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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -59.767773 0.0000000) to (12.200046 59.767773 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5454753 5.4334339 6.0068872 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.767773 0.0000000) to (12.200046 59.767773 9.0103308) create_atoms CPU = 0.003 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5454753 5.4334339 6.0068872 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.767773 0.0000000) to (12.200046 59.767773 9.0103308) create_atoms CPU = 0.003 seconds 530 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 39 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4324.037 0 -4324.037 19619.794 90 0 -4447.654 0 -4447.654 -997.81844 Loop time of 1.21855 on 1 procs for 90 steps with 1056 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4324.03701387124 -4447.64958970537 -4447.65398432978 Force two-norm initial, final = 155.09481 0.23652037 Force max component initial, final = 38.198146 0.055908975 Final line search alpha, max atom move = 1.0000000 0.055908975 Iterations, force evaluations = 90 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1481 | 1.1481 | 1.1481 | 0.0 | 94.22 Neigh | 0.032305 | 0.032305 | 0.032305 | 0.0 | 2.65 Comm | 0.017543 | 0.017543 | 0.017543 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02064 | | | 1.69 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4414.00 ave 4414 max 4414 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: 82084.0 ave 82084 max 82084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82084 Ave neighs/atom = 77.731061 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -4447.654 0 -4447.654 -997.81844 13140.118 92 0 -4447.6623 0 -4447.6623 -0.64000989 13128.055 Loop time of 0.0365149 on 1 procs for 2 steps with 1056 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 = -4447.65398432978 -4447.66007644994 -4447.66231685648 Force two-norm initial, final = 16.317608 0.34592537 Force max component initial, final = 13.408025 0.20057022 Final line search alpha, max atom move = 0.00017875007 3.5851940e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034239 | 0.034239 | 0.034239 | 0.0 | 93.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048831 | 0.00048831 | 0.00048831 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001787 | | | 4.89 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4519.00 ave 4519 max 4519 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: 82168.0 ave 82168 max 82168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82168 Ave neighs/atom = 77.810606 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.707 | 4.707 | 4.707 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4447.6623 0 -4447.6623 -0.64000989 Loop time of 6.846e-06 on 1 procs for 0 steps with 1056 atoms 160.7% 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 | | 6.846e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4511.00 ave 4511 max 4511 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: 82192.0 ave 82192 max 82192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82192 Ave neighs/atom = 77.833333 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.707 | 4.707 | 4.707 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 -4447.6623 -4447.6623 12.206782 119.41272 9.0063463 -0.64000989 -0.64000989 7.6302533 14.91692 -24.467202 2.3566475 488.79394 Loop time of 6.685e-06 on 1 procs for 0 steps with 1056 atoms 239.3% 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 | | 6.685e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4511.00 ave 4511 max 4511 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41096.0 ave 41096 max 41096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82192.0 ave 82192 max 82192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82192 Ave neighs/atom = 77.833333 Neighbor list builds = 0 Dangerous builds = 0 1056 -4447.66221125648 eV 2.35664750401181 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01