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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -62.179355 0.0000000) to (35.897235 62.179355 6.0968422) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226516 5.5798826 6.0968422 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.179355 0.0000000) to (35.897235 62.179355 6.0968422) create_atoms CPU = 0.002 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226516 5.5798826 6.0968422 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.179355 0.0000000) to (35.897235 62.179355 6.0968422) create_atoms CPU = 0.002 seconds 1251 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2480 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.945 | 6.945 | 6.945 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10969.919 0 -10969.919 1215.9161 40 0 -10996.435 0 -10996.435 -3883.0114 Loop time of 1.85637 on 1 procs for 40 steps with 2480 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10969.9191219227 -10996.4255039737 -10996.4346288463 Force two-norm initial, final = 24.464219 0.30671351 Force max component initial, final = 3.8805342 0.032033795 Final line search alpha, max atom move = 1.0000000 0.032033795 Iterations, force evaluations = 40 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8068 | 1.8068 | 1.8068 | 0.0 | 97.33 Neigh | 0.030492 | 0.030492 | 0.030492 | 0.0 | 1.64 Comm | 0.010547 | 0.010547 | 0.010547 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00851 | | | 0.46 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 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: 555136.0 ave 555136 max 555136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 555136 Ave neighs/atom = 223.84516 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.945 | 6.945 | 6.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -10996.435 0 -10996.435 -3883.0114 27217.12 42 0 -10996.484 0 -10996.484 -1478.0209 27180.393 Loop time of 0.0987631 on 1 procs for 2 steps with 2480 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 = -10996.4346288463 -10996.4804627493 -10996.4835593405 Force two-norm initial, final = 78.791330 2.3300394 Force max component initial, final = 75.691637 1.8038258 Final line search alpha, max atom move = 8.0401483e-05 0.00014503027 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09681 | 0.09681 | 0.09681 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037507 | 0.00037507 | 0.00037507 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001579 | | | 1.60 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 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: 554938.0 ave 554938 max 554938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554938 Ave neighs/atom = 223.76532 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.083 | 7.083 | 7.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10996.484 0 -10996.484 -1478.0209 Loop time of 1.677e-06 on 1 procs for 0 steps with 2480 atoms 178.9% 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 | | 1.677e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 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: 555004.0 ave 555004 max 555004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 555004 Ave neighs/atom = 223.79194 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.083 | 7.083 | 7.083 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 -10996.484 -10996.484 35.895571 124.35871 6.0888974 -1478.0209 -1478.0209 106.32346 -4625.2542 84.868009 2.2399164 916.51179 Loop time of 1.918e-06 on 1 procs for 0 steps with 2480 atoms 260.7% 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 | | 1.918e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688.0 ave 12688 max 12688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 277502.0 ave 277502 max 277502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 555004.0 ave 555004 max 555004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 555004 Ave neighs/atom = 223.79194 Neighbor list builds = 0 Dangerous builds = 0 2480 -10928.8752829956 eV 2.23991635391701 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02