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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -52.765531 0.0000000) to (30.464194 52.765531 7.0510907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5280415 6.2816109 7.0510907 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -52.765531 0.0000000) to (30.464194 52.765531 7.0510907) create_atoms CPU = 0.005 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5280415 6.2816109 7.0510907 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.765531 0.0000000) to (30.464194 52.765531 7.0510907) create_atoms CPU = 0.004 seconds 676 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 35 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.626 | 4.626 | 4.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4301.5983 0 -4301.5983 27751.1 59 0 -4511.0553 0 -4511.0553 2609.9489 Loop time of 10.3181 on 1 procs for 59 steps with 1344 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 = -4301.59829530905 -4511.05193803156 -4511.05527347144 Force two-norm initial, final = 398.17944 0.12753211 Force max component initial, final = 73.342426 0.010853080 Final line search alpha, max atom move = 1.0000000 0.010853080 Iterations, force evaluations = 59 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.276 | 10.276 | 10.276 | 0.0 | 99.59 Neigh | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.13 Comm | 0.011464 | 0.011464 | 0.011464 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01689 | | | 0.16 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4251.00 ave 4251 max 4251 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: 72496.0 ave 72496 max 72496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72496 Ave neighs/atom = 53.940476 Neighbor list builds = 1 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.626 | 4.626 | 4.626 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -4511.0553 0 -4511.0553 2609.9489 22668.684 64 0 -4511.2039 0 -4511.2039 -131.89427 22735.022 Loop time of 0.750001 on 1 procs for 5 steps with 1344 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 = -4511.05527347142 -4511.20295577879 -4511.20394267042 Force two-norm initial, final = 79.233226 4.6084959 Force max component initial, final = 75.110904 4.5316670 Final line search alpha, max atom move = 0.00020241291 0.00091726789 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74567 | 0.74567 | 0.74567 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071696 | 0.00071696 | 0.00071696 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003613 | | | 0.48 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4299.00 ave 4299 max 4299 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: 72568.0 ave 72568 max 72568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72568 Ave neighs/atom = 53.994048 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.764 | 4.764 | 4.764 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4511.2039 0 -4511.2039 -131.89427 Loop time of 6.355e-06 on 1 procs for 0 steps with 1344 atoms 188.8% 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 | | 6.355e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4299.00 ave 4299 max 4299 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: 72528.0 ave 72528 max 72528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72528 Ave neighs/atom = 53.964286 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.764 | 4.764 | 4.764 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 -4511.2039 -4511.2039 30.456201 105.97348 7.0440504 -131.89427 -131.89427 -33.077933 -43.569301 -319.03559 2.5881658 882.77207 Loop time of 2.6511e-05 on 1 procs for 0 steps with 1344 atoms 147.1% 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 | | 2.651e-05 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4299.00 ave 4299 max 4299 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36264.0 ave 36264 max 36264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72528.0 ave 72528 max 72528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72528 Ave neighs/atom = 53.964286 Neighbor list builds = 0 Dangerous builds = 0 1344 -4511.20394267042 eV 2.58816582973368 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11