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 = 4.0501807 4.0501807 4.0501807 Created orthogonal box = (0.0000000 -71.540456 0.0000000) to (41.303901 71.540456 7.0151188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3544464 6.4202973 7.0151188 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -71.540456 0.0000000) to (41.303901 71.540456 7.0151188) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3544464 6.4202973 7.0151188 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -71.540456 0.0000000) to (41.303901 71.540456 7.0151188) create_atoms CPU = 0.003 seconds 1249 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 10 35 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 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2494 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_131650261510_005#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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 6.129 | 6.129 | 6.129 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8839.8064 0 -8839.8064 6046.6879 50 0 -8916.8179 0 -8916.8179 4642.1452 Loop time of 1.74451 on 1 procs for 50 steps with 2494 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8839.80644016462 -8916.81031112239 -8916.81785158976 Force two-norm initial, final = 73.677226 0.17708824 Force max component initial, final = 16.207618 0.054498326 Final line search alpha, max atom move = 1.0000000 0.054498326 Iterations, force evaluations = 50 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6495 | 1.6495 | 1.6495 | 0.0 | 94.55 Neigh | 0.072214 | 0.072214 | 0.072214 | 0.0 | 4.14 Comm | 0.011074 | 0.011074 | 0.011074 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01176 | | | 0.67 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 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: 349128.0 ave 349128 max 349128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 349128 Ave neighs/atom = 139.98717 Neighbor list builds = 3 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.129 | 6.129 | 6.129 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -8916.8179 0 -8916.8179 4642.1452 41457.948 58 0 -8917.4962 0 -8917.4962 143.65213 41700.442 Loop time of 0.226945 on 1 procs for 8 steps with 2494 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8916.81785158977 -8917.49152476346 -8917.49623013764 Force two-norm initial, final = 231.01553 6.6426262 Force max component initial, final = 200.51207 4.9717588 Final line search alpha, max atom move = 0.00014982727 0.00074490502 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19483 | 0.19483 | 0.19483 | 0.0 | 85.85 Neigh | 0.025345 | 0.025345 | 0.025345 | 0.0 | 11.17 Comm | 0.0012446 | 0.0012446 | 0.0012446 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005528 | | | 2.44 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 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: 348724.0 ave 348724 max 348724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348724 Ave neighs/atom = 139.82518 Neighbor list builds = 1 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 6.267 | 6.267 | 6.267 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8917.4962 0 -8917.4962 143.65213 Loop time of 2.495e-06 on 1 procs for 0 steps with 2494 atoms 160.3% 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 | | 2.495e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 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: 348728.0 ave 348728 max 348728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348728 Ave neighs/atom = 139.82678 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 6.267 | 6.267 | 6.267 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 -8917.4962 -8917.4962 41.306059 144.14359 7.0037651 143.65213 143.65213 114.17829 192.43913 124.33899 2.5934874 1331.106 Loop time of 2.636e-06 on 1 procs for 0 steps with 2494 atoms 303.5% 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 | | 2.636e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 174364.0 ave 174364 max 174364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 348728.0 ave 348728 max 348728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348728 Ave neighs/atom = 139.82678 Neighbor list builds = 0 Dangerous builds = 0 2494 -8917.49385167389 eV 2.59348736385988 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02