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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -66.301357 0.0000000) to (46.882139 66.301357 5.7275649) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9973342 6.4322212 5.7275649 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -66.301357 0.0000000) to (46.882139 66.301357 5.7275649) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9973342 6.4322212 5.7275649 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -66.301357 0.0000000) to (46.882139 66.301357 5.7275649) create_atoms CPU = 0.003 seconds 1080 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 38 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2144 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_971738391444_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.228 | 5.228 | 5.228 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7133.6441 0 -7133.6441 2392.2933 95 0 -7170.5613 0 -7170.5613 1469.3001 Loop time of 19.8151 on 1 procs for 95 steps with 2144 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 = -7133.64409311869 -7170.55441097088 -7170.56132401056 Force two-norm initial, final = 42.967990 0.26962873 Force max component initial, final = 6.5679939 0.013877142 Final line search alpha, max atom move = 1.0000000 0.013877142 Iterations, force evaluations = 95 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.74 | 19.74 | 19.74 | 0.0 | 99.62 Neigh | 0.027527 | 0.027527 | 0.027527 | 0.0 | 0.14 Comm | 0.024122 | 0.024122 | 0.024122 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02343 | | | 0.12 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8390.00 ave 8390 max 8390 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: 172448.0 ave 172448 max 172448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172448 Ave neighs/atom = 80.432836 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.222 | 5.222 | 5.222 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -7170.5613 0 -7170.5613 1469.3001 35606.547 98 0 -7170.6191 0 -7170.6191 34.642422 35672.888 Loop time of 0.489738 on 1 procs for 3 steps with 2144 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 = -7170.56132401056 -7170.61864078591 -7170.61909318637 Force two-norm initial, final = 63.015148 2.4992584 Force max component initial, final = 53.874526 2.4015733 Final line search alpha, max atom move = 0.00020339950 0.00048847880 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4878 | 0.4878 | 0.4878 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031024 | 0.00031024 | 0.00031024 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00163 | | | 0.33 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7886.00 ave 7886 max 7886 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: 171296.0 ave 171296 max 171296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171296 Ave neighs/atom = 79.895522 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.359 | 5.359 | 5.359 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7170.6191 0 -7170.6191 34.642422 Loop time of 2.23e-06 on 1 procs for 0 steps with 2144 atoms 179.4% 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 | | 2.23e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7814.00 ave 7814 max 7814 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: 169760.0 ave 169760 max 169760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169760 Ave neighs/atom = 79.179104 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.359 | 5.359 | 5.359 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 -7170.6191 -7170.6191 46.899819 132.86657 5.7246823 34.642422 34.642422 18.045417 108.07649 -22.194641 2.5555209 856.44229 Loop time of 2.515e-06 on 1 procs for 0 steps with 2144 atoms 238.6% 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 | | 2.515e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7814.00 ave 7814 max 7814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84880.0 ave 84880 max 84880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 169760.0 ave 169760 max 169760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169760 Ave neighs/atom = 79.179104 Neighbor list builds = 0 Dangerous builds = 0 2144 -7170.61909318637 eV 2.55552085230761 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21