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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -47.726185 0.0000000) to (33.747509 47.726185 5.1464469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2786063 6.1045120 5.1464469 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -47.726185 0.0000000) to (33.747509 47.726185 5.1464469) create_atoms CPU = 0.002 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2786063 6.1045120 5.1464469 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -47.726185 0.0000000) to (33.747509 47.726185 5.1464469) create_atoms CPU = 0.002 seconds 694 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 ghost atom cutoff = 8 binsize = 4, bins = 9 24 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1376 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_945691923444_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 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3925.5115 0 -3925.5115 115225.67 73 0 -4501.5486 0 -4501.5486 4887.2719 Loop time of 1.82783 on 1 procs for 73 steps with 1376 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3925.51147680409 -4501.54421714045 -4501.54862646703 Force two-norm initial, final = 929.98197 0.17149867 Force max component initial, final = 140.73643 0.011364910 Final line search alpha, max atom move = 1.0000000 0.011364910 Iterations, force evaluations = 73 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.789 | 1.789 | 1.789 | 0.0 | 97.88 Neigh | 0.015427 | 0.015427 | 0.015427 | 0.0 | 0.84 Comm | 0.01268 | 0.01268 | 0.01268 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01071 | | | 0.59 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8480.00 ave 8480 max 8480 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: 241600.0 ave 241600 max 241600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241600 Ave neighs/atom = 175.58140 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.497 | 5.497 | 5.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -4501.5486 0 -4501.5486 4887.2719 16578.145 77 0 -4501.6641 0 -4501.6641 -18.812132 16634.394 Loop time of 0.111358 on 1 procs for 4 steps with 1376 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 = -4501.54862646704 -4501.66408822826 -4501.66409172115 Force two-norm initial, final = 92.394080 0.41123739 Force max component initial, final = 68.446900 0.27929584 Final line search alpha, max atom move = 0.0071084781 0.0019853684 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10782 | 0.10782 | 0.10782 | 0.0 | 96.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057767 | 0.00057767 | 0.00057767 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002955 | | | 2.65 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8705.00 ave 8705 max 8705 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: 241604.0 ave 241604 max 241604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241604 Ave neighs/atom = 175.58430 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 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.635 | 5.635 | 5.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4501.6641 0 -4501.6641 -18.812132 Loop time of 2.168e-06 on 1 procs for 0 steps with 1376 atoms 138.4% 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 | | 2.168e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8705.00 ave 8705 max 8705 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: 241460.0 ave 241460 max 241460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241460 Ave neighs/atom = 175.47965 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 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.635 | 5.635 | 5.635 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 -4501.6641 -4501.6641 33.799055 95.676527 5.1439532 -18.812132 -18.812132 -26.942053 -18.019337 -11.475005 2.3438348 1000.2772 Loop time of 2.42e-06 on 1 procs for 0 steps with 1376 atoms 247.9% 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 | | 2.42e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8705.00 ave 8705 max 8705 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120730.0 ave 120730 max 120730 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 241460.0 ave 241460 max 241460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241460 Ave neighs/atom = 175.47965 Neighbor list builds = 0 Dangerous builds = 0 1376 -4501.66409172115 eV 2.34383477030448 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02