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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -72.716372 0.0000000) to (51.418240 72.716372 5.7131378) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9827239 6.7329974 5.7131378 Created 1296 atoms using lattice units in orthogonal box = (0.0000000 -72.716372 0.0000000) to (51.418240 72.716372 5.7131378) create_atoms CPU = 0.004 seconds 1296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9827239 6.7329974 5.7131378 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -72.716372 0.0000000) to (51.418240 72.716372 5.7131378) create_atoms CPU = 0.004 seconds 1300 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 9 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2596 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 9 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 13.23 | 13.23 | 13.23 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7237.3433 0 -7237.3433 13765.834 96 0 -7476.4688 0 -7476.4688 2400.4465 Loop time of 8.80637 on 1 procs for 96 steps with 2596 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7237.34331919153 -7476.4620099048 -7476.46878883774 Force two-norm initial, final = 183.15258 0.24954332 Force max component initial, final = 31.169536 0.030269848 Final line search alpha, max atom move = 0.97877914 0.029627496 Iterations, force evaluations = 96 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.6731 | 8.6731 | 8.6731 | 0.0 | 98.49 Neigh | 0.053827 | 0.053827 | 0.053827 | 0.0 | 0.61 Comm | 0.04725 | 0.04725 | 0.04725 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03222 | | | 0.37 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19501.0 ave 19501 max 19501 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: 1.09394e+06 ave 1.09394e+06 max 1.09394e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1093936 Ave neighs/atom = 421.39291 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 9 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.85 | 12.85 | 12.85 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -7476.4688 0 -7476.4688 2400.4465 42722.248 100 0 -7476.7344 0 -7476.7344 45.531986 42853.256 Loop time of 0.263034 on 1 procs for 4 steps with 2596 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 = -7476.46878883779 -7476.72940503278 -7476.73436782163 Force two-norm initial, final = 155.41174 2.5124799 Force max component initial, final = 147.57796 2.2518662 Final line search alpha, max atom move = 6.8932155e-05 0.00015522599 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25814 | 0.25814 | 0.25814 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009078 | 0.0009078 | 0.0009078 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003989 | | | 1.52 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20095.0 ave 20095 max 20095 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: 1.06238e+06 ave 1.06238e+06 max 1.06238e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1062376 Ave neighs/atom = 409.23575 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 9 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 12.37 | 12.37 | 12.37 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7476.7344 0 -7476.7344 45.531986 Loop time of 2.146e-06 on 1 procs for 0 steps with 2596 atoms 186.4% 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 | | 2.146e-06 | | |100.00 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20004.0 ave 20004 max 20004 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: 1.04103e+06 ave 1.04103e+06 max 1.04103e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1041032 Ave neighs/atom = 401.01387 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 9 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 12.37 | 12.37 | 12.37 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 -7476.7344 -7476.7344 51.589372 145.29588 5.7170276 45.531986 45.531986 37.742738 14.604228 84.248991 2.6844339 2221.7092 Loop time of 2.557e-06 on 1 procs for 0 steps with 2596 atoms 312.9% 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 | | 2.557e-06 | | |100.00 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20004.0 ave 20004 max 20004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 520516.0 ave 520516 max 520516 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.04103e+06 ave 1.04103e+06 max 1.04103e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1041032 Ave neighs/atom = 401.01387 Neighbor list builds = 0 Dangerous builds = 0 2596 -7476.73436782163 eV 2.6844338652054 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09