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 = 3.7004859 3.7004859 3.7004859 Created orthogonal box = (0.0000000 -38.456578 0.0000000) to (27.192907 38.456578 5.2332774) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0428682 4.9851120 5.2332774 Created 431 atoms using lattice units in orthogonal box = (0.0000000 -38.456578 0.0000000) to (27.192907 38.456578 5.2332774) create_atoms CPU = 0.001 seconds 431 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0428682 4.9851120 5.2332774 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -38.456578 0.0000000) to (27.192907 38.456578 5.2332774) create_atoms CPU = 0.001 seconds 439 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 10 29 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 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 870 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_857282754307_003#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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -822.77473 0 -822.77473 127515.26 87 0 -1297.0012 0 -1297.0012 8115.2458 Loop time of 0.416106 on 1 procs for 87 steps with 870 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 = -822.774733512731 -1296.99999204572 -1297.00119698866 Force two-norm initial, final = 929.01384 0.11552122 Force max component initial, final = 207.53963 0.028299518 Final line search alpha, max atom move = 1.0000000 0.028299518 Iterations, force evaluations = 87 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37948 | 0.37948 | 0.37948 | 0.0 | 91.20 Neigh | 0.015955 | 0.015955 | 0.015955 | 0.0 | 3.83 Comm | 0.0088763 | 0.0088763 | 0.0088763 | 0.0 | 2.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0118 | | | 2.84 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3297.00 ave 3297 max 3297 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: 47008.0 ave 47008 max 47008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47008 Ave neighs/atom = 54.032184 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -1297.0012 0 -1297.0012 8115.2458 10945.359 93 0 -1297.2391 0 -1297.2391 -3.3070858 11025.003 Loop time of 0.023764 on 1 procs for 6 steps with 870 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 = -1297.00119698866 -1297.23906138019 -1297.23913624456 Force two-norm initial, final = 98.723756 0.23830763 Force max component initial, final = 68.797498 0.14160235 Final line search alpha, max atom move = 0.00078898646 0.00011172234 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020923 | 0.020923 | 0.020923 | 0.0 | 88.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045246 | 0.00045246 | 0.00045246 | 0.0 | 1.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002389 | | | 10.05 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3294.00 ave 3294 max 3294 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: 47040.0 ave 47040 max 47040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47040 Ave neighs/atom = 54.068966 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.677 | 4.677 | 4.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1297.2391 0 -1297.2391 -3.3070858 Loop time of 2.967e-06 on 1 procs for 0 steps with 870 atoms 168.5% 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 | | 2.967e-06 | | |100.00 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3282.00 ave 3282 max 3282 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: 47000.0 ave 47000 max 47000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47000 Ave neighs/atom = 54.022989 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.677 | 4.677 | 4.677 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 -1297.2391 -1297.2391 27.281952 76.897746 5.2552052 -3.3070858 -3.3070858 9.4334828 1.3094326 -20.664173 2.3711247 367.64886 Loop time of 2.788e-06 on 1 procs for 0 steps with 870 atoms 179.3% 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 | | 2.788e-06 | | |100.00 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3282.00 ave 3282 max 3282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23500.0 ave 23500 max 23500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47000.0 ave 47000 max 47000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47000 Ave neighs/atom = 54.022989 Neighbor list builds = 0 Dangerous builds = 0 870 -1297.23913624456 eV 2.37112466824033 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00