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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -36.760840 0.0000000) to (31.832700 36.760840 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7135615 5.6549593 6.2429061 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -36.760840 0.0000000) to (31.832700 36.760840 6.2429061) create_atoms CPU = 0.001 seconds 630 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7135615 5.6549593 6.2429061 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -36.760840 0.0000000) to (31.832700 36.760840 6.2429061) create_atoms CPU = 0.001 seconds 630 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 1226 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5141.0621 0 -5141.0621 -3927.7377 97 0 -5183.9362 0 -5183.9362 -22849.893 Loop time of 7.10383 on 1 procs for 97 steps with 1226 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 = -5141.06208664849 -5183.93169579443 -5183.9361723997 Force two-norm initial, final = 26.446255 0.20962505 Force max component initial, final = 6.1589836 0.032657522 Final line search alpha, max atom move = 1.0000000 0.032657522 Iterations, force evaluations = 97 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0671 | 7.0671 | 7.0671 | 0.0 | 99.48 Neigh | 0.020408 | 0.020408 | 0.020408 | 0.0 | 0.29 Comm | 0.0071379 | 0.0071379 | 0.0071379 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009185 | | | 0.13 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4663.00 ave 4663 max 4663 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: 94160.0 ave 94160 max 94160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94160 Ave neighs/atom = 76.802610 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -5183.9362 0 -5183.9362 -22849.893 14610.857 111 0 -5185.805 0 -5185.805 -3078.6669 14424.989 Loop time of 0.739251 on 1 procs for 14 steps with 1226 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 = -5183.93617239969 -5185.80497308175 -5185.80500586875 Force two-norm initial, final = 309.89444 0.83481811 Force max component initial, final = 287.67598 0.35375328 Final line search alpha, max atom move = 0.0013080145 0.00046271444 Iterations, force evaluations = 14 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73521 | 0.73521 | 0.73521 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059532 | 0.00059532 | 0.00059532 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003448 | | | 0.47 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4660.00 ave 4660 max 4660 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: 94280.0 ave 94280 max 94280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94280 Ave neighs/atom = 76.900489 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5185.805 0 -5185.805 -3078.6669 Loop time of 1.725e-06 on 1 procs for 0 steps with 1226 atoms 173.9% 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 | | 1.725e-06 | | |100.00 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4678.00 ave 4678 max 4678 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: 94564.0 ave 94564 max 94564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94564 Ave neighs/atom = 77.132137 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.777 | 4.777 | 4.777 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 -5185.805 -5185.805 31.423322 73.52168 6.2437853 -3078.6669 -3078.6669 38.785909 -9309.0339 34.247211 2.2830363 1163.9045 Loop time of 1.656e-06 on 1 procs for 0 steps with 1226 atoms 181.2% 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 | | 1.656e-06 | | |100.00 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4678.00 ave 4678 max 4678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47282.0 ave 47282 max 47282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94564.0 ave 94564 max 94564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94564 Ave neighs/atom = 77.132137 Neighbor list builds = 0 Dangerous builds = 0 1226 -5185.80500586875 eV 2.28303625858868 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08