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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -59.934527 0.0000000) to (48.936336 59.934527 9.9204335) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0332469 5.7471464 6.6136223 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -59.934527 0.0000000) to (48.936336 59.934527 9.9204335) create_atoms CPU = 0.002 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0332469 5.7471464 6.6136223 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -59.934527 0.0000000) to (48.936336 59.934527 9.9204335) create_atoms CPU = 0.002 seconds 1755 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3502 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_664470114311_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.395 | 7.395 | 7.395 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11598.409 0 -11598.409 5081.3073 87 0 -11736.676 0 -11736.676 3471.4106 Loop time of 4.17319 on 1 procs for 87 steps with 3502 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 = -11598.4094742587 -11736.6649450401 -11736.6762155608 Force two-norm initial, final = 56.268857 0.24766151 Force max component initial, final = 7.4505325 0.031291522 Final line search alpha, max atom move = 1.0000000 0.031291522 Iterations, force evaluations = 87 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.999 | 3.999 | 3.999 | 0.0 | 95.83 Neigh | 0.13632 | 0.13632 | 0.13632 | 0.0 | 3.27 Comm | 0.016152 | 0.016152 | 0.016152 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02169 | | | 0.52 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11436.0 ave 11436 max 11436 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: 609032.0 ave 609032 max 609032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609032 Ave neighs/atom = 173.90977 Neighbor list builds = 4 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.395 | 7.395 | 7.395 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -11736.676 0 -11736.676 3471.4106 58192.79 95 0 -11737.537 0 -11737.537 49.678133 58442.209 Loop time of 0.293749 on 1 procs for 8 steps with 3502 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 = -11736.6762155608 -11737.5336942059 -11737.5373813851 Force two-norm initial, final = 271.50430 3.1711606 Force max component initial, final = 257.41131 1.9418798 Final line search alpha, max atom move = 0.00010395959 0.00020187703 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28661 | 0.28661 | 0.28661 | 0.0 | 97.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095955 | 0.00095955 | 0.00095955 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00618 | | | 2.10 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11429.0 ave 11429 max 11429 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: 609282.0 ave 609282 max 609282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609282 Ave neighs/atom = 173.98115 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.533 | 7.533 | 7.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11737.537 0 -11737.537 49.678133 Loop time of 2.44e-06 on 1 procs for 0 steps with 3502 atoms 163.9% 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 | | 2.44e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11450.0 ave 11450 max 11450 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: 608702.0 ave 608702 max 608702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 608702 Ave neighs/atom = 173.81553 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.533 | 7.533 | 7.533 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 -11737.537 -11737.537 48.834087 120.76179 9.910008 49.678133 49.678133 43.270259 53.632562 52.131577 2.521246 2241.3673 Loop time of 2.712e-06 on 1 procs for 0 steps with 3502 atoms 258.1% 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 | | 2.712e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11450.0 ave 11450 max 11450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 304351.0 ave 304351 max 304351 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 608702.0 ave 608702 max 608702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 608702 Ave neighs/atom = 173.81553 Neighbor list builds = 0 Dangerous builds = 0 3502 -11716.2472714728 eV 2.52124598389047 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05