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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -36.028196 0.0000000) to (25.475782 36.028196 5.0449566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4957262 5.6514818 5.0449566 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.028196 0.0000000) to (25.475782 36.028196 5.0449566) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4957262 5.6514818 5.0449566 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.028196 0.0000000) to (25.475782 36.028196 5.0449566) create_atoms CPU = 0.001 seconds 410 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 26 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 818 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_058735400462_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3225.0578 0 -3225.0578 79496.256 107 0 -3442.8515 0 -3442.8515 59277.701 Loop time of 4.63825 on 1 procs for 107 steps with 818 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3225.05776609383 -3442.84844190794 -3442.85154106784 Force two-norm initial, final = 241.41682 0.21029654 Force max component initial, final = 73.377853 0.024653756 Final line search alpha, max atom move = 1.0000000 0.024653756 Iterations, force evaluations = 107 202 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6189 | 4.6189 | 4.6189 | 0.0 | 99.58 Neigh | 0.0038234 | 0.0038234 | 0.0038234 | 0.0 | 0.08 Comm | 0.0072871 | 0.0072871 | 0.0072871 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008241 | | | 0.18 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3560.00 ave 3560 max 3560 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: 49084.0 ave 49084 max 49084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49084 Ave neighs/atom = 60.004890 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -3442.8515 0 -3442.8515 59277.701 9260.9911 151 0 -3449.324 0 -3449.324 -76.35542 9586.8707 Loop time of 1.00535 on 1 procs for 44 steps with 818 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3442.85154106784 -3449.3210376664 -3449.32404741614 Force two-norm initial, final = 594.24580 5.7914386 Force max component initial, final = 367.41617 4.2544504 Final line search alpha, max atom move = 8.6499546e-05 0.00036800803 Iterations, force evaluations = 44 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99234 | 0.99234 | 0.99234 | 0.0 | 98.71 Neigh | 0.0036609 | 0.0036609 | 0.0036609 | 0.0 | 0.36 Comm | 0.0014712 | 0.0014712 | 0.0014712 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007878 | | | 0.78 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3498.00 ave 3498 max 3498 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: 48072.0 ave 48072 max 48072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48072 Ave neighs/atom = 58.767726 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.671 | 4.671 | 4.671 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3449.324 0 -3449.324 -76.35542 Loop time of 1.761e-06 on 1 procs for 0 steps with 818 atoms 170.4% 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 | | 1.761e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3498.00 ave 3498 max 3498 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: 47952.0 ave 47952 max 47952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47952 Ave neighs/atom = 58.621027 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.671 | 4.671 | 4.671 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 -3449.324 -3449.324 26.460843 72.064371 5.0275059 -76.35542 -76.35542 592.19288 -711.09077 -110.16837 2.3265435 909.62596 Loop time of 1.52e-06 on 1 procs for 0 steps with 818 atoms 197.4% 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 | | 1.52e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3498.00 ave 3498 max 3498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23976.0 ave 23976 max 23976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47952.0 ave 47952 max 47952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47952 Ave neighs/atom = 58.621027 Neighbor list builds = 0 Dangerous builds = 0 818 -3449.32404741614 eV 2.3265435147102 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05