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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -35.911290 0.0000000) to (31.100090 35.911290 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -35.911290 0.0000000) to (31.100090 35.911290 6.0992294) create_atoms CPU = 0.001 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -35.911290 0.0000000) to (31.100090 35.911290 6.0992294) create_atoms CPU = 0.001 seconds 627 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 = 11 24 3 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 5 atoms, new total = 1245 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_912636107108_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 = 11 24 3 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) = 4.638 | 4.638 | 4.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5106.9566 0 -5106.9566 81232.613 100 0 -5501.3222 0 -5501.3222 11129.744 Loop time of 6.97875 on 1 procs for 100 steps with 1245 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 = -5106.95662050948 -5501.31727342751 -5501.32215083124 Force two-norm initial, final = 497.38523 0.28290389 Force max component initial, final = 145.73196 0.070357900 Final line search alpha, max atom move = 0.70281668 0.049448706 Iterations, force evaluations = 100 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9371 | 6.9371 | 6.9371 | 0.0 | 99.40 Neigh | 0.022106 | 0.022106 | 0.022106 | 0.0 | 0.32 Comm | 0.0086094 | 0.0086094 | 0.0086094 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01098 | | | 0.16 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4800.00 ave 4800 max 4800 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: 96668.0 ave 96668 max 96668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96668 Ave neighs/atom = 77.644980 Neighbor list builds = 3 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 = 11 24 3 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 : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.638 | 4.638 | 4.638 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -5501.3222 0 -5501.3222 11129.744 13623.78 107 0 -5501.9383 0 -5501.9383 166.79336 13703.742 Loop time of 0.352266 on 1 procs for 7 steps with 1245 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 = -5501.32215083124 -5501.93477305119 -5501.9382552001 Force two-norm initial, final = 202.69454 2.8091203 Force max component initial, final = 184.54018 2.0904867 Final line search alpha, max atom move = 0.00011739504 0.00024541277 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34986 | 0.34986 | 0.34986 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034717 | 0.00034717 | 0.00034717 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002064 | | | 0.59 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4806.00 ave 4806 max 4806 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: 96702.0 ave 96702 max 96702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96702 Ave neighs/atom = 77.672289 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 = 11 25 3 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5501.9383 0 -5501.9383 166.79336 Loop time of 2.109e-06 on 1 procs for 0 steps with 1245 atoms 189.7% 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 | | 2.109e-06 | | |100.00 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4791.00 ave 4791 max 4791 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: 96564.0 ave 96564 max 96564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96564 Ave neighs/atom = 77.561446 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 = 11 25 3 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) = 4.777 | 4.777 | 4.777 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 -5501.9383 -5501.9383 31.12888 72.28467 6.0901706 166.79336 166.79336 55.777358 200.55593 244.04679 2.2285396 869.71745 Loop time of 2.292e-06 on 1 procs for 0 steps with 1245 atoms 174.5% 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 | | 2.292e-06 | | |100.00 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4791.00 ave 4791 max 4791 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48282.0 ave 48282 max 48282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96564.0 ave 96564 max 96564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96564 Ave neighs/atom = 77.561446 Neighbor list builds = 0 Dangerous builds = 0 1245 -5501.93825520011 eV 2.22853964728043 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07