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 = 3.1599882 3.1599882 3.1599882 Created orthogonal box = (0.0000000 -56.879788 0.0000000) to (40.220084 56.879788 4.4688982) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4619867 5.2666470 4.4688982 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -56.879788 0.0000000) to (40.220084 56.879788 4.4688982) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4619867 5.2666470 4.4688982 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -56.879788 0.0000000) to (40.220084 56.879788 4.4688982) create_atoms CPU = 0.002 seconds 650 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 13 35 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 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_698578166685_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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -28853.768 0 -28853.768 42528.215 42 0 -29047.732 0 -29047.732 17147.404 Loop time of 29.3749 on 1 procs for 42 steps with 1298 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 = -28853.7683039275 -29047.7084160826 -29047.7318753907 Force two-norm initial, final = 148.14270 0.54056178 Force max component initial, final = 26.565820 0.078114582 Final line search alpha, max atom move = 0.90935479 0.071033869 Iterations, force evaluations = 42 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.358 | 29.358 | 29.358 | 0.0 | 99.94 Neigh | 0.0073103 | 0.0073103 | 0.0073103 | 0.0 | 0.02 Comm | 0.0047205 | 0.0047205 | 0.0047205 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004925 | | | 0.02 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6398.00 ave 6398 max 6398 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: 83488.0 ave 83488 max 83488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83488 Ave neighs/atom = 64.320493 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -29047.732 0 -29047.732 17147.404 20447.085 48 0 -29048.776 0 -29048.776 650.74868 20575.599 Loop time of 3.21495 on 1 procs for 6 steps with 1298 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 = -29047.7318753907 -29048.7518645146 -29048.7762333741 Force two-norm initial, final = 405.85219 14.803260 Force max component initial, final = 336.17985 10.465917 Final line search alpha, max atom move = 3.6240749e-05 0.00037929268 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2126 | 3.2126 | 3.2126 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039845 | 0.00039845 | 0.00039845 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001965 | | | 0.06 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6398.00 ave 6398 max 6398 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: 83388.0 ave 83388 max 83388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83388 Ave neighs/atom = 64.243451 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.788 | 4.788 | 4.788 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -29048.776 0 -29048.776 650.74868 Loop time of 1.972e-06 on 1 procs for 0 steps with 1298 atoms 152.1% 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 | | 1.972e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6386.00 ave 6386 max 6386 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: 83272.0 ave 83272 max 83272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83272 Ave neighs/atom = 64.154083 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.788 | 4.788 | 4.788 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 -29048.776 -29048.776 40.242385 114.42818 4.4682329 650.74868 650.74868 463.90512 819.74766 668.59324 2.5104018 573.20896 Loop time of 1.691e-06 on 1 procs for 0 steps with 1298 atoms 177.4% 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 | | 1.691e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6386.00 ave 6386 max 6386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41636.0 ave 41636 max 41636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83272.0 ave 83272 max 83272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83272 Ave neighs/atom = 64.154083 Neighbor list builds = 0 Dangerous builds = 0 1298 -6624.7932325349 eV 2.51040182548071 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34