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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -52.683191 0.0000000) to (43.015645 52.683191 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3032987 5.0518128 5.8134559 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -52.683191 0.0000000) to (43.015645 52.683191 8.7201838) create_atoms CPU = 0.003 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3032987 5.0518128 5.8134559 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -52.683191 0.0000000) to (43.015645 52.683191 8.7201838) create_atoms CPU = 0.002 seconds 1759 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 28 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3504 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.438 | 7.438 | 7.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14036.85 0 -14036.85 76013.284 85 0 -15345.902 0 -15345.902 12460.936 Loop time of 4.93613 on 1 procs for 85 steps with 3504 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14036.8500246199 -15345.8873474066 -15345.9024340487 Force two-norm initial, final = 1233.4139 0.62217301 Force max component initial, final = 166.64335 0.14548324 Final line search alpha, max atom move = 1.0000000 0.14548324 Iterations, force evaluations = 85 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8418 | 4.8418 | 4.8418 | 0.0 | 98.09 Neigh | 0.039716 | 0.039716 | 0.039716 | 0.0 | 0.80 Comm | 0.023346 | 0.023346 | 0.023346 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03129 | | | 0.63 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11939.0 ave 11939 max 11939 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: 614690.0 ave 614690 max 614690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614690 Ave neighs/atom = 175.42523 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.436 | 7.436 | 7.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -15345.902 0 -15345.902 12460.936 39523.386 95 0 -15348.09 0 -15348.09 -207.20023 39755.448 Loop time of 0.410749 on 1 procs for 10 steps with 3504 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 = -15345.9024340486 -15348.0879726575 -15348.0895301975 Force two-norm initial, final = 623.00952 9.3604676 Force max component initial, final = 571.08079 6.8649306 Final line search alpha, max atom move = 0.00013634610 0.00093600648 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36124 | 0.36124 | 0.36124 | 0.0 | 87.95 Neigh | 0.039233 | 0.039233 | 0.039233 | 0.0 | 9.55 Comm | 0.0015826 | 0.0015826 | 0.0015826 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008693 | | | 2.12 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11732.0 ave 11732 max 11732 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: 612250.0 ave 612250 max 612250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612250 Ave neighs/atom = 174.72888 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.573 | 7.573 | 7.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15348.09 0 -15348.09 -207.20023 Loop time of 2.142e-06 on 1 procs for 0 steps with 3504 atoms 186.7% 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 | | 2.142e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11747.0 ave 11747 max 11747 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: 612316.0 ave 612316 max 612316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612316 Ave neighs/atom = 174.74772 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.573 | 7.573 | 7.573 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 -15348.09 -15348.09 42.891964 106.33784 8.7163143 -207.20023 -207.20023 -275.86674 -149.02493 -196.70902 2.3119169 1576.4411 Loop time of 5.454e-06 on 1 procs for 0 steps with 3504 atoms 201.7% 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 | | 5.454e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11747.0 ave 11747 max 11747 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306158.0 ave 306158 max 306158 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 612316.0 ave 612316 max 612316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612316 Ave neighs/atom = 174.74772 Neighbor list builds = 0 Dangerous builds = 0 3504 -15348.0895301975 eV 2.31191690941824 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06