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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -76.415440 0.0000000) to (38.207720 76.415440 4.0500102) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5809029 5.5809029 4.0500102 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -76.415440 0.0000000) to (38.207720 76.415440 4.0500102) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5809029 5.5809029 4.0500102 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.415440 0.0000000) to (38.207720 76.415440 4.0500102) create_atoms CPU = 0.002 seconds 714 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 11 41 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_120808805541_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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4707.2399 0 -4707.2399 19028.403 62 0 -4823.9219 0 -4823.9219 3736.4464 Loop time of 2.25404 on 1 procs for 62 steps with 1426 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 = -4707.23986714426 -4823.91840272058 -4823.92188033661 Force two-norm initial, final = 118.39165 0.14591056 Force max component initial, final = 22.653801 0.036230048 Final line search alpha, max atom move = 1.0000000 0.036230048 Iterations, force evaluations = 62 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2106 | 2.2106 | 2.2106 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023494 | 0.023494 | 0.023494 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01995 | | | 0.89 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8446.00 ave 8446 max 8446 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: 189472.0 ave 189472 max 189472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189472 Ave neighs/atom = 132.86957 Neighbor list builds = 0 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -4823.9219 0 -4823.9219 3736.4464 23649.304 68 0 -4824.1557 0 -4824.1557 -3.47078 23763.173 Loop time of 0.171573 on 1 procs for 6 steps with 1426 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 = -4823.92188033662 -4824.15520390003 -4824.15567114169 Force two-norm initial, final = 106.82562 0.59264732 Force max component initial, final = 89.850119 0.50038811 Final line search alpha, max atom move = 0.00018483422 9.2488846e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16448 | 0.16448 | 0.16448 | 0.0 | 95.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001581 | 0.001581 | 0.001581 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005517 | | | 3.22 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8437.00 ave 8437 max 8437 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: 182136.0 ave 182136 max 182136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182136 Ave neighs/atom = 127.72511 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.233 | 5.233 | 5.233 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4824.1557 0 -4824.1557 -3.47078 Loop time of 6.605e-06 on 1 procs for 0 steps with 1426 atoms 196.8% 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 | | 6.605e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8424.00 ave 8424 max 8424 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: 174448.0 ave 174448 max 174448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174448 Ave neighs/atom = 122.33380 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.233 | 5.233 | 5.233 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 -4824.1557 -4824.1557 38.157626 153.55773 4.0555653 -3.47078 -3.47078 14.438674 8.9327625 -33.783776 2.5724841 529.08297 Loop time of 7.316e-06 on 1 procs for 0 steps with 1426 atoms 273.4% 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 | | 7.316e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8424.00 ave 8424 max 8424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87224.0 ave 87224 max 87224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174448.0 ave 174448 max 174448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174448 Ave neighs/atom = 122.33380 Neighbor list builds = 0 Dangerous builds = 0 1426 -4824.15567114169 eV 2.57248407405804 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03