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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -34.501019 0.0000000) to (42.254946 34.501019 6.9940884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0518441 4.2535503 4.6627256 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -34.501019 0.0000000) to (42.254946 34.501019 6.9940884) create_atoms CPU = 0.004 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0518441 4.2535503 4.6627256 Created 881 atoms using lattice units in orthogonal box = (0.0000000 -34.501019 0.0000000) to (42.254946 34.501019 6.9940884) create_atoms CPU = 0.003 seconds 881 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1740 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_737567242631_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.551 | 5.551 | 5.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5896.8567 0 -5896.8567 152499.08 69 0 -7129.4793 0 -7129.4793 -821.34135 Loop time of 2.97638 on 1 procs for 69 steps with 1740 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 = -5896.85674581198 -7129.47453983442 -7129.4792585394 Force two-norm initial, final = 1936.6508 0.31223764 Force max component initial, final = 354.46932 0.085199238 Final line search alpha, max atom move = 1.0000000 0.085199238 Iterations, force evaluations = 69 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8287 | 2.8287 | 2.8287 | 0.0 | 95.04 Neigh | 0.10483 | 0.10483 | 0.10483 | 0.0 | 3.52 Comm | 0.019399 | 0.019399 | 0.019399 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02342 | | | 0.79 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 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: 236264.0 ave 236264 max 236264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236264 Ave neighs/atom = 135.78391 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.547 | 5.547 | 5.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -7129.4793 0 -7129.4793 -821.34135 20392.505 73 0 -7129.6465 0 -7129.6465 -118.6828 20385.004 Loop time of 0.152542 on 1 procs for 4 steps with 1740 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 = -7129.47925853941 -7129.64608582286 -7129.64652365502 Force two-norm initial, final = 80.856308 3.5250738 Force max component initial, final = 55.013948 3.0705174 Final line search alpha, max atom move = 0.00018603464 0.00057122259 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14809 | 0.14809 | 0.14809 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092332 | 0.00092332 | 0.00092332 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003526 | | | 2.31 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 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: 236282.0 ave 236282 max 236282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236282 Ave neighs/atom = 135.79425 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.685 | 5.685 | 5.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7129.6465 0 -7129.6465 -118.6828 Loop time of 6.626e-06 on 1 procs for 0 steps with 1740 atoms 196.2% 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 | | 6.626e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 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: 236278.0 ave 236278 max 236278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236278 Ave neighs/atom = 135.79195 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.685 | 5.685 | 5.685 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 -7129.6465 -7129.6465 42.149178 69.2148 6.9875144 -118.6828 -118.6828 -240.72583 13.763063 -129.08565 2.2451371 1591.5651 Loop time of 6.886e-06 on 1 procs for 0 steps with 1740 atoms 261.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118139.0 ave 118139 max 118139 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 236278.0 ave 236278 max 236278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236278 Ave neighs/atom = 135.79195 Neighbor list builds = 0 Dangerous builds = 0 1740 -7129.64652365502 eV 2.2451371308611 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03