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 = 3.4921275 3.4921275 3.4921275 Created orthogonal box = (0.0000000 -60.485423 0.0000000) to (24.693071 60.485423 8.5539306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9263370 5.2420700 5.7026204 Created 1195 atoms using lattice units in orthogonal box = (0.0000000 -60.485423 0.0000000) to (24.693071 60.485423 8.5539306) create_atoms CPU = 0.002 seconds 1195 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9263370 5.2420700 5.7026204 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -60.485423 0.0000000) to (24.693071 60.485423 8.5539306) create_atoms CPU = 0.002 seconds 1203 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 7 31 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2398 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_270337113239_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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 7 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 6.521 | 6.521 | 6.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7659.5847 0 -7659.5847 32089.095 70 0 -7951.002 0 -7951.002 1247.3432 Loop time of 2.64624 on 1 procs for 70 steps with 2398 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7659.58469034357 -7950.99464325126 -7951.00204987762 Force two-norm initial, final = 885.93218 0.23881387 Force max component initial, final = 322.23374 0.038835865 Final line search alpha, max atom move = 1.0000000 0.038835865 Iterations, force evaluations = 70 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5243 | 2.5243 | 2.5243 | 0.0 | 95.39 Neigh | 0.08935 | 0.08935 | 0.08935 | 0.0 | 3.38 Comm | 0.014771 | 0.014771 | 0.014771 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01779 | | | 0.67 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10270.0 ave 10270 max 10270 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: 477508.0 ave 477508 max 477508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 477508 Ave neighs/atom = 199.12761 Neighbor list builds = 3 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 7 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.522 | 6.522 | 6.522 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -7951.002 0 -7951.002 1247.3432 25551.803 74 0 -7951.0955 0 -7951.0955 -70.278126 25582.143 Loop time of 0.145056 on 1 procs for 4 steps with 2398 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7951.00204987762 -7951.09494337782 -7951.09547580074 Force two-norm initial, final = 58.372879 3.1653680 Force max component initial, final = 58.084678 2.7987906 Final line search alpha, max atom move = 0.00017454162 0.00048850544 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1411 | 0.1411 | 0.1411 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059139 | 0.00059139 | 0.00059139 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003368 | | | 2.32 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10281.0 ave 10281 max 10281 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: 477560.0 ave 477560 max 477560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 477560 Ave neighs/atom = 199.14929 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 7 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 6.660 | 6.660 | 6.660 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7951.0955 0 -7951.0955 -70.278126 Loop time of 2.36e-06 on 1 procs for 0 steps with 2398 atoms 169.5% 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 | | 2.36e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10293.0 ave 10293 max 10293 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: 477310.0 ave 477310 max 477310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 477310 Ave neighs/atom = 199.04504 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 7 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 6.660 | 6.660 | 6.660 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 -7951.0955 -7951.0955 24.665897 121.35209 8.5465876 -70.278126 -70.278126 -79.841252 44.141035 -175.13416 2.2821009 905.27233 Loop time of 2.328e-06 on 1 procs for 0 steps with 2398 atoms 343.6% 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 | | 2.328e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10293.0 ave 10293 max 10293 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 238655.0 ave 238655 max 238655 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 477310.0 ave 477310 max 477310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 477310 Ave neighs/atom = 199.04504 Neighbor list builds = 0 Dangerous builds = 0 2398 -7849.84320600097 eV 2.28210094218991 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04