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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -60.244545 0.0000000) to (49.189465 60.244545 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0644546 5.7768742 6.6478321 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -60.244545 0.0000000) to (49.189465 60.244545 9.9717481) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0644546 5.7768742 6.6478321 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -60.244545 0.0000000) to (49.189465 60.244545 9.9717481) create_atoms CPU = 0.002 seconds 1756 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 40 4 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 3486 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 40 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.220 | 5.220 | 5.220 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11313.517 0 -11313.517 19042.752 93 0 -11707.788 0 -11707.788 -1198.6694 Loop time of 15.424 on 1 procs for 93 steps with 3486 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11313.5166155102 -11707.7858111878 -11707.7884857244 Force two-norm initial, final = 494.96640 0.44728779 Force max component initial, final = 72.522765 0.096292057 Final line search alpha, max atom move = 1.0000000 0.096292057 Iterations, force evaluations = 93 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.307 | 15.307 | 15.307 | 0.0 | 99.24 Neigh | 0.073338 | 0.073338 | 0.073338 | 0.0 | 0.48 Comm | 0.015514 | 0.015514 | 0.015514 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02861 | | | 0.19 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7268.00 ave 7268 max 7268 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: 187740.0 ave 187740 max 187740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187740 Ave neighs/atom = 53.855422 Neighbor list builds = 4 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 40 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.217 | 5.217 | 5.217 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -11707.788 0 -11707.788 -1198.6694 59100.496 95 0 -11707.843 0 -11707.843 0.64845088 59027.596 Loop time of 0.468716 on 1 procs for 2 steps with 3486 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 = -11707.7884857244 -11707.8333328836 -11707.843050108 Force two-norm initial, final = 89.937375 5.9206682 Force max component initial, final = 64.730148 4.3947127 Final line search alpha, max atom move = 3.3917017e-05 0.00014905555 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46649 | 0.46649 | 0.46649 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030649 | 0.00030649 | 0.00030649 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001922 | | | 0.41 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6887.00 ave 6887 max 6887 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: 187584.0 ave 187584 max 187584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187584 Ave neighs/atom = 53.810671 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 40 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.355 | 5.355 | 5.355 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11707.843 0 -11707.843 0.64845088 Loop time of 2.285e-06 on 1 procs for 0 steps with 3486 atoms 175.1% 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 | | 2.285e-06 | | |100.00 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6894.00 ave 6894 max 6894 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: 187582.0 ave 187582 max 187582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187582 Ave neighs/atom = 53.810098 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 40 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.355 | 5.355 | 5.355 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 -11707.843 -11707.843 49.14719 120.55596 9.9624861 0.64845088 0.64845088 119.18246 -10.934356 -106.30275 2.4831784 2041.0108 Loop time of 2.531e-06 on 1 procs for 0 steps with 3486 atoms 276.6% 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 | | 2.531e-06 | | |100.00 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6894.00 ave 6894 max 6894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93791.0 ave 93791 max 93791 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187582.0 ave 187582 max 187582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187582 Ave neighs/atom = 53.810098 Neighbor list builds = 0 Dangerous builds = 0 3486 -11707.843050108 eV 2.48317844415671 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16