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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -59.119740 0.0000000) to (20.901984 59.119740 5.1457129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7005412 6.2702754 5.1457129 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.119740 0.0000000) to (20.901984 59.119740 5.1457129) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7005412 6.2702754 5.1457129 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.119740 0.0000000) to (20.901984 59.119740 5.1457129) create_atoms CPU = 0.001 seconds 530 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 25 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.889 | 5.889 | 5.889 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3323.6336 0 -3323.6336 68608.701 49 0 -3589.9028 0 -3589.9028 2440.7326 Loop time of 1.61408 on 1 procs for 49 steps with 1056 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 = -3323.6336362656 -3589.89960944759 -3589.90284907732 Force two-norm initial, final = 815.28503 0.15657447 Force max component initial, final = 271.71322 0.0092476383 Final line search alpha, max atom move = 1.0000000 0.0092476383 Iterations, force evaluations = 49 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5818 | 1.5818 | 1.5818 | 0.0 | 98.00 Neigh | 0.018236 | 0.018236 | 0.018236 | 0.0 | 1.13 Comm | 0.0081902 | 0.0081902 | 0.0081902 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005826 | | | 0.36 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10135.0 ave 10135 max 10135 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: 336100.0 ave 336100 max 336100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336100 Ave neighs/atom = 318.27652 Neighbor list builds = 1 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.888 | 5.888 | 5.888 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -3589.9028 0 -3589.9028 2440.7326 12717.319 54 0 -3590.0145 0 -3590.0145 -86.968624 12739.725 Loop time of 0.152763 on 1 procs for 5 steps with 1056 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 = -3589.90284907731 -3590.01436191798 -3590.01454244514 Force two-norm initial, final = 58.994568 1.5379453 Force max component initial, final = 57.872975 1.1800856 Final line search alpha, max atom move = 0.00037900799 0.00044726187 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14923 | 0.14923 | 0.14923 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063448 | 0.00063448 | 0.00063448 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002898 | | | 1.90 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10007.0 ave 10007 max 10007 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: 336096.0 ave 336096 max 336096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336096 Ave neighs/atom = 318.27273 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.026 | 6.026 | 6.026 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3590.0145 0 -3590.0145 -86.968624 Loop time of 2.269e-06 on 1 procs for 0 steps with 1056 atoms 176.3% 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 | | 2.269e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10007.0 ave 10007 max 10007 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: 335896.0 ave 335896 max 335896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335896 Ave neighs/atom = 318.08333 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.026 | 6.026 | 6.026 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 -3590.0145 -3590.0145 20.860245 118.66607 5.1465254 -86.968624 -86.968624 -120.91512 -148.94565 8.9549026 2.3655293 377.40463 Loop time of 2.746e-06 on 1 procs for 0 steps with 1056 atoms 182.1% 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 | | 2.746e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10007.0 ave 10007 max 10007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167948.0 ave 167948 max 167948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 335896.0 ave 335896 max 335896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335896 Ave neighs/atom = 318.08333 Neighbor list builds = 0 Dangerous builds = 0 1056 -3590.01454244514 eV 2.36552932677132 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02