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 = 3.4301372 3.4301372 3.4301372 Created orthogonal box = (0.0000000 -36.462859 0.0000000) to (36.462859 36.462859 3.4301372) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8402025 4.8402025 3.4301372 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -36.462859 0.0000000) to (36.462859 36.462859 3.4301372) create_atoms CPU = 0.001 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8402025 4.8402025 3.4301372 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -36.462859 0.0000000) to (36.462859 36.462859 3.4301372) create_atoms CPU = 0.000 seconds 454 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 = 10 19 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_044341472608_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 ghost atom cutoff = 8 binsize = 4, bins = 10 19 1 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) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3286.0659 0 -3286.0659 142476.7 36 0 -3603.8837 0 -3603.8837 38234.353 Loop time of 0.645993 on 1 procs for 36 steps with 906 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 = -3286.0658528596 -3603.88071107406 -3603.88368776351 Force two-norm initial, final = 791.77615 0.21436719 Force max component initial, final = 324.66950 0.040664527 Final line search alpha, max atom move = 1.0000000 0.040664527 Iterations, force evaluations = 36 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62616 | 0.62616 | 0.62616 | 0.0 | 96.93 Neigh | 0.011181 | 0.011181 | 0.011181 | 0.0 | 1.73 Comm | 0.0051693 | 0.0051693 | 0.0051693 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00348 | | | 0.54 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8616.00 ave 8616 max 8616 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: 185352.0 ave 185352 max 185352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185352 Ave neighs/atom = 204.58278 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 = 10 19 1 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -3603.8837 0 -3603.8837 38234.353 9121.0098 47 0 -3605.8182 0 -3605.8182 -173.86576 9206.4785 Loop time of 0.150263 on 1 procs for 11 steps with 906 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 = -3603.88368776351 -3605.81806211857 -3605.81821882692 Force two-norm initial, final = 434.72302 2.0230866 Force max component initial, final = 383.41924 1.1912440 Final line search alpha, max atom move = 0.00048847451 0.00058189235 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14461 | 0.14461 | 0.14461 | 0.0 | 96.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099986 | 0.00099986 | 0.00099986 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004649 | | | 3.09 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8616.00 ave 8616 max 8616 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: 185532.0 ave 185532 max 185532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185532 Ave neighs/atom = 204.78146 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 = 10 19 1 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) = 5.149 | 5.149 | 5.149 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3605.8182 0 -3605.8182 -173.86576 Loop time of 2.382e-06 on 1 procs for 0 steps with 906 atoms 167.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8604.00 ave 8604 max 8604 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: 182472.0 ave 182472 max 182472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182472 Ave neighs/atom = 201.40397 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 = 10 19 1 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) = 5.149 | 5.149 | 5.149 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 -3605.8182 -3605.8182 36.398125 73.653216 3.4341781 -173.86576 -173.86576 -145.85886 -168.18547 -207.55294 2.2446523 261.05004 Loop time of 2.622e-06 on 1 procs for 0 steps with 906 atoms 228.8% 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 | | 2.622e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8604.00 ave 8604 max 8604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91236.0 ave 91236 max 91236 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 182472.0 ave 182472 max 182472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182472 Ave neighs/atom = 201.40397 Neighbor list builds = 0 Dangerous builds = 0 906 -3605.81821882692 eV 2.24465232417686 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01