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 -46.531011 0.0000000) to (32.902394 46.531011 5.7275716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9792956 6.3451379 5.7275716 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -46.531011 0.0000000) to (32.902394 46.531011 5.7275716) create_atoms CPU = 0.005 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9792956 6.3451379 5.7275716 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.531011 0.0000000) to (32.902394 46.531011 5.7275716) create_atoms CPU = 0.003 seconds 532 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 = 8 23 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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 = 8 23 2 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) = 5.009 | 5.009 | 5.009 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3480.8249 0 -3480.8249 -555.58125 78 0 -3513.6629 0 -3513.6629 -2944.3869 Loop time of 2.22362 on 1 procs for 78 steps with 1048 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 = -3480.82491525323 -3513.65970016852 -3513.66291081549 Force two-norm initial, final = 18.200252 0.13625370 Force max component initial, final = 3.5978610 0.023235861 Final line search alpha, max atom move = 1.0000000 0.023235861 Iterations, force evaluations = 78 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1411 | 2.1411 | 2.1411 | 0.0 | 96.29 Neigh | 0.042721 | 0.042721 | 0.042721 | 0.0 | 1.92 Comm | 0.020715 | 0.020715 | 0.020715 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01914 | | | 0.86 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5924.00 ave 5924 max 5924 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: 146160.0 ave 146160 max 146160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146160 Ave neighs/atom = 139.46565 Neighbor list builds = 2 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 = 8 23 2 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.009 | 5.009 | 5.009 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -3513.6629 0 -3513.6629 -2944.3869 17537.614 82 0 -3513.7343 0 -3513.7343 -14.345991 17472.357 Loop time of 0.129188 on 1 procs for 4 steps with 1048 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3513.66291081545 -3513.73429727708 -3513.73430250496 Force two-norm initial, final = 57.093799 0.33225402 Force max component initial, final = 41.692072 0.22097781 Final line search alpha, max atom move = 0.013991176 0.0030917395 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12456 | 0.12456 | 0.12456 | 0.0 | 96.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001068 | 0.001068 | 0.001068 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003556 | | | 2.75 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5892.00 ave 5892 max 5892 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: 146080.0 ave 146080 max 146080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146080 Ave neighs/atom = 139.38931 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 = 8 23 2 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) = 5.147 | 5.147 | 5.147 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3513.7343 0 -3513.7343 -14.345991 Loop time of 6.445e-06 on 1 procs for 0 steps with 1048 atoms 201.7% 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 | | 6.445e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5892.00 ave 5892 max 5892 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: 146168.0 ave 146168 max 146168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146168 Ave neighs/atom = 139.47328 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 = 8 23 2 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) = 5.147 | 5.147 | 5.147 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 -3513.7343 -3513.7343 32.873292 92.812916 5.7266398 -14.345991 -14.345991 -5.2103409 -17.567752 -20.259881 2.6581091 598.61365 Loop time of 7.277e-06 on 1 procs for 0 steps with 1048 atoms 247.4% 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 | | 7.277e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5892.00 ave 5892 max 5892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73084.0 ave 73084 max 73084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146168.0 ave 146168 max 146168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146168 Ave neighs/atom = 139.47328 Neighbor list builds = 0 Dangerous builds = 0 1048 -3513.73430261418 eV 2.65810909322827 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02