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 = 3.1706996 3.1706996 3.1706996 Created orthogonal box = (0.0000000 -51.906589 0.0000000) to (36.703501 51.906589 4.4840464) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4781345 5.0357139 4.4840464 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -51.906589 0.0000000) to (36.703501 51.906589 4.4840464) create_atoms CPU = 0.001 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4781345 5.0357139 4.4840464 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -51.906589 0.0000000) to (36.703501 51.906589 4.4840464) create_atoms CPU = 0.001 seconds 538 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 32 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1072 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_468686727341_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11433.234 0 -11433.234 2498.9243 75 0 -11597.567 0 -11597.567 5703.5949 Loop time of 38.0265 on 1 procs for 75 steps with 1072 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 = -11433.2339036324 -11597.5554632991 -11597.5666297221 Force two-norm initial, final = 97.217014 0.35340494 Force max component initial, final = 19.859734 0.025315398 Final line search alpha, max atom move = 1.0000000 0.025315398 Iterations, force evaluations = 75 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.003 | 38.003 | 38.003 | 0.0 | 99.94 Neigh | 0.011494 | 0.011494 | 0.011494 | 0.0 | 0.03 Comm | 0.0059178 | 0.0059178 | 0.0059178 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006182 | | | 0.02 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5488.00 ave 5488 max 5488 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: 68944.0 ave 68944 max 68944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68944 Ave neighs/atom = 64.313433 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -11597.567 0 -11597.567 5703.5949 17085.594 79 0 -11597.833 0 -11597.833 -90.729551 17123.207 Loop time of 1.86772 on 1 procs for 4 steps with 1072 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 = -11597.5666297221 -11597.8221646372 -11597.8334561769 Force two-norm initial, final = 145.03542 2.4252006 Force max component initial, final = 135.34350 1.6672324 Final line search alpha, max atom move = 5.9998683e-05 0.00010003175 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8664 | 1.8664 | 1.8664 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024515 | 0.00024515 | 0.00024515 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001117 | | | 0.06 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5496.00 ave 5496 max 5496 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: 68880.0 ave 68880 max 68880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68880 Ave neighs/atom = 64.253731 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.740 | 4.740 | 4.740 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11597.833 0 -11597.833 -90.729551 Loop time of 1.597e-06 on 1 procs for 0 steps with 1072 atoms 187.9% 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 | | 1.597e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5496.00 ave 5496 max 5496 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: 68864.0 ave 68864 max 68864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68864 Ave neighs/atom = 64.238806 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.740 | 4.740 | 4.740 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 -11597.833 -11597.833 36.629579 104.19491 4.4864896 -90.729551 -90.729551 -154.99162 -156.57247 39.375444 2.3963897 560.34259 Loop time of 1.566e-06 on 1 procs for 0 steps with 1072 atoms 127.7% 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 | | 1.566e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5496.00 ave 5496 max 5496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34432.0 ave 34432 max 34432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68864.0 ave 68864 max 68864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68864 Ave neighs/atom = 64.238806 Neighbor list builds = 0 Dangerous builds = 0 1072 -3317.46890594306 eV 2.39638971059989 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:41