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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -47.707720 0.0000000) to (58.429785 47.707720 9.8764362) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6776897 6.1338496 6.5842908 Created 1677 atoms using lattice units in orthogonal box = (0.0000000 -47.707720 0.0000000) to (58.429785 47.707720 9.8764362) create_atoms CPU = 0.003 seconds 1677 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6776897 6.1338496 6.5842908 Created 1701 atoms using lattice units in orthogonal box = (0.0000000 -47.707720 0.0000000) to (58.429785 47.707720 9.8764362) create_atoms CPU = 0.003 seconds 1701 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 22 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 3360 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_019873715786_000#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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.973 | 6.973 | 6.973 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10987.203 0 -10987.203 8299.3767 75 0 -11254.228 0 -11254.228 5140.2086 Loop time of 4.04218 on 1 procs for 75 steps with 3360 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 = -10987.2029722315 -11254.2177490994 -11254.2283333948 Force two-norm initial, final = 75.104448 0.23914277 Force max component initial, final = 6.9454960 0.033626007 Final line search alpha, max atom move = 1.0000000 0.033626007 Iterations, force evaluations = 75 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9644 | 3.9644 | 3.9644 | 0.0 | 98.07 Neigh | 0.034924 | 0.034924 | 0.034924 | 0.0 | 0.86 Comm | 0.017338 | 0.017338 | 0.017338 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02555 | | | 0.63 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10756.0 ave 10756 max 10756 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: 581720.0 ave 581720 max 581720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581720 Ave neighs/atom = 173.13095 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.973 | 6.973 | 6.973 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -11254.228 0 -11254.228 5140.2086 55062.155 84 0 -11255.362 0 -11255.362 30.365969 55394.846 Loop time of 0.290064 on 1 procs for 9 steps with 3360 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 = -11254.2283333948 -11255.3616663341 -11255.3618534044 Force two-norm initial, final = 349.14589 2.6587699 Force max component initial, final = 312.53140 2.5532135 Final line search alpha, max atom move = 0.00029573645 0.00075507830 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28286 | 0.28286 | 0.28286 | 0.0 | 97.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096496 | 0.00096496 | 0.00096496 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006242 | | | 2.15 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10748.0 ave 10748 max 10748 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: 583850.0 ave 583850 max 583850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583850 Ave neighs/atom = 173.76488 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.111 | 7.111 | 7.111 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11255.362 0 -11255.362 30.365969 Loop time of 2.086e-06 on 1 procs for 0 steps with 3360 atoms 143.8% 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 | | 2.086e-06 | | |100.00 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10748.0 ave 10748 max 10748 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: 583392.0 ave 583392 max 583392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583392 Ave neighs/atom = 173.62857 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.111 | 7.111 | 7.111 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 -11255.362 -11255.362 58.41727 96.179865 9.8592514 30.365969 30.365969 12.344862 74.437818 4.3152271 2.6719403 2020.5285 Loop time of 2.631e-06 on 1 procs for 0 steps with 3360 atoms 304.1% 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 | | 2.631e-06 | | |100.00 Nlocal: 3360.00 ave 3360 max 3360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10748.0 ave 10748 max 10748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291696.0 ave 291696 max 291696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 583392.0 ave 583392 max 583392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583392 Ave neighs/atom = 173.62857 Neighbor list builds = 0 Dangerous builds = 0 3360 -11255.3618534044 eV 2.6719403091431 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04