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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -52.251765 0.0000000) to (36.944990 52.251765 5.1733334) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7952926 4.6101270 5.1733334 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -52.251765 0.0000000) to (36.944990 52.251765 5.1733334) create_atoms CPU = 0.001 seconds 822 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7952926 4.6101270 5.1733334 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -52.251765 0.0000000) to (36.944990 52.251765 5.1733334) create_atoms CPU = 0.001 seconds 822 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 = 11 29 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 34 atoms, new total = 1610 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_634187028437_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 = 11 29 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) = 5.531 | 5.531 | 5.531 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6215.3006 0 -6215.3006 -1766.7542 852 0 -6340.8071 0 -6340.8071 -73334.14 Loop time of 17.8594 on 1 procs for 852 steps with 1610 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 = -6215.30056916211 -6340.80158729616 -6340.80711669112 Force two-norm initial, final = 30.507112 0.22776208 Force max component initial, final = 6.0483445 0.044487346 Final line search alpha, max atom move = 1.0000000 0.044487346 Iterations, force evaluations = 852 1607 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.387 | 17.387 | 17.387 | 0.0 | 97.36 Neigh | 0.22022 | 0.22022 | 0.22022 | 0.0 | 1.23 Comm | 0.13289 | 0.13289 | 0.13289 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1189 | | | 0.67 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8237.00 ave 8237 max 8237 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: 215528.0 ave 215528 max 215528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215528 Ave neighs/atom = 133.86832 Neighbor list builds = 17 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 = 11 29 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 : 852 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.535 | 5.535 | 5.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 852 0 -6340.8071 0 -6340.8071 -73334.14 19973.629 896 0 -6377.4994 0 -6377.4994 -219.17259 18911.128 Loop time of 0.503151 on 1 procs for 44 steps with 1610 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 = -6340.80711669115 -6377.49843081563 -6377.49940220675 Force two-norm initial, final = 1550.1203 8.2700723 Force max component initial, final = 1337.3534 6.7388714 Final line search alpha, max atom move = 0.00045944840 0.0030961637 Iterations, force evaluations = 44 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48531 | 0.48531 | 0.48531 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028362 | 0.0028362 | 0.0028362 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01501 | | | 2.98 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8234.00 ave 8234 max 8234 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: 215698.0 ave 215698 max 215698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215698 Ave neighs/atom = 133.97391 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 = 11 29 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) = 5.676 | 5.676 | 5.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6377.4994 0 -6377.4994 -219.17259 Loop time of 1.653e-06 on 1 procs for 0 steps with 1610 atoms 181.5% 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 | | 1.653e-06 | | |100.00 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8627.00 ave 8627 max 8627 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: 227364.0 ave 227364 max 227364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227364 Ave neighs/atom = 141.21988 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 = 11 29 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) = 5.676 | 5.676 | 5.676 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 -6377.4994 -6377.4994 36.534485 104.50353 4.9531729 -219.17259 -219.17259 220.27634 -1424.4236 546.62955 2.2502457 4409.3249 Loop time of 2.22e-06 on 1 procs for 0 steps with 1610 atoms 180.2% 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 | | 2.22e-06 | | |100.00 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8627.00 ave 8627 max 8627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113682.0 ave 113682 max 113682 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227364.0 ave 227364 max 227364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227364 Ave neighs/atom = 141.21988 Neighbor list builds = 0 Dangerous builds = 0 1610 -6149.81058770643 eV 2.25024571457085 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18