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 = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -59.242523 0.0000000) to (20.945395 59.242523 5.1563998) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7123804 6.2832979 5.1563998 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.242523 0.0000000) to (20.945395 59.242523 5.1563998) create_atoms CPU = 0.006 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7123804 6.2832979 5.1563998 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.242523 0.0000000) to (20.945395 59.242523 5.1563998) create_atoms CPU = 0.005 seconds 530 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 28 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_331285495617_004#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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.471 | 5.471 | 5.471 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3935.7787 0 -3935.7787 30334.849 64 0 -4112.6824 0 -4112.6824 2420.4828 Loop time of 2.72697 on 1 procs for 64 steps with 1056 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 = -3935.77868324815 -4112.67872562122 -4112.68239065924 Force two-norm initial, final = 305.45507 0.24957653 Force max component initial, final = 98.724110 0.035183103 Final line search alpha, max atom move = 1.0000000 0.035183103 Iterations, force evaluations = 64 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6523 | 2.6523 | 2.6523 | 0.0 | 97.26 Neigh | 0.033633 | 0.033633 | 0.033633 | 0.0 | 1.23 Comm | 0.023919 | 0.023919 | 0.023919 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01708 | | | 0.63 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8835.00 ave 8835 max 8835 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: 235364.0 ave 235364 max 235364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235364 Ave neighs/atom = 222.88258 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.471 | 5.471 | 5.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -4112.6824 0 -4112.6824 2420.4828 12796.72 70 0 -4113.0499 0 -4113.0499 -32.19668 12815.672 Loop time of 0.181578 on 1 procs for 6 steps with 1056 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 = -4112.68239065923 -4113.04903737023 -4113.04985031082 Force two-norm initial, final = 123.03234 1.0621840 Force max component initial, final = 111.76592 0.71613921 Final line search alpha, max atom move = 0.00024131606 0.00017281589 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17546 | 0.17546 | 0.17546 | 0.0 | 96.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014143 | 0.0014143 | 0.0014143 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004701 | | | 2.59 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8889.00 ave 8889 max 8889 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: 235232.0 ave 235232 max 235232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235232 Ave neighs/atom = 222.75758 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.609 | 5.609 | 5.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4113.0499 0 -4113.0499 -32.19668 Loop time of 6.585e-06 on 1 procs for 0 steps with 1056 atoms 182.2% 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 | | 6.585e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8889.00 ave 8889 max 8889 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: 235128.0 ave 235128 max 235128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235128 Ave neighs/atom = 222.65909 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.609 | 5.609 | 5.609 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 -4113.0499 -4113.0499 20.869378 119.0613 5.1577614 -32.19668 -32.19668 -89.20463 55.892087 -63.277498 2.3569314 434.46814 Loop time of 7.247e-06 on 1 procs for 0 steps with 1056 atoms 248.4% 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 | | 7.247e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8889.00 ave 8889 max 8889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117564.0 ave 117564 max 117564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235128.0 ave 235128 max 235128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235128 Ave neighs/atom = 222.65909 Neighbor list builds = 0 Dangerous builds = 0 1056 -4113.04985031082 eV 2.35693136271875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03