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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -37.913654 0.0000000) to (46.434553 37.913654 8.8547219) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9098523 5.5147133 5.9031479 Created 1316 atoms using lattice units in orthogonal box = (0.0000000 -37.913654 0.0000000) to (46.434553 37.913654 8.8547219) create_atoms CPU = 0.006 seconds 1316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9098523 5.5147133 5.9031479 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -37.913654 0.0000000) to (46.434553 37.913654 8.8547219) create_atoms CPU = 0.005 seconds 1322 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 13 20 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2638 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.075 | 6.075 | 6.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8831.0759 0 -8831.0759 55167.949 63 0 -9296.4782 0 -9296.4782 5846.6247 Loop time of 4.26717 on 1 procs for 63 steps with 2638 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 = -8831.07587557036 -9296.46955319125 -9296.47818221695 Force two-norm initial, final = 536.48537 0.31627217 Force max component initial, final = 128.49062 0.037106811 Final line search alpha, max atom move = 1.0000000 0.037106811 Iterations, force evaluations = 63 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0268 | 4.0268 | 4.0268 | 0.0 | 94.37 Neigh | 0.18508 | 0.18508 | 0.18508 | 0.0 | 4.34 Comm | 0.024074 | 0.024074 | 0.024074 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03121 | | | 0.73 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8892.00 ave 8892 max 8892 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: 379158.0 ave 379158 max 379158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379158 Ave neighs/atom = 143.72934 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.075 | 6.075 | 6.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -9296.4782 0 -9296.4782 5846.6247 31177.54 69 0 -9296.9884 0 -9296.9884 -141.55465 31311.238 Loop time of 0.303844 on 1 procs for 6 steps with 2638 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9296.47818221692 -9296.98726016807 -9296.98840707761 Force two-norm initial, final = 225.88132 6.4652893 Force max component initial, final = 200.33486 5.0884367 Final line search alpha, max atom move = 9.7137204e-05 0.00049427651 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29554 | 0.29554 | 0.29554 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001493 | 0.001493 | 0.001493 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006806 | | | 2.24 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8891.00 ave 8891 max 8891 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: 379574.0 ave 379574 max 379574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379574 Ave neighs/atom = 143.88704 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.213 | 6.213 | 6.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9296.9884 0 -9296.9884 -141.55465 Loop time of 6.295e-06 on 1 procs for 0 steps with 2638 atoms 190.6% 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 | | 6.295e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8891.00 ave 8891 max 8891 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: 377966.0 ave 377966 max 377966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 377966 Ave neighs/atom = 143.27748 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.213 | 6.213 | 6.213 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 -9296.9884 -9296.9884 46.454884 76.222702 8.8426924 -141.55465 -141.55465 -199.79173 35.146183 -260.0184 2.3205103 1500.7908 Loop time of 6.385e-06 on 1 procs for 0 steps with 2638 atoms 313.2% 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 | | 6.385e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8891.00 ave 8891 max 8891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 188983.0 ave 188983 max 188983 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 377966.0 ave 377966 max 377966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 377966 Ave neighs/atom = 143.27748 Neighbor list builds = 0 Dangerous builds = 0 2638 -9297.00159707762 eV 2.32051031040592 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05