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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -52.095123 0.0000000) to (42.532616 52.095123 8.6222635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2437472 4.9950853 5.7481757 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -52.095123 0.0000000) to (42.532616 52.095123 8.6222635) create_atoms CPU = 0.006 seconds 1760 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2437472 4.9950853 5.7481757 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -52.095123 0.0000000) to (42.532616 52.095123 8.6222635) create_atoms CPU = 0.006 seconds 1760 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 3472 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15313.048 0 -15313.048 5666.8985 52 0 -15385.593 0 -15385.593 -6602.1999 Loop time of 7.40176 on 1 procs for 52 steps with 3472 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 = -15313.0475902012 -15385.5777574911 -15385.5926837676 Force two-norm initial, final = 73.399709 0.39330556 Force max component initial, final = 10.050255 0.031551274 Final line search alpha, max atom move = 1.0000000 0.031551274 Iterations, force evaluations = 52 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2421 | 7.2421 | 7.2421 | 0.0 | 97.84 Neigh | 0.097736 | 0.097736 | 0.097736 | 0.0 | 1.32 Comm | 0.028844 | 0.028844 | 0.028844 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03311 | | | 0.45 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13048.0 ave 13048 max 13048 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: 772800.0 ave 772800 max 772800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 772800 Ave neighs/atom = 222.58065 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -15385.593 0 -15385.593 -6602.1999 38209.421 55 0 -15385.84 0 -15385.84 -1001.1075 38088.33 Loop time of 0.44034 on 1 procs for 3 steps with 3472 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15385.5926837676 -15385.8394127703 -15385.8397330408 Force two-norm initial, final = 219.91765 0.43504466 Force max component initial, final = 157.45033 0.11438068 Final line search alpha, max atom move = 0.00025919227 2.9646588e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43236 | 0.43236 | 0.43236 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017146 | 0.0017146 | 0.0017146 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006263 | | | 1.42 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12941.0 ave 12941 max 12941 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: 771712.0 ave 771712 max 771712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 771712 Ave neighs/atom = 222.26728 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15385.84 0 -15385.84 -1001.1075 Loop time of 6.656e-06 on 1 procs for 0 steps with 3472 atoms 210.3% 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 | | 6.656e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12947.0 ave 12947 max 12947 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: 771904.0 ave 771904 max 771904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 771904 Ave neighs/atom = 222.32258 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.31 | 11.31 | 11.31 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 -15385.84 -15385.84 42.461021 104.19025 8.6094307 -1001.1075 -1001.1075 -2.8311578 -2995.687 -4.8042351 2.2133354 1670.6631 Loop time of 7.116e-06 on 1 procs for 0 steps with 3472 atoms 281.1% 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 | | 7.116e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12947.0 ave 12947 max 12947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 385952.0 ave 385952 max 385952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 771904.0 ave 771904 max 771904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 771904 Ave neighs/atom = 222.32258 Neighbor list builds = 0 Dangerous builds = 0 3472 -15291.1881459912 eV 2.21333541849684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09