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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -55.239063 0.0000000) to (39.059916 55.239063 5.1736123) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1673552 6.2991914 5.1736123 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -55.239063 0.0000000) to (39.059916 55.239063 5.1736123) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1673552 6.2991914 5.1736123 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -55.239063 0.0000000) to (39.059916 55.239063 5.1736123) create_atoms CPU = 0.002 seconds 916 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 ghost atom cutoff = 8 binsize = 4, bins = 10 28 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1828 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_942420706858_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 ghost atom cutoff = 8 binsize = 4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.984 | 5.984 | 5.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7077.7801 0 -7077.7801 61944.158 419 0 -7386.2631 0 -7386.2631 -61870.766 Loop time of 13.9032 on 1 procs for 419 steps with 1828 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 = -7077.78009321012 -7386.25685262089 -7386.2631449023 Force two-norm initial, final = 325.54080 0.24295216 Force max component initial, final = 77.804870 0.013801526 Final line search alpha, max atom move = 1.0000000 0.013801526 Iterations, force evaluations = 419 824 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.535 | 13.535 | 13.535 | 0.0 | 97.35 Neigh | 0.19777 | 0.19777 | 0.19777 | 0.0 | 1.42 Comm | 0.09488 | 0.09488 | 0.09488 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07519 | | | 0.54 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10688.0 ave 10688 max 10688 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: 315488.0 ave 315488 max 315488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315488 Ave neighs/atom = 172.58643 Neighbor list builds = 10 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 ghost atom cutoff = 8 binsize = 4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 419 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.986 | 5.986 | 5.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 419 0 -7386.2631 0 -7386.2631 -61870.766 22325.515 518 0 -7468.0771 0 -7468.0771 -493.27336 21662.805 Loop time of 1.68011 on 1 procs for 99 steps with 1828 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 = -7386.26314490242 -7468.07467557403 -7468.07714558187 Force two-norm initial, final = 1988.1921 13.906725 Force max component initial, final = 1465.2453 8.6403776 Final line search alpha, max atom move = 0.00015589941 0.0013470297 Iterations, force evaluations = 99 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.513 | 1.513 | 1.513 | 0.0 | 90.05 Neigh | 0.1135 | 0.1135 | 0.1135 | 0.0 | 6.76 Comm | 0.0095586 | 0.0095586 | 0.0095586 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04409 | | | 2.62 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9473.00 ave 9473 max 9473 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: 309144.0 ave 309144 max 309144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309144 Ave neighs/atom = 169.11597 Neighbor list builds = 6 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 ghost atom cutoff = 8 binsize = 4, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.114 | 6.114 | 6.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7468.0771 0 -7468.0771 -493.27336 Loop time of 2.139e-06 on 1 procs for 0 steps with 1828 atoms 140.3% 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 | | 2.139e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9473.00 ave 9473 max 9473 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: 309040.0 ave 309040 max 309040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309040 Ave neighs/atom = 169.05908 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 ghost atom cutoff = 8 binsize = 4, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.114 | 6.114 | 6.114 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 -7468.0771 -7468.0771 36.910097 104.67307 5.6070513 -493.27336 -493.27336 -603.86836 -547.4559 -328.49581 2.2956357 4134.4999 Loop time of 2.61e-06 on 1 procs for 0 steps with 1828 atoms 229.9% 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 | | 2.61e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9473.00 ave 9473 max 9473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 154520.0 ave 154520 max 154520 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 309040.0 ave 309040 max 309040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309040 Ave neighs/atom = 169.05908 Neighbor list builds = 0 Dangerous builds = 0 1828 -7468.0771455818 eV 2.29563569224143 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15