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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -50.943356 0.0000000) to (12.007464 50.943356 5.1200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4579383 6.1749523 5.1200000 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -50.943356 0.0000000) to (12.007464 50.943356 5.1200000) create_atoms CPU = 0.003 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4579383 6.1749523 5.1200000 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.943356 0.0000000) to (12.007464 50.943356 5.1200000) create_atoms CPU = 0.003 seconds 266 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 528 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_390178379548_001#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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1789.907 0 -1789.907 36606.481 48 0 -1863.8084 0 -1863.8084 6144.798 Loop time of 1.90374 on 1 procs for 48 steps with 528 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 = -1789.90701716481 -1863.80669427697 -1863.80841843927 Force two-norm initial, final = 156.01725 0.11934077 Force max component initial, final = 49.461992 0.029571393 Final line search alpha, max atom move = 1.0000000 0.029571393 Iterations, force evaluations = 48 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8808 | 1.8808 | 1.8808 | 0.0 | 98.80 Neigh | 0.0070255 | 0.0070255 | 0.0070255 | 0.0 | 0.37 Comm | 0.0085327 | 0.0085327 | 0.0085327 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007336 | | | 0.39 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3602.00 ave 3602 max 3602 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: 40868.0 ave 40868 max 40868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40868 Ave neighs/atom = 77.401515 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -1863.8084 0 -1863.8084 6144.798 6263.8134 53 0 -1863.9053 0 -1863.9053 248.61677 6289.5016 Loop time of 0.152293 on 1 procs for 5 steps with 528 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 = -1863.80841843927 -1863.903870703 -1863.9053190647 Force two-norm initial, final = 48.078102 1.8095273 Force max component initial, final = 43.362414 1.3543107 Final line search alpha, max atom move = 0.00035099685 0.00047535880 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14934 | 0.14934 | 0.14934 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064997 | 0.00064997 | 0.00064997 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002306 | | | 1.51 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3602.00 ave 3602 max 3602 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: 40892.0 ave 40892 max 40892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40892 Ave neighs/atom = 77.446970 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 ghost atom cutoff = 6 binsize = 3, bins = 5 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1863.9053 0 -1863.9053 248.61677 Loop time of 6.445e-06 on 1 procs for 0 steps with 528 atoms 170.7% 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 | | 6.445e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3602.00 ave 3602 max 3602 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: 40856.0 ave 40856 max 40856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40856 Ave neighs/atom = 77.378788 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 ghost atom cutoff = 6 binsize = 3, bins = 5 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.645 | 4.645 | 4.645 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 -1863.9053 -1863.9053 12.009877 102.33657 5.1173702 248.61677 248.61677 122.87665 346.51795 276.45572 2.3782863 279.0737 Loop time of 6.936e-06 on 1 procs for 0 steps with 528 atoms 259.5% 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 | | 6.936e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3602.00 ave 3602 max 3602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20428.0 ave 20428 max 20428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40856.0 ave 40856 max 40856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40856 Ave neighs/atom = 77.378788 Neighbor list builds = 0 Dangerous builds = 0 528 -1863.9053190647 eV 2.37828626475742 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02