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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296739 5.3548974 5.7481360 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) create_atoms CPU = 0.004 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296739 5.3548974 5.7481360 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) create_atoms CPU = 0.003 seconds 1688 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 20 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3352 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_010613863288_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.837 | 7.837 | 7.837 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14720.853 0 -14720.853 9962.8505 70 0 -14847.045 0 -14847.045 3773.0685 Loop time of 3.81372 on 1 procs for 70 steps with 3352 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 = -14720.8528696726 -14847.033961244 -14847.0451026094 Force two-norm initial, final = 125.97252 0.37494848 Force max component initial, final = 21.397498 0.051258920 Final line search alpha, max atom move = 1.0000000 0.051258920 Iterations, force evaluations = 70 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5573 | 3.5573 | 3.5573 | 0.0 | 93.28 Neigh | 0.21733 | 0.21733 | 0.21733 | 0.0 | 5.70 Comm | 0.016723 | 0.016723 | 0.016723 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02233 | | | 0.59 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12392.0 ave 12392 max 12392 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: 752472.0 ave 752472 max 752472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752472 Ave neighs/atom = 224.48449 Neighbor list builds = 5 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.857 | 7.857 | 7.857 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -14847.045 0 -14847.045 3773.0685 36635.936 73 0 -14847.214 0 -14847.214 167.72597 36710.959 Loop time of 0.181218 on 1 procs for 3 steps with 3352 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 = -14847.0451026094 -14847.2071703808 -14847.2141293733 Force two-norm initial, final = 170.03168 8.3053746 Force max component initial, final = 152.19891 7.7729257 Final line search alpha, max atom move = 3.7252171e-05 0.00028955836 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17763 | 0.17763 | 0.17763 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051939 | 0.00051939 | 0.00051939 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003072 | | | 1.69 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12399.0 ave 12399 max 12399 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: 752398.0 ave 752398 max 752398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752398 Ave neighs/atom = 224.46241 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.994 | 7.994 | 7.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14847.214 0 -14847.214 167.72597 Loop time of 2.686e-06 on 1 procs for 0 steps with 3352 atoms 148.9% 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 | | 2.686e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12399.0 ave 12399 max 12399 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: 752008.0 ave 752008 max 752008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752008 Ave neighs/atom = 224.34606 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.994 | 7.994 | 7.994 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 -14847.214 -14847.214 51.014858 83.476423 8.6205547 167.72597 167.72597 117.99735 339.95881 45.221755 2.2002521 1752.7032 Loop time of 3.021e-06 on 1 procs for 0 steps with 3352 atoms 231.7% 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 | | 3.021e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12399.0 ave 12399 max 12399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 376004.0 ave 376004 max 376004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 752008.0 ave 752008 max 752008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752008 Ave neighs/atom = 224.34606 Neighbor list builds = 0 Dangerous builds = 0 3352 -14847.2141293733 eV 2.20025205272352 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04