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 -41.745971 0.0000000) to (29.518859 41.745971 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7275398 6.2307419 5.1000820 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.745971 0.0000000) to (29.518859 41.745971 5.1000820) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7275398 6.2307419 5.1000820 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.745971 0.0000000) to (29.518859 41.745971 5.1000820) create_atoms CPU = 0.002 seconds 538 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 4 atoms, new total = 1070 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) = 7.086 | 7.086 | 7.086 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4230.5843 0 -4230.5843 41900.724 85 0 -4484.612 0 -4484.612 646.14761 Loop time of 4.65019 on 1 procs for 85 steps with 1070 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 = -4230.58425886899 -4484.60773040838 -4484.61202525067 Force two-norm initial, final = 375.26904 0.29403555 Force max component initial, final = 117.53999 0.035531214 Final line search alpha, max atom move = 1.0000000 0.035531214 Iterations, force evaluations = 85 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5873 | 4.5873 | 4.5873 | 0.0 | 98.65 Neigh | 0.029966 | 0.029966 | 0.029966 | 0.0 | 0.64 Comm | 0.022057 | 0.022057 | 0.022057 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01085 | | | 0.23 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12896.0 ave 12896 max 12896 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: 658964.0 ave 658964 max 658964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658964 Ave neighs/atom = 615.85421 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 = 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.087 | 7.087 | 7.087 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -4484.612 0 -4484.612 646.14761 12569.595 92 0 -4485.1579 0 -4485.1579 -0.95689317 12573.489 Loop time of 0.30127 on 1 procs for 7 steps with 1070 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 = -4484.61202525063 -4485.15778192993 -4485.15791040061 Force two-norm initial, final = 149.14327 0.52224131 Force max component initial, final = 116.76587 0.10332017 Final line search alpha, max atom move = 0.00056786666 5.8672079e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29562 | 0.29562 | 0.29562 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010474 | 0.0010474 | 0.0010474 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004602 | | | 1.53 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12680.0 ave 12680 max 12680 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: 658404.0 ave 658404 max 658404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658404 Ave neighs/atom = 615.33084 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 15 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) = 7.225 | 7.225 | 7.225 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4485.1579 0 -4485.1579 -0.95689317 Loop time of 1.991e-06 on 1 procs for 0 steps with 1070 atoms 200.9% 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 | | 1.991e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12735.0 ave 12735 max 12735 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: 657992.0 ave 657992 max 657992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657992 Ave neighs/atom = 614.94579 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 15 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) = 7.225 | 7.225 | 7.225 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 -4485.1579 -4485.1579 29.363833 83.925319 5.1021127 -0.95689317 -0.95689317 1.0483275 9.251805 -13.170812 2.3435113 609.82361 Loop time of 2.624e-06 on 1 procs for 0 steps with 1070 atoms 266.8% 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 | | 2.624e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12735.0 ave 12735 max 12735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328996.0 ave 328996 max 328996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 657992.0 ave 657992 max 657992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657992 Ave neighs/atom = 614.94579 Neighbor list builds = 0 Dangerous builds = 0 1070 -4485.15791040059 eV 2.34351134663111 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05