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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -55.403427 0.0000000) to (33.927531 55.403427 8.6176016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4721825 5.3616220 5.7450677 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -55.403427 0.0000000) to (33.927531 55.403427 8.6176016) create_atoms CPU = 0.002 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4721825 5.3616220 5.7450677 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -55.403427 0.0000000) to (33.927531 55.403427 8.6176016) create_atoms CPU = 0.002 seconds 1492 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2976 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_306032198193_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.55 | 12.55 | 12.55 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9851.3675 0 -9851.3675 223664.98 90 0 -13012.095 0 -13012.095 6597.127 Loop time of 8.44083 on 1 procs for 90 steps with 2976 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9851.36745290231 -13012.0833900941 -13012.0954969464 Force two-norm initial, final = 4067.0072 0.37370657 Force max component initial, final = 693.20002 0.067304699 Final line search alpha, max atom move = 1.0000000 0.067304699 Iterations, force evaluations = 90 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3373 | 8.3373 | 8.3373 | 0.0 | 98.77 Neigh | 0.048896 | 0.048896 | 0.048896 | 0.0 | 0.58 Comm | 0.029408 | 0.029408 | 0.029408 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02526 | | | 0.30 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14475.0 ave 14475 max 14475 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: 974582.0 ave 974582 max 974582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 974582 Ave neighs/atom = 327.48051 Neighbor list builds = 1 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.55 | 12.55 | 12.55 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -13012.095 0 -13012.095 6597.127 32397.037 95 0 -13012.587 0 -13012.587 -190.88333 32524.292 Loop time of 0.357719 on 1 procs for 5 steps with 2976 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 = -13012.0954969465 -13012.5850037867 -13012.5866981959 Force two-norm initial, final = 264.63534 7.5759894 Force max component initial, final = 238.58969 5.5672906 Final line search alpha, max atom move = 7.8622975e-05 0.00043771695 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35286 | 0.35286 | 0.35286 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093881 | 0.00093881 | 0.00093881 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003924 | | | 1.10 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14762.0 ave 14762 max 14762 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: 978530.0 ave 978530 max 978530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 978530 Ave neighs/atom = 328.80712 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.07 | 12.07 | 12.07 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13012.587 0 -13012.587 -190.88333 Loop time of 2.278e-06 on 1 procs for 0 steps with 2976 atoms 131.7% 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 | | 2.278e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14762.0 ave 14762 max 14762 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: 963536.0 ave 963536 max 963536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 963536 Ave neighs/atom = 323.76882 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.07 | 12.07 | 12.07 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 -13012.587 -13012.587 33.923774 111.27888 8.6157074 -190.88333 -190.88333 -274.21948 -51.752103 -246.67841 2.1806184 874.45439 Loop time of 2.649e-06 on 1 procs for 0 steps with 2976 atoms 226.5% 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 | | 2.649e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14762.0 ave 14762 max 14762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 481768.0 ave 481768 max 481768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 963536.0 ave 963536 max 963536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 963536 Ave neighs/atom = 323.76882 Neighbor list builds = 0 Dangerous builds = 0 2976 -13012.5866981959 eV 2.18061842767533 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09