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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -45.817736 0.0000000) to (22.907295 45.817736 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8899180 3.8899180 3.1465590 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -45.817736 0.0000000) to (22.907295 45.817736 3.1465590) create_atoms CPU = 0.002 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8899180 3.8899180 3.1465590 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -45.817736 0.0000000) to (22.907295 45.817736 3.1465590) create_atoms CPU = 0.001 seconds 213 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 420 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2832.8419 0 -2832.8419 -6212.3997 43 0 -2844.3385 0 -2844.3385 -13096.21 Loop time of 2.12351 on 1 procs for 43 steps with 420 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2832.84185196343 -2844.33663260067 -2844.33851107011 Force two-norm initial, final = 26.053776 0.39996174 Force max component initial, final = 12.819207 0.17752313 Final line search alpha, max atom move = 0.052759847 0.0093660931 Iterations, force evaluations = 43 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1112 | 2.1112 | 2.1112 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0063139 | 0.0063139 | 0.0063139 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005996 | | | 0.28 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3135.00 ave 3135 max 3135 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: 23994.0 ave 23994 max 23994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23994 Ave neighs/atom = 57.128571 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -2844.3385 0 -2844.3385 -13096.21 6605.0074 47 0 -2844.4837 0 -2844.4837 -1207.7249 6574.8318 Loop time of 0.149064 on 1 procs for 4 steps with 420 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2844.33851107011 -2844.48230264442 -2844.48367590728 Force two-norm initial, final = 83.191233 0.38135971 Force max component initial, final = 70.213491 0.13238347 Final line search alpha, max atom move = 0.00024845156 3.2890879e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14721 | 0.14721 | 0.14721 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004011 | 0.0004011 | 0.0004011 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001452 | | | 0.97 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3140.00 ave 3140 max 3140 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: 24076.0 ave 24076 max 24076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24076 Ave neighs/atom = 57.323810 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2844.4837 0 -2844.4837 -1207.7249 Loop time of 6.225e-06 on 1 procs for 0 steps with 420 atoms 176.7% 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 | | 6.225e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3140.00 ave 3140 max 3140 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: 24080.0 ave 24080 max 24080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24080 Ave neighs/atom = 57.333333 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.576 | 4.576 | 4.576 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 -2844.4837 -2844.4837 22.879049 91.635473 3.1360505 -1207.7249 -1207.7249 15.717431 -3661.7423 22.850288 2.312972 261.56418 Loop time of 6.445e-06 on 1 procs for 0 steps with 420 atoms 263.8% 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 | | 6.445e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3140.00 ave 3140 max 3140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12040.0 ave 12040 max 12040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24080.0 ave 24080 max 24080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24080 Ave neighs/atom = 57.333333 Neighbor list builds = 0 Dangerous builds = 0 420 -2844.48367590728 eV 2.3129719597162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02