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 = 3.1501383 3.1501383 3.1501383 Created orthogonal box = (0.0000000 -49.206733 0.0000000) to (24.603366 49.206733 3.1501383) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4366726 4.4366726 3.1501383 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -49.206733 0.0000000) to (24.603366 49.206733 3.1501383) create_atoms CPU = 0.002 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4366726 4.4366726 3.1501383 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -49.206733 0.0000000) to (24.603366 49.206733 3.1501383) create_atoms CPU = 0.001 seconds 245 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 = 8.100217 ghost atom cutoff = 8.100217 binsize = 4.0501085, bins = 7 25 1 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 8.100217049417179 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 489 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_230319944007_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 = 8.100217 ghost atom cutoff = 8.100217 binsize = 4.0501085, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217049417179 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3159.2081 0 -3159.2081 61733.54 39 0 -3317.1961 0 -3317.1961 10900.862 Loop time of 0.602236 on 1 procs for 39 steps with 489 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3159.20810254873 -3317.19337806574 -3317.19611964483 Force two-norm initial, final = 329.29590 0.19659118 Force max component initial, final = 135.42116 0.070398126 Final line search alpha, max atom move = 0.84718209 0.059640032 Iterations, force evaluations = 39 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58793 | 0.58793 | 0.58793 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0083419 | 0.0083419 | 0.0083419 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005959 | | | 0.99 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5181.00 ave 5181 max 5181 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: 66918.0 ave 66918 max 66918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66918 Ave neighs/atom = 136.84663 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 = 8.100217 ghost atom cutoff = 8.100217 binsize = 4.0501085, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217049417179 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -3317.1961 0 -3317.1961 10900.862 7627.4379 45 0 -3317.4675 0 -3317.4675 -322.27332 7660.3344 Loop time of 0.072073 on 1 procs for 6 steps with 489 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3317.19611964483 -3317.46554774482 -3317.46749959802 Force two-norm initial, final = 109.87991 2.7878447 Force max component initial, final = 100.49881 2.1461461 Final line search alpha, max atom move = 0.00015671266 0.00033632827 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068391 | 0.068391 | 0.068391 | 0.0 | 94.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008521 | 0.0008521 | 0.0008521 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002829 | | | 3.93 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5178.00 ave 5178 max 5178 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: 67794.0 ave 67794 max 67794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67794 Ave neighs/atom = 138.63804 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 = 8.100217 ghost atom cutoff = 8.100217 binsize = 4.0501085, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217049417179 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3317.4675 0 -3317.4675 -322.27332 Loop time of 5.703e-06 on 1 procs for 0 steps with 489 atoms 157.8% 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 | | 5.703e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5180.00 ave 5180 max 5180 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: 67622.0 ave 67622 max 67622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67622 Ave neighs/atom = 138.28630 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 = 8.100217 ghost atom cutoff = 8.100217 binsize = 4.0501085, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217049417179 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) = 4.631 | 4.631 | 4.631 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 -3317.4675 -3317.4675 24.611736 98.955955 3.1453107 -322.27332 -322.27332 -449.02408 -234.64514 -283.15074 2.4677837 128.43335 Loop time of 6.655e-06 on 1 procs for 0 steps with 489 atoms 240.4% 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 | | 6.655e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5180.00 ave 5180 max 5180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33811.0 ave 33811 max 33811 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67622.0 ave 67622 max 67622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67622 Ave neighs/atom = 138.28630 Neighbor list builds = 0 Dangerous builds = 0 489 -3317.46749959802 eV 2.46778374594083 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01