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 = 3.6800447 3.6800447 3.6800447 Created orthogonal box = (0.0000000 -47.127567 0.0000000) to (33.324222 47.127567 5.2043691) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6895013 6.3219907 5.2043691 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -47.127567 0.0000000) to (33.324222 47.127567 5.2043691) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6895013 6.3219907 5.2043691 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -47.127567 0.0000000) to (33.324222 47.127567 5.2043691) create_atoms CPU = 0.002 seconds 660 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 33 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_142799717516_005#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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5462.4739 0 -5462.4739 4346.1146 77 0 -5539.6101 0 -5539.6101 -14870.99 Loop time of 0.681312 on 1 procs for 77 steps with 1304 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5462.47390394754 -5539.60466622314 -5539.61008040336 Force two-norm initial, final = 77.136206 0.22999000 Force max component initial, final = 18.542702 0.025036887 Final line search alpha, max atom move = 1.0000000 0.025036887 Iterations, force evaluations = 77 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65349 | 0.65349 | 0.65349 | 0.0 | 95.92 Neigh | 0.0069377 | 0.0069377 | 0.0069377 | 0.0 | 1.02 Comm | 0.0089743 | 0.0089743 | 0.0089743 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01191 | | | 1.75 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4816.00 ave 4816 max 4816 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: 72448.0 ave 72448 max 72448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72448 Ave neighs/atom = 55.558282 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -5539.6101 0 -5539.6101 -14870.99 16346.814 88 0 -5540.9091 0 -5540.9091 110.69248 16176.605 Loop time of 0.0442892 on 1 procs for 11 steps with 1304 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 = -5539.61008040336 -5540.90745791319 -5540.90909730312 Force two-norm initial, final = 289.35812 2.0097248 Force max component initial, final = 249.70992 1.2467031 Final line search alpha, max atom move = 0.00017238769 0.00021491626 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040724 | 0.040724 | 0.040724 | 0.0 | 91.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005418 | 0.0005418 | 0.0005418 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003023 | | | 6.83 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5069.00 ave 5069 max 5069 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: 72952.0 ave 72952 max 72952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72952 Ave neighs/atom = 55.944785 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.785 | 4.785 | 4.785 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5540.9091 0 -5540.9091 110.69248 Loop time of 1.568e-06 on 1 procs for 0 steps with 1304 atoms 127.6% 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 | | 1.568e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5095.00 ave 5095 max 5095 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: 73512.0 ave 73512 max 73512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73512 Ave neighs/atom = 56.374233 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.785 | 4.785 | 4.785 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 -5540.9091 -5540.9091 32.977258 94.273676 5.2033424 110.69248 110.69248 92.504795 116.12004 123.45262 2.3770727 800.22954 Loop time of 1.92e-06 on 1 procs for 0 steps with 1304 atoms 156.2% 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 | | 1.92e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5095.00 ave 5095 max 5095 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36756.0 ave 36756 max 36756 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73512.0 ave 73512 max 73512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73512 Ave neighs/atom = 56.374233 Neighbor list builds = 0 Dangerous builds = 0 1304 -5540.90909730312 eV 2.37707271080247 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00