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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4487538 6.6048871 5.7200000 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) create_atoms CPU = 0.002 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4487538 6.6048871 5.7200000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) create_atoms CPU = 0.001 seconds 434 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 860 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_131642768288_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2794.9898 0 -2794.9898 15254.718 58 0 -2881.5443 0 -2881.5443 508.24616 Loop time of 3.16046 on 1 procs for 58 steps with 860 atoms 95.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2794.98977201545 -2881.541775534 -2881.54426030066 Force two-norm initial, final = 169.17701 0.11104479 Force max component initial, final = 46.914064 0.013430868 Final line search alpha, max atom move = 1.0000000 0.013430868 Iterations, force evaluations = 58 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1457 | 3.1457 | 3.1457 | 0.0 | 99.53 Neigh | 0.0047158 | 0.0047158 | 0.0047158 | 0.0 | 0.15 Comm | 0.0047443 | 0.0047443 | 0.0047443 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005274 | | | 0.17 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4187.00 ave 4187 max 4187 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: 66772.0 ave 66772 max 66772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66772 Ave neighs/atom = 77.641860 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -2881.5443 0 -2881.5443 508.24616 14292.126 61 0 -2881.5639 0 -2881.5639 -45.485064 14302.312 Loop time of 0.146119 on 1 procs for 3 steps with 860 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 = -2881.54426030063 -2881.56249313282 -2881.56390286522 Force two-norm initial, final = 16.332365 0.85391885 Force max component initial, final = 14.413432 0.76757141 Final line search alpha, max atom move = 0.00015405892 0.00011825123 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.145 | 0.145 | 0.145 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001909 | 0.0001909 | 0.0001909 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009286 | | | 0.64 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4304.00 ave 4304 max 4304 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: 66708.0 ave 66708 max 66708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66708 Ave neighs/atom = 77.567442 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.714 | 4.714 | 4.714 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2881.5639 0 -2881.5639 -45.485064 Loop time of 1.947e-06 on 1 procs for 0 steps with 860 atoms 205.4% 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 | | 1.947e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4304.00 ave 4304 max 4304 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: 66704.0 ave 66704 max 66704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66704 Ave neighs/atom = 77.562791 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.714 | 4.714 | 4.714 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 -2881.5639 -2881.5639 21.023686 119.117 5.7111505 -45.485064 -45.485064 -37.742289 -12.860889 -85.852014 2.5843662 584.00949 Loop time of 2.339e-06 on 1 procs for 0 steps with 860 atoms 256.5% 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 | | 2.339e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4304.00 ave 4304 max 4304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33352.0 ave 33352 max 33352 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66704.0 ave 66704 max 66704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66704 Ave neighs/atom = 77.562791 Neighbor list builds = 0 Dangerous builds = 0 860 -2881.56390286522 eV 2.58436618337358 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03