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 = 3.6148132 3.6148132 3.6148132 Created orthogonal box = (0.0000000 -42.771047 0.0000000) to (52.383620 42.771047 8.8544479) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9866995 5.4991346 5.9029653 Created 1667 atoms using lattice units in orthogonal box = (0.0000000 -42.771047 0.0000000) to (52.383620 42.771047 8.8544479) create_atoms CPU = 0.003 seconds 1667 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9866995 5.4991346 5.9029653 Created 1691 atoms using lattice units in orthogonal box = (0.0000000 -42.771047 0.0000000) to (52.383620 42.771047 8.8544479) create_atoms CPU = 0.003 seconds 1691 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 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 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3358 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_380822813353_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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 14.95 | 14.95 | 14.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11527.005 0 -11527.005 25406.076 131 0 -11844.005 0 -11844.005 2711.7449 Loop time of 20.482 on 1 procs for 131 steps with 3358 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11527.0046759701 -11843.9928558188 -11844.0046190089 Force two-norm initial, final = 211.28737 0.31358986 Force max component initial, final = 24.263869 0.057236145 Final line search alpha, max atom move = 1.0000000 0.057236145 Iterations, force evaluations = 131 212 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.823 | 19.823 | 19.823 | 0.0 | 96.78 Neigh | 0.53246 | 0.53246 | 0.53246 | 0.0 | 2.60 Comm | 0.071976 | 0.071976 | 0.071976 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05458 | | | 0.27 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17747.0 ave 17747 max 17747 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: 1.54942e+06 ave 1.54942e+06 max 1.54942e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1549422 Ave neighs/atom = 461.41215 Neighbor list builds = 6 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 131 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 14.95 | 14.95 | 14.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 131 0 -11844.005 0 -11844.005 2711.7449 39676.822 135 0 -11844.228 0 -11844.228 -139.1743 39761.6 Loop time of 0.550499 on 1 procs for 4 steps with 3358 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 = -11844.0046190089 -11844.2257071004 -11844.2282875261 Force two-norm initial, final = 148.35066 9.6287144 Force max component initial, final = 141.96753 7.4660106 Final line search alpha, max atom move = 5.4801072e-05 0.00040914539 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54484 | 0.54484 | 0.54484 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092103 | 0.00092103 | 0.00092103 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004736 | | | 0.86 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17643.0 ave 17643 max 17643 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: 1.54675e+06 ave 1.54675e+06 max 1.54675e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1546750 Ave neighs/atom = 460.61644 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 14.46 | 14.46 | 14.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11844.228 0 -11844.228 -139.1743 Loop time of 2.718e-06 on 1 procs for 0 steps with 3358 atoms 184.0% 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 | | 2.718e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17546.0 ave 17546 max 17546 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: 1.54480e+06 ave 1.5448e+06 max 1.5448e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1544798 Ave neighs/atom = 460.03514 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 14.46 | 14.46 | 14.46 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 -11844.228 -11844.228 52.36739 85.820615 8.8473111 -139.1743 -139.1743 -221.22157 104.29586 -300.59719 2.2708436 1675.2677 Loop time of 2.777e-06 on 1 procs for 0 steps with 3358 atoms 288.1% 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 | | 2.777e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17546.0 ave 17546 max 17546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 772399.0 ave 772399 max 772399 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.54480e+06 ave 1.5448e+06 max 1.5448e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1544798 Ave neighs/atom = 460.03514 Neighbor list builds = 0 Dangerous builds = 0 3358 -11844.2282875261 eV 2.27084358408293 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22