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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -65.657284 0.0000000) to (23.213355 65.657284 5.7147330) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3309151 4.9740366 5.7147330 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -65.657284 0.0000000) to (23.213355 65.657284 5.7147330) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3309151 4.9740366 5.7147330 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.657284 0.0000000) to (23.213355 65.657284 5.7147330) create_atoms CPU = 0.001 seconds 530 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 27 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1054 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3886.0273 0 -3886.0273 29593.453 90 0 -4108.1352 0 -4108.1352 2510.1991 Loop time of 4.22349 on 1 procs for 90 steps with 1054 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3886.02728637552 -4108.13115234128 -4108.13516386957 Force two-norm initial, final = 426.55729 0.15856383 Force max component initial, final = 103.35768 0.025012011 Final line search alpha, max atom move = 1.0000000 0.025012011 Iterations, force evaluations = 90 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1247 | 4.1247 | 4.1247 | 0.0 | 97.66 Neigh | 0.062431 | 0.062431 | 0.062431 | 0.0 | 1.48 Comm | 0.021117 | 0.021117 | 0.021117 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0152 | | | 0.36 Nlocal: 1054.00 ave 1054 max 1054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9089.00 ave 9089 max 9089 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: 260456.0 ave 260456 max 260456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260456 Ave neighs/atom = 247.11195 Neighbor list builds = 3 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -4108.1352 0 -4108.1352 2510.1991 17419.945 94 0 -4108.2005 0 -4108.2005 -15.442752 17473.597 Loop time of 0.202093 on 1 procs for 4 steps with 1054 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 = -4108.13516386959 -4108.19989668124 -4108.20050195662 Force two-norm initial, final = 50.263183 0.45188715 Force max component initial, final = 41.209352 0.38791227 Final line search alpha, max atom move = 0.00016903789 6.5571872e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19739 | 0.19739 | 0.19739 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085927 | 0.00085927 | 0.00085927 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003842 | | | 1.90 Nlocal: 1054.00 ave 1054 max 1054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9076.00 ave 9076 max 9076 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: 260416.0 ave 260416 max 260416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260416 Ave neighs/atom = 247.07400 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.617 | 5.617 | 5.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4108.2005 0 -4108.2005 -15.442752 Loop time of 3.532e-06 on 1 procs for 0 steps with 1054 atoms 141.6% 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 | | 3.532e-06 | | |100.00 Nlocal: 1054.00 ave 1054 max 1054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9046.00 ave 9046 max 9046 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: 260224.0 ave 260224 max 260224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260224 Ave neighs/atom = 246.89184 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.617 | 5.617 | 5.617 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 -4108.2005 -4108.2005 23.209004 131.74454 5.7146969 -15.442752 -15.442752 -14.271163 3.5108548 -35.567947 2.687788 549.48143 Loop time of 3.799e-06 on 1 procs for 0 steps with 1054 atoms 210.6% 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 | | 3.799e-06 | | |100.00 Nlocal: 1054.00 ave 1054 max 1054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9046.00 ave 9046 max 9046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130112.0 ave 130112 max 130112 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 260224.0 ave 260224 max 260224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260224 Ave neighs/atom = 246.89184 Neighbor list builds = 0 Dangerous builds = 0 1054 -4108.20050195662 eV 2.68778798455119 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05