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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -48.632392 0.0000000) to (59.562272 48.632392 9.8588175) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7114508 5.9957743 6.5725450 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -48.632392 0.0000000) to (59.562272 48.632392 9.8588175) create_atoms CPU = 0.003 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7114508 5.9957743 6.5725450 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.632392 0.0000000) to (59.562272 48.632392 9.8588175) create_atoms CPU = 0.002 seconds 1755 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 24 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3504 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_149316865608_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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.958 | 6.958 | 6.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9002.4956 0 -9002.4956 15797.982 62 0 -9247.3824 0 -9247.3824 4159.2623 Loop time of 3.05951 on 1 procs for 62 steps with 3504 atoms 90.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9002.49560023077 -9247.373573456 -9247.38237384073 Force two-norm initial, final = 151.94508 0.27458701 Force max component initial, final = 16.965640 0.073475545 Final line search alpha, max atom move = 1.0000000 0.073475545 Iterations, force evaluations = 62 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9482 | 2.9482 | 2.9482 | 0.0 | 96.36 Neigh | 0.066269 | 0.066269 | 0.066269 | 0.0 | 2.17 Comm | 0.012786 | 0.012786 | 0.012786 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03222 | | | 1.05 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10925.0 ave 10925 max 10925 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: 492376.0 ave 492376 max 492376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 492376 Ave neighs/atom = 140.51826 Neighbor list builds = 2 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/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) = 6.961 | 6.961 | 6.961 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -9247.3824 0 -9247.3824 4159.2623 57115.201 71 0 -9248.401 0 -9248.401 4.0053941 57405.187 Loop time of 0.295077 on 1 procs for 9 steps with 3504 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 = -9247.38237384075 -9248.40098344337 -9248.40100173714 Force two-norm initial, final = 307.86471 0.63512406 Force max component initial, final = 284.70539 0.34993012 Final line search alpha, max atom move = 0.00081045482 0.00028360255 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28768 | 0.28768 | 0.28768 | 0.0 | 97.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010298 | 0.0010298 | 0.0010298 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006369 | | | 2.16 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10935.0 ave 10935 max 10935 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: 492416.0 ave 492416 max 492416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 492416 Ave neighs/atom = 140.52968 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 7.099 | 7.099 | 7.099 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9248.401 0 -9248.401 4.0053941 Loop time of 1.974e-06 on 1 procs for 0 steps with 3504 atoms 202.6% 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 | | 1.974e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10938.0 ave 10938 max 10938 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: 491484.0 ave 491484 max 491484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491484 Ave neighs/atom = 140.26370 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 7.099 | 7.099 | 7.099 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 -9248.401 -9248.401 59.528632 98.039727 9.8361045 4.0053941 4.0053941 -2.1938237 4.4659706 9.7440355 2.5314044 1989.9236 Loop time of 2.514e-06 on 1 procs for 0 steps with 3504 atoms 278.4% 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 | | 2.514e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10938.0 ave 10938 max 10938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 245742.0 ave 245742 max 245742 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 491484.0 ave 491484 max 491484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491484 Ave neighs/atom = 140.26370 Neighbor list builds = 0 Dangerous builds = 0 3504 -9140.7081438167 eV 2.53140436421196 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03