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 -36.379699 0.0000000) to (31.505743 36.379699 6.1787846) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6548770 5.5968767 6.1787846 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -36.379699 0.0000000) to (31.505743 36.379699 6.1787846) create_atoms CPU = 0.001 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6548770 5.5968767 6.1787846 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -36.379699 0.0000000) to (31.505743 36.379699 6.1787846) create_atoms CPU = 0.001 seconds 627 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 = 12 26 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1247 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 26 3 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) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4833.6095 0 -4833.6095 75498.459 79 0 -5249.1359 0 -5249.1359 56681.7 Loop time of 4.54188 on 1 procs for 79 steps with 1247 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 = -4833.60948640638 -5249.13070208836 -5249.13588044312 Force two-norm initial, final = 534.07574 0.30488330 Force max component initial, final = 118.58235 0.077591119 Final line search alpha, max atom move = 1.0000000 0.077591119 Iterations, force evaluations = 79 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5057 | 4.5057 | 4.5057 | 0.0 | 99.20 Neigh | 0.019784 | 0.019784 | 0.019784 | 0.0 | 0.44 Comm | 0.0069348 | 0.0069348 | 0.0069348 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009466 | | | 0.21 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4459.00 ave 4459 max 4459 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: 75134.0 ave 75134 max 75134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75134 Ave neighs/atom = 60.251804 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 26 3 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.628 | 4.628 | 4.628 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -5249.1359 0 -5249.1359 56681.7 14163.868 89 0 -5253.7047 0 -5253.7047 -653.18463 14430.798 Loop time of 0.387863 on 1 procs for 10 steps with 1247 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 = -5249.13588044312 -5253.7007158325 -5253.70470289177 Force two-norm initial, final = 871.59144 12.536074 Force max component initial, final = 561.74991 10.498500 Final line search alpha, max atom move = 6.6026921e-05 0.00069318363 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38472 | 0.38472 | 0.38472 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042989 | 0.00042989 | 0.00042989 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002708 | | | 0.70 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4457.00 ave 4457 max 4457 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: 75272.0 ave 75272 max 75272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75272 Ave neighs/atom = 60.362470 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 = 12 27 3 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) = 4.767 | 4.767 | 4.767 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5253.7047 0 -5253.7047 -653.18463 Loop time of 2.116e-06 on 1 procs for 0 steps with 1247 atoms 141.8% 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 | | 2.116e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4425.00 ave 4425 max 4425 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: 71486.0 ave 71486 max 71486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71486 Ave neighs/atom = 57.326383 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 = 12 27 3 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) = 4.767 | 4.767 | 4.767 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 -5253.7047 -5253.7047 31.621302 73.440408 6.2140612 -653.18463 -653.18463 -1169.8691 -123.01463 -666.67015 2.2573932 1111.6393 Loop time of 2.273e-06 on 1 procs for 0 steps with 1247 atoms 220.0% 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 | | 2.273e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4425.00 ave 4425 max 4425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35743.0 ave 35743 max 35743 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71486.0 ave 71486 max 71486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71486 Ave neighs/atom = 57.326383 Neighbor list builds = 0 Dangerous builds = 0 1247 -5253.70470289177 eV 2.25739320230483 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05