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 = 2.8436425 2.8436425 2.8436425 Created orthogonal box = (0.0000000 -56.301250 0.0000000) to (34.477333 56.301250 6.9654732) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9871746 4.0215178 4.6436488 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -56.301250 0.0000000) to (34.477333 56.301250 6.9654732) create_atoms CPU = 0.005 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9871746 4.0215178 4.6436488 Created 1181 atoms using lattice units in orthogonal box = (0.0000000 -56.301250 0.0000000) to (34.477333 56.301250 6.9654732) create_atoms CPU = 0.004 seconds 1181 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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2352 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_044341472608_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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.508 | 6.508 | 6.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6832.8967 0 -6832.8967 220395.08 108 0 -9445.4336 0 -9445.4336 3721.6014 Loop time of 8.2548 on 1 procs for 108 steps with 2352 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 = -6832.89668658787 -9445.42519757972 -9445.43357574191 Force two-norm initial, final = 4115.8538 0.31334176 Force max component initial, final = 543.34607 0.045545457 Final line search alpha, max atom move = 0.80673147 0.036742953 Iterations, force evaluations = 108 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0931 | 8.0931 | 8.0931 | 0.0 | 98.04 Neigh | 0.056787 | 0.056787 | 0.056787 | 0.0 | 0.69 Comm | 0.055811 | 0.055811 | 0.055811 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04905 | | | 0.59 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10706.0 ave 10706 max 10706 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: 399210.0 ave 399210 max 399210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 399210 Ave neighs/atom = 169.73214 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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.508 | 6.508 | 6.508 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -9445.4336 0 -9445.4336 3721.6014 27041.596 110 0 -9445.5108 0 -9445.5108 0.83326468 27096.822 Loop time of 0.20661 on 1 procs for 2 steps with 2352 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 = -9445.43357574192 -9445.50418918202 -9445.5107696186 Force two-norm initial, final = 112.00706 2.7537246 Force max component initial, final = 75.775396 1.9660233 Final line search alpha, max atom move = 6.0212977e-05 0.00011838011 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20152 | 0.20152 | 0.20152 | 0.0 | 97.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012624 | 0.0012624 | 0.0012624 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003826 | | | 1.85 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10737.0 ave 10737 max 10737 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: 398516.0 ave 398516 max 398516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398516 Ave neighs/atom = 169.43707 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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.646 | 6.646 | 6.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9445.5108 0 -9445.5108 0.83326468 Loop time of 6.275e-06 on 1 procs for 0 steps with 2352 atoms 191.2% 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 | | 6.275e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10740.0 ave 10740 max 10740 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: 398358.0 ave 398358 max 398358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398358 Ave neighs/atom = 169.36990 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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.646 | 6.646 | 6.646 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 -9445.5108 -9445.5108 34.472809 112.72383 6.9731012 0.83326468 0.83326468 6.9904329 111.88337 -116.37401 2.2871845 1646.8959 Loop time of 6.756e-06 on 1 procs for 0 steps with 2352 atoms 251.6% 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 | | 6.756e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10740.0 ave 10740 max 10740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 199179.0 ave 199179 max 199179 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 398358.0 ave 398358 max 398358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398358 Ave neighs/atom = 169.36990 Neighbor list builds = 0 Dangerous builds = 0 2352 -9445.5107696186 eV 2.28718454804865 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09