666 -92.523884 25468.135 Loop time of 0.155428 on 1 procs for 6 steps with 2144 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 = -7525.99522264246 -7526.66634025596 -7526.66664347356 Force two-norm initial, final = 270.71265 2.8806722 Force max component initial, final = 191.40008 2.1207526 Final line search alpha, max atom move = 0.00023194533 0.00049189866 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14752 | 0.14752 | 0.14752 | 0.0 | 94.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016563 | 0.0016563 | 0.0016563 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006255 | | | 4.02 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9180.00 ave 9180 max 9180 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: 184544.0 ave 184544 max 184544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184544 Ave neighs/atom = 86.074627 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 5.379 | 5.379 | 5.379 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7526.6666 0 -7526.6666 -92.523884 Loop time of 6.515e-06 on 1 procs for 0 steps with 2144 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9482.00 ave 9482 max 9482 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: 184304.0 ave 184304 max 184304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184304 Ave neighs/atom = 85.962687 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 5.379 | 5.379 | 5.379 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 -7526.6666 -7526.6666 41.990358 118.87816 5.1020593 -92.523884 -92.523884 -116.46465 -27.96183 -133.14517 2.4494038 1021.9672 Loop time of 7.347e-06 on 1 procs for 0 steps with 2144 atoms 285.8% 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 | | 7.347e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9482.00 ave 9482 max 9482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92152.0 ave 92152 max 92152 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184304.0 ave 184304 max 184304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184304 Ave neighs/atom = 85.962687 Neighbor list builds = 0 Dangerous builds = 0 2144 -7526.66664347356 eV 2.44940381846383 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04