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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -41.433262 0.0000000) to (29.297741 41.433262 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4390516 5.6499903 5.1000820 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.433262 0.0000000) to (29.297741 41.433262 5.1000820) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4390516 5.6499903 5.1000820 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.433262 0.0000000) to (29.297741 41.433262 5.1000820) create_atoms CPU = 0.001 seconds 532 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.087 | 7.087 | 7.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4218.5814 0 -4218.5814 25726.653 88 0 -4374.8885 0 -4374.8885 -4280.4057 Loop time of 4.88627 on 1 procs for 88 steps with 1048 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 = -4218.58135667423 -4374.88486239248 -4374.88846990476 Force two-norm initial, final = 222.14943 0.25001973 Force max component initial, final = 50.243042 0.024683371 Final line search alpha, max atom move = 1.0000000 0.024683371 Iterations, force evaluations = 88 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7877 | 4.7877 | 4.7877 | 0.0 | 97.98 Neigh | 0.060704 | 0.060704 | 0.060704 | 0.0 | 1.24 Comm | 0.025043 | 0.025043 | 0.025043 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01282 | | | 0.26 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12438.0 ave 12438 max 12438 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: 641144.0 ave 641144 max 641144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 641144 Ave neighs/atom = 611.77863 Neighbor list builds = 2 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.083 | 7.083 | 7.083 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4374.8885 0 -4374.8885 -4280.4057 12381.989 92 0 -4375.0856 0 -4375.0856 -570.57468 12354.491 Loop time of 0.189583 on 1 procs for 4 steps with 1048 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 = -4374.88846990475 -4375.08215370661 -4375.08555089483 Force two-norm initial, final = 98.519214 9.0253546 Force max component initial, final = 82.363526 8.2279194 Final line search alpha, max atom move = 0.00012043278 0.00099091123 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18644 | 0.18644 | 0.18644 | 0.0 | 98.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005974 | 0.0005974 | 0.0005974 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002545 | | | 1.34 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12438.0 ave 12438 max 12438 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: 641600.0 ave 641600 max 641600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 641600 Ave neighs/atom = 612.21374 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.221 | 7.221 | 7.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4375.0856 0 -4375.0856 -570.57468 Loop time of 2.33e-06 on 1 procs for 0 steps with 1048 atoms 214.6% 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 | | 2.33e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12460.0 ave 12460 max 12460 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: 642080.0 ave 642080 max 642080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 642080 Ave neighs/atom = 612.67176 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.221 | 7.221 | 7.221 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 -4375.0856 -4375.0856 29.240019 82.644136 5.1125217 -570.57468 -570.57468 -1064.9251 -221.6614 -425.13758 2.308216 744.77498 Loop time of 2.771e-06 on 1 procs for 0 steps with 1048 atoms 216.5% 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 | | 2.771e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12460.0 ave 12460 max 12460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 321040.0 ave 321040 max 321040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 642080.0 ave 642080 max 642080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 642080 Ave neighs/atom = 612.67176 Neighbor list builds = 0 Dangerous builds = 0 1048 -4375.08555089483 eV 2.30821595071908 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05