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 = 4.0500047 4.0500047 4.0500047 Created orthogonal box = (0.0000000 -48.936393 0.0000000) to (59.934596 48.936393 9.9204450) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7471531 6.0332539 6.6136300 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -48.936393 0.0000000) to (59.934596 48.936393 9.9204450) create_atoms CPU = 0.007 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7471531 6.0332539 6.6136300 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -48.936393 0.0000000) to (59.934596 48.936393 9.9204450) create_atoms CPU = 0.006 seconds 1758 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3504 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_651801486679_005#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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 7.002 | 7.002 | 7.002 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11631.756 0 -11631.756 4740.8713 22 0 -11746.687 0 -11746.687 3254.1172 Loop time of 1.78207 on 1 procs for 22 steps with 3504 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 = -11631.7557949482 -11746.6764999795 -11746.6869308046 Force two-norm initial, final = 41.637465 0.22343064 Force max component initial, final = 5.1960144 0.012540599 Final line search alpha, max atom move = 1.0000000 0.012540599 Iterations, force evaluations = 22 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7599 | 1.7599 | 1.7599 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.009265 | 0.009265 | 0.009265 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0129 | | | 0.72 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10850.0 ave 10850 max 10850 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: 491112.0 ave 491112 max 491112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491112 Ave neighs/atom = 140.15753 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.620 | 6.620 | 6.620 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -11746.687 0 -11746.687 3254.1172 58192.992 30 0 -11747.441 0 -11747.441 4.392645 58430.77 Loop time of 0.538957 on 1 procs for 8 steps with 3504 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 = -11746.6869308047 -11747.4411531621 -11747.441214337 Force two-norm initial, final = 253.36031 0.84038386 Force max component initial, final = 238.34162 0.62948654 Final line search alpha, max atom move = 0.00039289146 0.00024731988 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52464 | 0.52464 | 0.52464 | 0.0 | 97.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024873 | 0.0024873 | 0.0024873 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01183 | | | 2.19 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10719.0 ave 10719 max 10719 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: 489000.0 ave 489000 max 489000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489000 Ave neighs/atom = 139.55479 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.758 | 6.758 | 6.758 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11747.441 0 -11747.441 4.392645 Loop time of 6.515e-06 on 1 procs for 0 steps with 3504 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10751.0 ave 10751 max 10751 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: 488688.0 ave 488688 max 488688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488688 Ave neighs/atom = 139.46575 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.758 | 6.758 | 6.758 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 -11747.441 -11747.441 59.889352 98.554792 9.8995225 4.392645 4.392645 -9.3954349 5.3492005 17.224169 2.557892 2075.8013 Loop time of 6.725e-06 on 1 procs for 0 steps with 3504 atoms 267.7% 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 | | 6.725e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10751.0 ave 10751 max 10751 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244344.0 ave 244344 max 244344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 488688.0 ave 488688 max 488688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488688 Ave neighs/atom = 139.46575 Neighbor list builds = 0 Dangerous builds = 0 3504 -11747.4412147022 eV 2.55789203894392 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03