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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -43.690605 0.0000000) to (5.0449566 43.690605 6.1787847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0449566 5.8254141 6.1787847 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -43.690605 0.0000000) to (5.0449566 43.690605 6.1787847) create_atoms CPU = 0.003 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0449566 5.8254141 6.1787847 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.690605 0.0000000) to (5.0449566 43.690605 6.1787847) create_atoms CPU = 0.002 seconds 122 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 32 3 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 242 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_856956178669_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -740.96757 0 -740.96757 199753.4 64 0 -1020.6005 0 -1020.6005 69640.288 Loop time of 2.20503 on 1 procs for 64 steps with 242 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 = -740.967571796617 -1020.59957224317 -1020.60051957509 Force two-norm initial, final = 598.16305 0.11265506 Force max component initial, final = 166.10562 0.012889268 Final line search alpha, max atom move = 1.0000000 0.012889268 Iterations, force evaluations = 64 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1907 | 2.1907 | 2.1907 | 0.0 | 99.35 Neigh | 0.0028607 | 0.0028607 | 0.0028607 | 0.0 | 0.13 Comm | 0.0063925 | 0.0063925 | 0.0063925 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005098 | | | 0.23 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2338.00 ave 2338 max 2338 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: 15088.0 ave 15088 max 15088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15088 Ave neighs/atom = 62.347107 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.447 | 4.447 | 4.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -1020.6005 0 -1020.6005 69640.288 2723.8209 102 0 -1023.3883 0 -1023.3883 1.6226505 2814.0771 Loop time of 0.82702 on 1 procs for 38 steps with 242 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 = -1020.60051957509 -1023.38762746772 -1023.38826660369 Force two-norm initial, final = 212.28801 1.7357787 Force max component initial, final = 159.31115 1.2632939 Final line search alpha, max atom move = 0.0030415350 0.0038423525 Iterations, force evaluations = 38 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8061 | 0.8061 | 0.8061 | 0.0 | 97.47 Neigh | 0.0093489 | 0.0093489 | 0.0093489 | 0.0 | 1.13 Comm | 0.0027622 | 0.0027622 | 0.0027622 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008805 | | | 1.06 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2326.00 ave 2326 max 2326 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: 14188.0 ave 14188 max 14188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14188 Ave neighs/atom = 58.628099 Neighbor list builds = 3 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1023.3883 0 -1023.3883 1.6226505 Loop time of 9.331e-06 on 1 procs for 0 steps with 242 atoms 139.3% 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 | | 9.331e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2326.00 ave 2326 max 2326 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: 14328.0 ave 14328 max 14328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14328 Ave neighs/atom = 59.206612 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.585 | 4.585 | 4.585 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 -1023.3883 -1023.3883 4.9861147 90.646272 6.2262101 1.6226505 1.6226505 -327.18272 -392.71809 724.76876 2.4274852 99.300043 Loop time of 6.174e-06 on 1 procs for 0 steps with 242 atoms 243.0% 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 | | 6.174e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2326.00 ave 2326 max 2326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7164.00 ave 7164 max 7164 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 14328.0 ave 14328 max 14328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14328 Ave neighs/atom = 59.206612 Neighbor list builds = 0 Dangerous builds = 0 242 -1023.38826660369 eV 2.42748522976788 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03