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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -62.175603 0.0000000) to (35.897101 62.175603 6.0968195) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226309 5.5798618 6.0968195 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -62.175603 0.0000000) to (35.897101 62.175603 6.0968195) create_atoms CPU = 0.003 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226309 5.5798618 6.0968195 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.175603 0.0000000) to (35.897101 62.175603 6.0968195) create_atoms CPU = 0.002 seconds 1250 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2490 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10920.189 0 -10920.189 6597.5213 91 0 -11048.586 0 -11048.586 6092.2149 Loop time of 3.53911 on 1 procs for 91 steps with 2490 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10920.1886743058 -11048.5759145646 -11048.5859444707 Force two-norm initial, final = 57.497397 0.36789429 Force max component initial, final = 10.514242 0.097426070 Final line search alpha, max atom move = 0.60590259 0.059030708 Iterations, force evaluations = 91 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4057 | 3.4057 | 3.4057 | 0.0 | 96.23 Neigh | 0.083653 | 0.083653 | 0.083653 | 0.0 | 2.36 Comm | 0.025421 | 0.025421 | 0.025421 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02431 | | | 0.69 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12146.0 ave 12146 max 12146 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: 434692.0 ave 434692 max 434692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434692 Ave neighs/atom = 174.57510 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -11048.586 0 -11048.586 6092.2149 27215.274 95 0 -11048.931 0 -11048.931 367.15921 27302.98 Loop time of 0.140502 on 1 procs for 4 steps with 2490 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 = -11048.5859444708 -11048.9236692823 -11048.9310802456 Force two-norm initial, final = 212.44405 12.141203 Force max component initial, final = 187.96267 10.609340 Final line search alpha, max atom move = 5.3049658e-05 0.00056282183 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13632 | 0.13632 | 0.13632 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069295 | 0.00069295 | 0.00069295 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003486 | | | 2.48 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12124.0 ave 12124 max 12124 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: 435082.0 ave 435082 max 435082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 435082 Ave neighs/atom = 174.73173 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.676 | 6.676 | 6.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11048.931 0 -11048.931 367.15921 Loop time of 2.421e-06 on 1 procs for 0 steps with 2490 atoms 165.2% 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 | | 2.421e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12121.0 ave 12121 max 12121 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: 434926.0 ave 434926 max 434926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434926 Ave neighs/atom = 174.66908 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.676 | 6.676 | 6.676 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 -11048.931 -11048.931 35.921549 124.7586 6.0923454 367.15921 367.15921 185.45274 624.61028 291.41461 2.2432337 968.47216 Loop time of 2.55e-06 on 1 procs for 0 steps with 2490 atoms 235.3% 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 | | 2.55e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12121.0 ave 12121 max 12121 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217463.0 ave 217463 max 217463 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 434926.0 ave 434926 max 434926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434926 Ave neighs/atom = 174.66908 Neighbor list builds = 0 Dangerous builds = 0 2490 -11048.9310802456 eV 2.24323370071749 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04