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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -47.936049 0.0000000) to (29.354715 47.936049 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3372210 5.4472783 5.9005198 Created 1045 atoms using lattice units in orthogonal box = (0.0000000 -47.936049 0.0000000) to (29.354715 47.936049 8.8507797) create_atoms CPU = 0.002 seconds 1045 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3372210 5.4472783 5.9005198 Created 1069 atoms using lattice units in orthogonal box = (0.0000000 -47.936049 0.0000000) to (29.354715 47.936049 8.8507797) create_atoms CPU = 0.001 seconds 1069 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 30 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2109 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.124 | 5.124 | 5.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7413.6335 0 -7413.6335 6970.3737 62 0 -7453.4343 0 -7453.4343 1968.6092 Loop time of 6.49524 on 1 procs for 62 steps with 2109 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 = -7413.63349120574 -7453.42772657431 -7453.43426299963 Force two-norm initial, final = 63.988770 0.20461482 Force max component initial, final = 19.045228 0.045889563 Final line search alpha, max atom move = 1.0000000 0.045889563 Iterations, force evaluations = 62 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4565 | 6.4565 | 6.4565 | 0.0 | 99.40 Neigh | 0.01521 | 0.01521 | 0.01521 | 0.0 | 0.23 Comm | 0.0098131 | 0.0098131 | 0.0098131 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01367 | | | 0.21 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6445.00 ave 6445 max 6445 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: 182126.0 ave 182126 max 182126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182126 Ave neighs/atom = 86.356567 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.124 | 5.124 | 5.124 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -7453.4343 0 -7453.4343 1968.6092 24908.733 66 0 -7453.5707 0 -7453.5707 -221.07393 24946.824 Loop time of 0.346556 on 1 procs for 4 steps with 2109 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 = -7453.43426299962 -7453.56874887133 -7453.57073558392 Force two-norm initial, final = 82.028518 7.9896544 Force max component initial, final = 81.670313 6.4413959 Final line search alpha, max atom move = 8.3020158e-05 0.00053476571 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34392 | 0.34392 | 0.34392 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036622 | 0.00036622 | 0.00036622 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00227 | | | 0.65 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6428.00 ave 6428 max 6428 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: 182092.0 ave 182092 max 182092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182092 Ave neighs/atom = 86.340446 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.262 | 5.262 | 5.262 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7453.5707 0 -7453.5707 -221.07393 Loop time of 2.296e-06 on 1 procs for 0 steps with 2109 atoms 174.2% 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 | | 2.296e-06 | | |100.00 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6428.00 ave 6428 max 6428 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: 182000.0 ave 182000 max 182000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182000 Ave neighs/atom = 86.296823 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.262 | 5.262 | 5.262 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 -7453.5707 -7453.5707 29.327339 96.189979 8.8432676 -221.07393 -221.07393 -413.30426 48.948683 -298.86622 2.4074592 756.90291 Loop time of 2.691e-06 on 1 procs for 0 steps with 2109 atoms 260.1% 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 | | 2.691e-06 | | |100.00 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6428.00 ave 6428 max 6428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91000.0 ave 91000 max 91000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 182000.0 ave 182000 max 182000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182000 Ave neighs/atom = 86.296823 Neighbor list builds = 0 Dangerous builds = 0 2109 -7453.57073558392 eV 2.40745922586014 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07