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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -69.333891 0.0000000) to (40.027848 69.333891 6.2768674) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9057481 5.3039548 6.2768674 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.333891 0.0000000) to (40.027848 69.333891 6.2768674) create_atoms CPU = 0.003 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9057481 5.3039548 6.2768674 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.333891 0.0000000) to (40.027848 69.333891 6.2768674) create_atoms CPU = 0.003 seconds 1465 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 40 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 2899 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_427873955970_001#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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.203 | 6.203 | 6.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12071.596 0 -12071.596 -3410.7793 433 0 -12275.033 0 -12275.033 -19963.563 Loop time of 290.886 on 1 procs for 433 steps with 2899 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 = -12071.5958655483 -12275.0205831981 -12275.0326272054 Force two-norm initial, final = 27.252862 0.34839198 Force max component initial, final = 6.9965076 0.098525297 Final line search alpha, max atom move = 1.0000000 0.098525297 Iterations, force evaluations = 433 772 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 289.83 | 289.83 | 289.83 | 0.0 | 99.64 Neigh | 0.67742 | 0.67742 | 0.67742 | 0.0 | 0.23 Comm | 0.19206 | 0.19206 | 0.19206 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1906 | | | 0.07 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11039.0 ave 11039 max 11039 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: 348188.0 ave 348188 max 348188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348188 Ave neighs/atom = 120.10624 Neighbor list builds = 16 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 433 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.201 | 6.201 | 6.201 Mbytes Step Temp E_pair E_mol TotEng Press Volume 433 0 -12275.033 0 -12275.033 -19963.563 34840.21 449 0 -12280.475 0 -12280.475 -10292.782 34624.525 Loop time of 8.2666 on 1 procs for 16 steps with 2899 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 = -12275.0326272054 -12280.4743434116 -12280.4746290517 Force two-norm initial, final = 655.36335 6.5822440 Force max component initial, final = 637.55849 4.7150478 Final line search alpha, max atom move = 0.0025511052 0.012028583 Iterations, force evaluations = 16 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2444 | 8.2444 | 8.2444 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032516 | 0.0032516 | 0.0032516 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01893 | | | 0.23 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11028.0 ave 11028 max 11028 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: 347944.0 ave 347944 max 347944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 347944 Ave neighs/atom = 120.02208 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.338 | 6.338 | 6.338 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12280.475 0 -12280.475 -10292.782 Loop time of 3.535e-06 on 1 procs for 0 steps with 2899 atoms 169.7% 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 | | 3.535e-06 | | |100.00 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10997.0 ave 10997 max 10997 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: 350402.0 ave 350402 max 350402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350402 Ave neighs/atom = 120.86996 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.338 | 6.338 | 6.338 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 -12280.475 -12280.475 39.435126 138.66778 6.3317684 -10292.782 -10292.782 214.94811 -31290.157 196.8625 2.2610987 9955.475 Loop time of 3.84e-06 on 1 procs for 0 steps with 2899 atoms 208.3% 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 | | 3.84e-06 | | |100.00 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10997.0 ave 10997 max 10997 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 175201.0 ave 175201 max 175201 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 350402.0 ave 350402 max 350402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350402 Ave neighs/atom = 120.86996 Neighbor list builds = 0 Dangerous builds = 0 2899 -12280.4746290517 eV 2.2610987120674 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:05:01