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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -63.853855 0.0000000) to (36.866040 63.853855 6.2613856) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6716985 5.7304742 6.2613856 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -63.853855 0.0000000) to (36.866040 63.853855 6.2613856) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6716985 5.7304742 6.2613856 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.853855 0.0000000) to (36.866040 63.853855 6.2613856) create_atoms CPU = 0.002 seconds 1249 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2490 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_028979335952_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.106 | 6.106 | 6.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8344.4091 0 -8344.4091 31512.67 77 0 -8776.8193 0 -8776.8193 1855.3502 Loop time of 18.5671 on 1 procs for 77 steps with 2490 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 = -8344.40909968764 -8776.8105274777 -8776.81930261626 Force two-norm initial, final = 633.01754 0.34095148 Force max component initial, final = 180.25822 0.053407792 Final line search alpha, max atom move = 0.77871881 0.041589652 Iterations, force evaluations = 77 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.475 | 18.475 | 18.475 | 0.0 | 99.51 Neigh | 0.057554 | 0.057554 | 0.057554 | 0.0 | 0.31 Comm | 0.015789 | 0.015789 | 0.015789 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01845 | | | 0.10 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9141.00 ave 9141 max 9141 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: 329726.0 ave 329726 max 329726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329726 Ave neighs/atom = 132.42008 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.108 | 6.108 | 6.108 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -8776.8193 0 -8776.8193 1855.3502 29479.089 80 0 -8776.8888 0 -8776.8888 -40.299779 29518.512 Loop time of 0.746504 on 1 procs for 3 steps with 2490 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 = -8776.81930261626 -8776.88816565331 -8776.8887514533 Force two-norm initial, final = 76.477099 2.1910918 Force max component initial, final = 61.705317 1.5134335 Final line search alpha, max atom move = 0.00014137648 0.00021396391 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74376 | 0.74376 | 0.74376 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040414 | 0.00040414 | 0.00040414 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002338 | | | 0.31 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9223.00 ave 9223 max 9223 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: 329678.0 ave 329678 max 329678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329678 Ave neighs/atom = 132.40080 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.246 | 6.246 | 6.246 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8776.8888 0 -8776.8888 -40.299779 Loop time of 2.585e-06 on 1 procs for 0 steps with 2490 atoms 193.4% 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 | | 2.585e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9198.00 ave 9198 max 9198 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: 329616.0 ave 329616 max 329616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329616 Ave neighs/atom = 132.37590 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.246 | 6.246 | 6.246 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 -8776.8888 -8776.8888 36.825723 127.82932 6.270652 -40.299779 -40.299779 -82.05481 36.548075 -75.392603 2.2572432 1187.2515 Loop time of 2.432e-06 on 1 procs for 0 steps with 2490 atoms 246.7% 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 | | 2.432e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9198.00 ave 9198 max 9198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164808.0 ave 164808 max 164808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 329616.0 ave 329616 max 329616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329616 Ave neighs/atom = 132.37590 Neighbor list builds = 0 Dangerous builds = 0 2490 -8776.8887514533 eV 2.25724321910845 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20