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 = 2.8147787 2.8147787 2.8147787 Created orthogonal box = (0.0000000 -34.011101 0.0000000) to (41.654921 34.011101 6.8947716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9943075 4.1931494 4.5965144 Created 873 atoms using lattice units in orthogonal box = (0.0000000 -34.011101 0.0000000) to (41.654921 34.011101 6.8947716) create_atoms CPU = 0.001 seconds 873 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9943075 4.1931494 4.5965144 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.011101 0.0000000) to (41.654921 34.011101 6.8947716) create_atoms CPU = 0.001 seconds 879 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 19 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1749 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.561 | 5.561 | 5.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3887.9856 0 -3887.9856 349643.99 136 0 -7167.8678 0 -7167.8678 6182.538 Loop time of 3.91422 on 1 procs for 136 steps with 1749 atoms 95.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3887.98557009379 -7167.86130434319 -7167.86779120291 Force two-norm initial, final = 4748.8482 0.38901774 Force max component initial, final = 782.44846 0.078419848 Final line search alpha, max atom move = 0.90419143 0.070906554 Iterations, force evaluations = 136 259 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8159 | 3.8159 | 3.8159 | 0.0 | 97.49 Neigh | 0.050033 | 0.050033 | 0.050033 | 0.0 | 1.28 Comm | 0.0239 | 0.0239 | 0.0239 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02444 | | | 0.62 Nlocal: 1749.00 ave 1749 max 1749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7412.00 ave 7412 max 7412 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: 289554.0 ave 289554 max 289554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289554 Ave neighs/atom = 165.55403 Neighbor list builds = 3 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 136 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.561 | 5.561 | 5.561 Mbytes Step Temp E_pair E_mol TotEng Press Volume 136 0 -7167.8678 0 -7167.8678 6182.538 19536.056 140 0 -7168.0876 0 -7168.0876 210.8822 19597.258 Loop time of 0.0915646 on 1 procs for 4 steps with 1749 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 = -7167.8677912029 -7168.08598897604 -7168.08757360958 Force two-norm initial, final = 148.73933 5.9715749 Force max component initial, final = 130.62012 5.0288268 Final line search alpha, max atom move = 9.0790823e-05 0.00045657133 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089136 | 0.089136 | 0.089136 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035839 | 0.00035839 | 0.00035839 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002071 | | | 2.26 Nlocal: 1749.00 ave 1749 max 1749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7410.00 ave 7410 max 7410 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: 289396.0 ave 289396 max 289396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289396 Ave neighs/atom = 165.46369 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.699 | 5.699 | 5.699 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7168.0876 0 -7168.0876 210.8822 Loop time of 2.211e-06 on 1 procs for 0 steps with 1749 atoms 180.9% 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 | | 2.211e-06 | | |100.00 Nlocal: 1749.00 ave 1749 max 1749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7405.00 ave 7405 max 7405 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: 289236.0 ave 289236 max 289236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289236 Ave neighs/atom = 165.37221 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.699 | 5.699 | 5.699 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 -7168.0876 -7168.0876 41.629546 68.070333 6.9156938 210.8822 210.8822 -35.608708 255.8753 412.38 2.2419282 1742.8226 Loop time of 2.506e-06 on 1 procs for 0 steps with 1749 atoms 239.4% 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 | | 2.506e-06 | | |100.00 Nlocal: 1749.00 ave 1749 max 1749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7405.00 ave 7405 max 7405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144618.0 ave 144618 max 144618 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 289236.0 ave 289236 max 289236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289236 Ave neighs/atom = 165.37221 Neighbor list builds = 0 Dangerous builds = 0 1749 -7168.08757360958 eV 2.24192820022125 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05