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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -38.136789 0.0000000) to (12.711235 38.136789 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7385986 3.7385986 3.0829274 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -38.136789 0.0000000) to (12.711235 38.136789 3.0829274) create_atoms CPU = 0.000 seconds 103 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7385986 3.7385986 3.0829274 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -38.136789 0.0000000) to (12.711235 38.136789 3.0829274) create_atoms CPU = 0.000 seconds 103 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 202 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_152208847456_000#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.787 | 4.787 | 4.787 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1263.5909 0 -1263.5909 42321.773 62 0 -1309.179 0 -1309.179 -11798.04 Loop time of 3.21544 on 1 procs for 62 steps with 202 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 = -1263.59094605901 -1309.17789022137 -1309.17901909057 Force two-norm initial, final = 141.42115 0.14674498 Force max component initial, final = 59.628223 0.021676213 Final line search alpha, max atom move = 1.0000000 0.021676213 Iterations, force evaluations = 62 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2054 | 3.2054 | 3.2054 | 0.0 | 99.69 Neigh | 0.0069005 | 0.0069005 | 0.0069005 | 0.0 | 0.21 Comm | 0.0021672 | 0.0021672 | 0.0021672 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001013 | | | 0.03 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2462.00 ave 2462 max 2462 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: 14998.0 ave 14998 max 14998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14998 Ave neighs/atom = 74.247525 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.786 | 4.786 | 4.786 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1309.179 0 -1309.179 -11798.04 2988.9948 74 0 -1309.3208 0 -1309.3208 2933.4981 2966.9214 Loop time of 0.368542 on 1 procs for 12 steps with 202 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 = -1309.17901909057 -1309.3206268952 -1309.32077200916 Force two-norm initial, final = 37.428985 0.64912678 Force max component initial, final = 31.770989 0.44081558 Final line search alpha, max atom move = 0.00074738006 0.00032945678 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36777 | 0.36777 | 0.36777 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001879 | 0.0001879 | 0.0001879 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005865 | | | 0.16 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2445.00 ave 2445 max 2445 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: 14898.0 ave 14898 max 14898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14898 Ave neighs/atom = 73.752475 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.924 | 4.924 | 4.924 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1309.3208 0 -1309.3208 2933.4981 Loop time of 4.9e-06 on 1 procs for 0 steps with 202 atoms 122.4% 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 | | 4.9e-06 | | |100.00 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2445.00 ave 2445 max 2445 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: 15178.0 ave 15178 max 15178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15178 Ave neighs/atom = 75.138614 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.924 | 4.924 | 4.924 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 -1309.3208 -1309.3208 12.759929 76.273577 3.0484822 2933.4981 2933.4981 238.9581 8502.8508 58.685392 2.5921082 321.31721 Loop time of 1.9e-06 on 1 procs for 0 steps with 202 atoms 157.9% 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 | | 1.9e-06 | | |100.00 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2445.00 ave 2445 max 2445 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7589.00 ave 7589 max 7589 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15178.0 ave 15178 max 15178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15178 Ave neighs/atom = 75.138614 Neighbor list builds = 0 Dangerous builds = 0 202 -1309.32077200916 eV 2.59210816329534 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03