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 -75.017096 0.0000000) to (26.522549 75.017096 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7848380 6.9783345 5.7200000 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -75.017096 0.0000000) to (26.522549 75.017096 5.7200000) create_atoms CPU = 0.003 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7848380 6.9783345 5.7200000 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -75.017096 0.0000000) to (26.522549 75.017096 5.7200000) create_atoms CPU = 0.002 seconds 690 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 = 9 47 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_099716416216_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 = 9 47 2 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) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4535.8564 0 -4535.8564 12914.983 68 0 -4622.9985 0 -4622.9985 2856.0559 Loop time of 6.23514 on 1 procs for 68 steps with 1378 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 = -4535.85643057178 -4622.99467257581 -4622.99851314171 Force two-norm initial, final = 120.82199 0.14974208 Force max component initial, final = 32.494353 0.032784760 Final line search alpha, max atom move = 1.0000000 0.032784760 Iterations, force evaluations = 68 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2157 | 6.2157 | 6.2157 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0092582 | 0.0092582 | 0.0092582 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01017 | | | 0.16 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5857.00 ave 5857 max 5857 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: 107020.0 ave 107020 max 107020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107020 Ave neighs/atom = 77.663280 Neighbor list builds = 0 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 = 9 47 2 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4622.9985 0 -4622.9985 2856.0559 22761.534 73 0 -4623.1357 0 -4623.1357 -1.3260859 22843.139 Loop time of 0.398844 on 1 procs for 5 steps with 1378 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 = -4622.99851314172 -4623.13452995801 -4623.13569794835 Force two-norm initial, final = 78.111729 0.20014210 Force max component initial, final = 68.308417 0.096216343 Final line search alpha, max atom move = 0.00010938982 1.0525088e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39616 | 0.39616 | 0.39616 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039715 | 0.00039715 | 0.00039715 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002286 | | | 0.57 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5857.00 ave 5857 max 5857 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: 106000.0 ave 106000 max 106000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106000 Ave neighs/atom = 76.923077 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 = 9 47 2 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) = 5.208 | 5.208 | 5.208 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4623.1357 0 -4623.1357 -1.3260859 Loop time of 2.471e-06 on 1 procs for 0 steps with 1378 atoms 161.9% 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 | | 2.471e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5857.00 ave 5857 max 5857 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: 105900.0 ave 105900 max 105900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105900 Ave neighs/atom = 76.850508 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 = 9 47 2 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) = 5.208 | 5.208 | 5.208 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 -4623.1357 -4623.1357 26.520028 150.67933 5.7164725 -1.3260859 -1.3260859 4.7014464 -1.9354252 -6.7442789 2.6182725 478.90106 Loop time of 2.498e-06 on 1 procs for 0 steps with 1378 atoms 240.2% 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 | | 2.498e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5857.00 ave 5857 max 5857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52950.0 ave 52950 max 52950 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105900.0 ave 105900 max 105900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105900 Ave neighs/atom = 76.850508 Neighbor list builds = 0 Dangerous builds = 0 1378 -4623.13569794835 eV 2.61827248392927 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07