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 = 4.0320829 4.0320829 4.0320829 Created orthogonal box = (0.0000000 -43.050865 0.0000000) to (24.855428 43.050865 6.9837724) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5409022 6.0422266 6.9837724 Created 455 atoms using lattice units in orthogonal box = (0.0000000 -43.050865 0.0000000) to (24.855428 43.050865 6.9837724) create_atoms CPU = 0.003 seconds 455 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5409022 6.0422266 6.9837724 Created 457 atoms using lattice units in orthogonal box = (0.0000000 -43.050865 0.0000000) to (24.855428 43.050865 6.9837724) create_atoms CPU = 0.002 seconds 457 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 7 23 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 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 911 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_450093727396_002#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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 4.979 | 4.979 | 4.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2984.3489 0 -2984.3489 9469.9384 72 0 -3049.9116 0 -3049.9116 4294.9811 Loop time of 1.7834 on 1 procs for 72 steps with 911 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 = -2984.34892695314 -3049.90863777196 -3049.91155179473 Force two-norm initial, final = 43.352480 0.15118515 Force max component initial, final = 6.7581466 0.049607060 Final line search alpha, max atom move = 1.0000000 0.049607060 Iterations, force evaluations = 72 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7126 | 1.7126 | 1.7126 | 0.0 | 96.03 Neigh | 0.035029 | 0.035029 | 0.035029 | 0.0 | 1.96 Comm | 0.018526 | 0.018526 | 0.018526 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01721 | | | 0.97 Nlocal: 911.000 ave 911 max 911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4830.00 ave 4830 max 4830 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: 114806.0 ave 114806 max 114806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114806 Ave neighs/atom = 126.02195 Neighbor list builds = 2 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.979 | 4.979 | 4.979 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -3049.9116 0 -3049.9116 4294.9811 14945.939 81 0 -3050.239 0 -3050.239 4.2497401 15023.89 Loop time of 0.153254 on 1 procs for 9 steps with 911 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 = -3049.91155179474 -3050.23857243129 -3050.23903838 Force two-norm initial, final = 88.920690 0.39372807 Force max component initial, final = 83.943960 0.15948362 Final line search alpha, max atom move = 0.00051716464 8.2479287e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14603 | 0.14603 | 0.14603 | 0.0 | 95.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013588 | 0.0013588 | 0.0013588 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005863 | | | 3.83 Nlocal: 911.000 ave 911 max 911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4820.00 ave 4820 max 4820 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: 114704.0 ave 114704 max 114704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114704 Ave neighs/atom = 125.90999 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 5.117 | 5.117 | 5.117 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3050.239 0 -3050.239 4.2497401 Loop time of 7.558e-06 on 1 procs for 0 steps with 911 atoms 172.0% 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 | | 7.558e-06 | | |100.00 Nlocal: 911.000 ave 911 max 911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4820.00 ave 4820 max 4820 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: 109710.0 ave 109710 max 109710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109710 Ave neighs/atom = 120.42810 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 5.117 | 5.117 | 5.117 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 -3050.239 -3050.239 24.847846 86.817825 6.9644168 4.2497401 4.2497401 -2.5312061 -1.6800758 16.960502 2.6182635 737.80792 Loop time of 6.936e-06 on 1 procs for 0 steps with 911 atoms 245.1% 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 | | 6.936e-06 | | |100.00 Nlocal: 911.000 ave 911 max 911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4820.00 ave 4820 max 4820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54855.0 ave 54855 max 54855 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109710.0 ave 109710 max 109710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109710 Ave neighs/atom = 120.42810 Neighbor list builds = 0 Dangerous builds = 0 911 -3050.23903838 eV 2.61826351338331 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02