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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.421633 0.0000000) to (37.418113 37.421633 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9670062 4.9670062 3.5200000 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -37.421633 0.0000000) to (37.418113 37.421633 3.5200000) create_atoms CPU = 0.002 seconds 453 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9670062 4.9670062 3.5200000 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -37.421633 0.0000000) to (37.418113 37.421633 3.5200000) create_atoms CPU = 0.002 seconds 453 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 ghost atom cutoff = 6 binsize = 3, bins = 13 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 891 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_444394830472_001#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 ghost atom cutoff = 6 binsize = 3, bins = 13 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3917.3804 0 -3917.3804 1870.3897 38 0 -3946.5938 0 -3946.5938 -15050.065 Loop time of 2.52358 on 1 procs for 38 steps with 891 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 = -3917.38044105999 -3946.59108289773 -3946.59376487196 Force two-norm initial, final = 40.806820 0.43337632 Force max component initial, final = 11.204496 0.092073756 Final line search alpha, max atom move = 1.0000000 0.092073756 Iterations, force evaluations = 38 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5078 | 2.5078 | 2.5078 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0077127 | 0.0077127 | 0.0077127 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008092 | | | 0.32 Nlocal: 891.000 ave 891 max 891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4537.00 ave 4537 max 4537 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: 68766.0 ave 68766 max 68766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68766 Ave neighs/atom = 77.178451 Neighbor list builds = 0 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 ghost atom cutoff = 6 binsize = 3, bins = 13 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -3946.5938 0 -3946.5938 -15050.065 9857.7383 45 0 -3946.8511 0 -3946.8511 -5057.3208 9801.3699 Loop time of 0.351677 on 1 procs for 7 steps with 891 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 = -3946.59376487196 -3946.85089410749 -3946.85113347788 Force two-norm initial, final = 99.623465 0.59331130 Force max component initial, final = 87.485617 0.13874245 Final line search alpha, max atom move = 0.00031463862 4.3653733e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34693 | 0.34693 | 0.34693 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00098615 | 0.00098615 | 0.00098615 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003759 | | | 1.07 Nlocal: 891.000 ave 891 max 891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4553.00 ave 4553 max 4553 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: 69220.0 ave 69220 max 69220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69220 Ave neighs/atom = 77.687991 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 ghost atom cutoff = 6 binsize = 3, bins = 13 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.687 | 4.687 | 4.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3946.8511 0 -3946.8511 -5057.3208 Loop time of 6.556e-06 on 1 procs for 0 steps with 891 atoms 167.8% 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 | | 6.556e-06 | | |100.00 Nlocal: 891.000 ave 891 max 891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 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: 69276.0 ave 69276 max 69276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69276 Ave neighs/atom = 77.750842 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 ghost atom cutoff = 6 binsize = 3, bins = 13 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.687 | 4.687 | 4.687 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 -3946.8511 -3946.8511 37.429979 74.843267 3.4987625 -5057.3208 -5057.3208 5.6143161 -15192.074 14.497624 2.3252743 243.25808 Loop time of 8.7e-06 on 1 procs for 0 steps with 891 atoms 436.8% 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 | | 8.7e-06 | | |100.00 Nlocal: 891.000 ave 891 max 891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34638.0 ave 34638 max 34638 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69276.0 ave 69276 max 69276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69276 Ave neighs/atom = 77.750842 Neighbor list builds = 0 Dangerous builds = 0 891 -3946.85113347788 eV 2.32527425134444 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03