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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -46.698077 0.0000000) to (28.596615 46.698077 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1993846 5.3065997 5.7481359 Created 1042 atoms using lattice units in orthogonal box = (0.0000000 -46.698077 0.0000000) to (28.596615 46.698077 8.6222039) create_atoms CPU = 0.002 seconds 1042 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1993846 5.3065997 5.7481359 Created 1066 atoms using lattice units in orthogonal box = (0.0000000 -46.698077 0.0000000) to (28.596615 46.698077 8.6222039) create_atoms CPU = 0.002 seconds 1066 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2106 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_444394830472_001#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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.098 | 5.098 | 5.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9335.0092 0 -9335.0092 3523.3275 33 0 -9349.3088 0 -9349.3088 3814.8262 Loop time of 2.32536 on 1 procs for 33 steps with 2106 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9335.00916552255 -9349.29982990596 -9349.3087702809 Force two-norm initial, final = 27.738727 0.29222549 Force max component initial, final = 4.2906705 0.032865893 Final line search alpha, max atom move = 1.0000000 0.032865893 Iterations, force evaluations = 33 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3124 | 2.3124 | 2.3124 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0051343 | 0.0051343 | 0.0051343 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007822 | | | 0.34 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6043.00 ave 6043 max 6043 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: 164184.0 ave 164184 max 164184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164184 Ave neighs/atom = 77.960114 Neighbor list builds = 0 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -9349.3088 0 -9349.3088 3814.8262 23028.302 38 0 -9349.5649 0 -9349.5649 -6.0905164 23076.913 Loop time of 0.292842 on 1 procs for 5 steps with 2106 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9349.30877028092 -9349.56464735956 -9349.5648995006 Force two-norm initial, final = 137.30647 0.74514366 Force max component initial, final = 135.63375 0.46129030 Final line search alpha, max atom move = 0.00021181314 9.7707347e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28919 | 0.28919 | 0.28919 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048027 | 0.00048027 | 0.00048027 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003175 | | | 1.08 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5998.00 ave 5998 max 5998 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: 163524.0 ave 163524 max 163524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163524 Ave neighs/atom = 77.646724 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9349.5649 0 -9349.5649 -6.0905164 Loop time of 2.478e-06 on 1 procs for 0 steps with 2106 atoms 161.4% 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 | | 2.478e-06 | | |100.00 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5998.00 ave 5998 max 5998 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: 163524.0 ave 163524 max 163524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163524 Ave neighs/atom = 77.646724 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.235 | 5.235 | 5.235 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 -9349.5649 -9349.5649 28.56149 93.766877 8.6168277 -6.0905164 -6.0905164 -31.986976 -11.690701 25.406128 2.3546881 819.03971 Loop time of 4.345e-06 on 1 procs for 0 steps with 2106 atoms 230.1% 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 | | 4.345e-06 | | |100.00 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5998.00 ave 5998 max 5998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81762.0 ave 81762 max 81762 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163524.0 ave 163524 max 163524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163524 Ave neighs/atom = 77.646724 Neighbor list builds = 0 Dangerous builds = 0 2106 -9349.5648995006 eV 2.35468810646859 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03