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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -43.539996 0.0000000) to (20.524951 43.539996 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0367502 5.9760778 4.9780318 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -43.539996 0.0000000) to (20.524951 43.539996 4.9780318) create_atoms CPU = 0.004 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0367502 5.9760778 4.9780318 Created 411 atoms using lattice units in orthogonal box = (0.0000000 -43.539996 0.0000000) to (20.524951 43.539996 4.9780318) create_atoms CPU = 0.003 seconds 411 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 816 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.401 | 5.401 | 5.401 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3571.0275 0 -3571.0275 2107.1819 55 0 -3617.997 0 -3617.997 8983.4295 Loop time of 2.68485 on 1 procs for 55 steps with 816 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 = -3571.02750434454 -3617.99388206667 -3617.99699600411 Force two-norm initial, final = 16.909095 0.16853014 Force max component initial, final = 3.5906494 0.013727549 Final line search alpha, max atom move = 1.0000000 0.013727549 Iterations, force evaluations = 55 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5966 | 2.5966 | 2.5966 | 0.0 | 96.71 Neigh | 0.058241 | 0.058241 | 0.058241 | 0.0 | 2.17 Comm | 0.017752 | 0.017752 | 0.017752 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0123 | | | 0.46 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7817.00 ave 7817 max 7817 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: 202404.0 ave 202404 max 202404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202404 Ave neighs/atom = 248.04412 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.401 | 5.401 | 5.401 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3617.997 0 -3617.997 8983.4295 8897.2986 61 0 -3618.274 0 -3618.274 202.214 8941.1931 Loop time of 0.221981 on 1 procs for 6 steps with 816 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 = -3617.9969960041 -3618.2718818698 -3618.27396833915 Force two-norm initial, final = 107.74158 2.0682189 Force max component initial, final = 99.731006 1.5178648 Final line search alpha, max atom move = 0.00019535353 0.00029652025 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21662 | 0.21662 | 0.21662 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013077 | 0.0013077 | 0.0013077 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004051 | | | 1.82 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7817.00 ave 7817 max 7817 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: 202080.0 ave 202080 max 202080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202080 Ave neighs/atom = 247.64706 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.539 | 5.539 | 5.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3618.274 0 -3618.274 202.214 Loop time of 7.397e-06 on 1 procs for 0 steps with 816 atoms 202.8% 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 | | 7.397e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7817.00 ave 7817 max 7817 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: 201936.0 ave 201936 max 201936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201936 Ave neighs/atom = 247.47059 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.539 | 5.539 | 5.539 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 -3618.274 -3618.274 20.502057 87.547015 4.9814606 202.214 202.214 216.68482 273.4456 116.51157 2.3636766 459.29806 Loop time of 8.239e-06 on 1 procs for 0 steps with 816 atoms 254.9% 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 | | 8.239e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7817.00 ave 7817 max 7817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100968.0 ave 100968 max 100968 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201936.0 ave 201936 max 201936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201936 Ave neighs/atom = 247.47059 Neighbor list builds = 0 Dangerous builds = 0 816 -3599.87345381341 eV 2.36367655391712 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03