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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -58.121897 0.0000000) to (29.059146 58.121897 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9177017 4.9177017 3.6043435 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.121897 0.0000000) to (29.059146 58.121897 3.6043435) create_atoms CPU = 0.003 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9177017 4.9177017 3.6043435 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.121897 0.0000000) to (29.059146 58.121897 3.6043435) create_atoms CPU = 0.002 seconds 522 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 39 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1036 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4359.4583 0 -4359.4583 6505.0132 28 0 -4385.726 0 -4385.726 -2168.9696 Loop time of 4.50655 on 1 procs for 28 steps with 1036 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 = -4359.4582575593 -4385.72214444549 -4385.72604071486 Force two-norm initial, final = 30.698996 0.20329379 Force max component initial, final = 8.1452077 0.060661463 Final line search alpha, max atom move = 1.0000000 0.060661463 Iterations, force evaluations = 28 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4797 | 4.4797 | 4.4797 | 0.0 | 99.40 Neigh | 0.012877 | 0.012877 | 0.012877 | 0.0 | 0.29 Comm | 0.0067807 | 0.0067807 | 0.0067807 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007244 | | | 0.16 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5480.00 ave 5480 max 5480 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: 80596.0 ave 80596 max 80596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80596 Ave neighs/atom = 77.795367 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -4385.726 0 -4385.726 -2168.9696 12175.276 33 0 -4385.8087 0 -4385.8087 -1835.3989 12172.666 Loop time of 0.650294 on 1 procs for 5 steps with 1036 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 = -4385.72604071486 -4385.80491362935 -4385.80871374053 Force two-norm initial, final = 27.517782 6.8522943 Force max component initial, final = 24.821729 5.6068541 Final line search alpha, max atom move = 0.00018672882 0.0010469613 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64641 | 0.64641 | 0.64641 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081135 | 0.00081135 | 0.00081135 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003076 | | | 0.47 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5472.00 ave 5472 max 5472 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: 80644.0 ave 80644 max 80644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80644 Ave neighs/atom = 77.841699 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.739 | 4.739 | 4.739 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4385.8087 0 -4385.8087 -1835.3989 Loop time of 7.147e-06 on 1 procs for 0 steps with 1036 atoms 209.9% 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 | | 7.147e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5472.00 ave 5472 max 5472 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: 80644.0 ave 80644 max 80644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80644 Ave neighs/atom = 77.841699 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.739 | 4.739 | 4.739 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 -4385.8087 -4385.8087 28.933089 116.24379 3.6192712 -1835.3989 -1835.3989 514.68593 -6761.9179 741.03523 2.2897751 370.97305 Loop time of 6.806e-06 on 1 procs for 0 steps with 1036 atoms 323.2% 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 | | 6.806e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5472.00 ave 5472 max 5472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40322.0 ave 40322 max 40322 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80644.0 ave 80644 max 80644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80644 Ave neighs/atom = 77.841699 Neighbor list builds = 0 Dangerous builds = 0 1036 -4385.80871374053 eV 2.28977514864441 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06