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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -53.497116 0.0000000) to (43.680212 53.497116 8.8549056) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3852316 5.1298604 5.9032704 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -53.497116 0.0000000) to (43.680212 53.497116 8.8549056) create_atoms CPU = 0.007 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3852316 5.1298604 5.9032704 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -53.497116 0.0000000) to (43.680212 53.497116 8.8549056) create_atoms CPU = 0.006 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 12 29 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3504 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_346334655118_005#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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 7.024 | 7.024 | 7.024 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11283.741 0 -11283.741 84399.49 65 0 -12359.253 0 -12359.253 6101.9549 Loop time of 5.71157 on 1 procs for 65 steps with 3504 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 = -11283.7406871865 -12359.2418373634 -12359.2527148228 Force two-norm initial, final = 1337.1811 0.34174304 Force max component initial, final = 206.48568 0.045773733 Final line search alpha, max atom move = 1.0000000 0.045773733 Iterations, force evaluations = 65 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5634 | 5.5634 | 5.5634 | 0.0 | 97.41 Neigh | 0.078727 | 0.078727 | 0.078727 | 0.0 | 1.38 Comm | 0.029817 | 0.029817 | 0.029817 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0396 | | | 0.69 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 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: 493140.0 ave 493140 max 493140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493140 Ave neighs/atom = 140.73630 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.022 | 7.022 | 7.022 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -12359.253 0 -12359.253 6101.9549 41383.674 71 0 -12359.94 0 -12359.94 -357.18365 41575.383 Loop time of 0.396556 on 1 procs for 6 steps with 3504 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12359.2527148226 -12359.9338209515 -12359.9396731556 Force two-norm initial, final = 305.67505 17.757523 Force max component initial, final = 269.75245 14.791269 Final line search alpha, max atom move = 5.1425337e-05 0.00076064601 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38556 | 0.38556 | 0.38556 | 0.0 | 97.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020088 | 0.0020088 | 0.0020088 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008983 | | | 2.27 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10969.0 ave 10969 max 10969 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: 491526.0 ave 491526 max 491526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491526 Ave neighs/atom = 140.27568 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 7.160 | 7.160 | 7.160 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12359.94 0 -12359.94 -357.18365 Loop time of 6.485e-06 on 1 procs for 0 steps with 3504 atoms 200.5% 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 | | 6.485e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10970.0 ave 10970 max 10970 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: 491060.0 ave 491060 max 491060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491060 Ave neighs/atom = 140.14269 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 7.160 | 7.160 | 7.160 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 -12359.94 -12359.94 43.649085 107.58321 8.8535332 -357.18365 -357.18365 -569.59997 -158.17408 -343.77691 2.300009 1547.1318 Loop time of 6.475e-06 on 1 procs for 0 steps with 3504 atoms 308.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10970.0 ave 10970 max 10970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 245530.0 ave 245530 max 245530 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 491060.0 ave 491060 max 491060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491060 Ave neighs/atom = 140.14269 Neighbor list builds = 0 Dangerous builds = 0 3504 -12359.9389691714 eV 2.30000898636517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07