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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -44.204191 0.0000000) to (54.138856 44.204191 8.9611272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1913971 5.4498317 5.9740848 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -44.204191 0.0000000) to (54.138856 44.204191 8.9611272) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1913971 5.4498317 5.9740848 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -44.204191 0.0000000) to (54.138856 44.204191 8.9611272) create_atoms CPU = 0.002 seconds 1756 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.993 | 6.993 | 6.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10396.952 0 -10396.952 206794.19 644 0 -14171.35 0 -14171.35 -51251.011 Loop time of 30.9162 on 1 procs for 644 steps with 3506 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 = -10396.9524318395 -14171.3358982776 -14171.3497206191 Force two-norm initial, final = 3766.5942 0.44313956 Force max component initial, final = 535.21395 0.14438534 Final line search alpha, max atom move = 1.0000000 0.14438534 Iterations, force evaluations = 644 1241 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.81 | 29.81 | 29.81 | 0.0 | 96.42 Neigh | 0.77259 | 0.77259 | 0.77259 | 0.0 | 2.50 Comm | 0.13273 | 0.13273 | 0.13273 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2009 | | | 0.65 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10619.0 ave 10619 max 10619 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: 529286.0 ave 529286 max 529286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 529286 Ave neighs/atom = 150.96577 Neighbor list builds = 23 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 644 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.990 | 6.990 | 6.990 Mbytes Step Temp E_pair E_mol TotEng Press Volume 644 0 -14171.35 0 -14171.35 -51251.011 42890.899 682 0 -14223.608 0 -14223.608 -11.963323 41493.739 Loop time of 1.06419 on 1 procs for 38 steps with 3506 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 = -14171.3497206193 -14223.6047026015 -14223.6077349353 Force two-norm initial, final = 2786.5177 8.1744513 Force max component initial, final = 2185.2811 3.8905711 Final line search alpha, max atom move = 0.00011635490 0.00045268700 Iterations, force evaluations = 38 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93625 | 0.93625 | 0.93625 | 0.0 | 87.98 Neigh | 0.10103 | 0.10103 | 0.10103 | 0.0 | 9.49 Comm | 0.0039901 | 0.0039901 | 0.0039901 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02293 | | | 2.15 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10609.0 ave 10609 max 10609 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: 557374.0 ave 557374 max 557374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557374 Ave neighs/atom = 158.97718 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.126 | 7.126 | 7.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14223.608 0 -14223.608 -11.963323 Loop time of 2.086e-06 on 1 procs for 0 steps with 3506 atoms 143.8% 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 | | 2.086e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10609.0 ave 10609 max 10609 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: 557398.0 ave 557398 max 557398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557398 Ave neighs/atom = 158.98403 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.126 | 7.126 | 7.126 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 -14223.608 -14223.608 53.073559 85.467742 9.1474938 -11.963323 -11.963323 36.088963 81.369955 -153.34889 2.2058189 7386.7302 Loop time of 2.253e-06 on 1 procs for 0 steps with 3506 atoms 310.7% 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 | | 2.253e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10609.0 ave 10609 max 10609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278699.0 ave 278699 max 278699 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 557398.0 ave 557398 max 557398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557398 Ave neighs/atom = 158.98403 Neighbor list builds = 0 Dangerous builds = 0 3506 -14223.6077349353 eV 2.20581887173884 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32