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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -53.615043 0.0000000) to (26.807522 53.615043 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6219865 4.6219865 3.5200000 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -53.615043 0.0000000) to (26.807522 53.615043 3.5200000) create_atoms CPU = 0.002 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6219865 4.6219865 3.5200000 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -53.615043 0.0000000) to (26.807522 53.615043 3.5200000) create_atoms CPU = 0.002 seconds 466 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 25 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 928 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.421 | 5.421 | 5.421 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4067.7984 0 -4067.7984 5821.8532 71 0 -4112.1654 0 -4112.1654 9233.3969 Loop time of 4.13688 on 1 procs for 71 steps with 928 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 = -4067.79844267367 -4112.16156207317 -4112.16541311021 Force two-norm initial, final = 23.704767 0.20156287 Force max component initial, final = 4.8626855 0.017115746 Final line search alpha, max atom move = 1.0000000 0.017115746 Iterations, force evaluations = 71 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0658 | 4.0658 | 4.0658 | 0.0 | 98.28 Neigh | 0.027086 | 0.027086 | 0.027086 | 0.0 | 0.65 Comm | 0.027078 | 0.027078 | 0.027078 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01687 | | | 0.41 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8856.00 ave 8856 max 8856 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: 230072.0 ave 230072 max 230072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230072 Ave neighs/atom = 247.92241 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.421 | 5.421 | 5.421 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4112.1654 0 -4112.1654 9233.3969 10118.496 76 0 -4112.3729 0 -4112.3729 58.590422 10170.513 Loop time of 0.227112 on 1 procs for 5 steps with 928 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 = -4112.16541311019 -4112.37170460072 -4112.37292827461 Force two-norm initial, final = 106.81194 1.5447936 Force max component initial, final = 85.034103 1.4178640 Final line search alpha, max atom move = 0.00027696514 0.00039269890 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22196 | 0.22196 | 0.22196 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012675 | 0.0012675 | 0.0012675 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003882 | | | 1.71 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8848.00 ave 8848 max 8848 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: 229376.0 ave 229376 max 229376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229376 Ave neighs/atom = 247.17241 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.559 | 5.559 | 5.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4112.3729 0 -4112.3729 58.590422 Loop time of 6.225e-06 on 1 procs for 0 steps with 928 atoms 192.8% 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 | | 6.225e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8853.00 ave 8853 max 8853 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: 229092.0 ave 229092 max 229092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229092 Ave neighs/atom = 246.86638 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.559 | 5.559 | 5.559 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 -4112.3729 -4112.3729 26.803073 107.7034 3.5231318 58.590422 58.590422 223.32122 31.172112 -78.722063 2.2011005 407.79831 Loop time of 7.217e-06 on 1 procs for 0 steps with 928 atoms 249.4% 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 | | 7.217e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8853.00 ave 8853 max 8853 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114546.0 ave 114546 max 114546 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229092.0 ave 229092 max 229092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229092 Ave neighs/atom = 246.86638 Neighbor list builds = 0 Dangerous builds = 0 928 -4091.44685293161 eV 2.2011005101642 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05