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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -44.666822 0.0000000) to (21.056142 44.666822 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1929829 6.1307403 5.1068645 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -44.666822 0.0000000) to (21.056142 44.666822 5.1068645) create_atoms CPU = 0.002 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1929829 6.1307403 5.1068645 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.666822 0.0000000) to (21.056142 44.666822 5.1068645) create_atoms CPU = 0.001 seconds 412 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3090.3385 0 -3090.3385 81414.544 546 0 -3478.8106 0 -3478.8106 3713.0039 Loop time of 68.2302 on 1 procs for 546 steps with 816 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 = -3090.33849914982 -3478.80744595623 -3478.8105612862 Force two-norm initial, final = 578.19918 0.17282615 Force max component initial, final = 120.94428 0.037899991 Final line search alpha, max atom move = 1.0000000 0.037899991 Iterations, force evaluations = 546 1059 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 68.027 | 68.027 | 68.027 | 0.0 | 99.70 Neigh | 0.090365 | 0.090365 | 0.090365 | 0.0 | 0.13 Comm | 0.062709 | 0.062709 | 0.062709 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05058 | | | 0.07 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4874.00 ave 4874 max 4874 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: 92184.0 ave 92184 max 92184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92184 Ave neighs/atom = 112.97059 Neighbor list builds = 14 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 546 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.573 | 4.573 | 4.573 Mbytes Step Temp E_pair E_mol TotEng Press Volume 546 0 -3478.8106 0 -3478.8106 3713.0039 9606.124 572 0 -3485.4609 0 -3485.4609 -17.985764 9613.1356 Loop time of 2.2131 on 1 procs for 26 steps with 816 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 = -3478.81056128621 -3485.46037924906 -3485.46093442209 Force two-norm initial, final = 408.89394 1.0935417 Force max component initial, final = 305.63916 0.39128697 Final line search alpha, max atom move = 0.00037859881 0.00014814078 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2064 | 2.2064 | 2.2064 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011323 | 0.0011323 | 0.0011323 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00554 | | | 0.25 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4799.00 ave 4799 max 4799 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: 91876.0 ave 91876 max 91876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91876 Ave neighs/atom = 112.59314 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.713 | 4.713 | 4.713 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3485.4609 0 -3485.4609 -17.985764 Loop time of 2.008e-06 on 1 procs for 0 steps with 816 atoms 149.4% 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 | | 2.008e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5062.00 ave 5062 max 5062 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: 91776.0 ave 91776 max 91776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91776 Ave neighs/atom = 112.47059 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.713 | 4.713 | 4.713 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 -3485.4609 -3485.4609 21.419331 90.154285 4.9782052 -17.985764 -17.985764 -23.680513 -65.813047 35.536267 2.3555951 2598.2058 Loop time of 1.757e-06 on 1 procs for 0 steps with 816 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 | | 1.757e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5062.00 ave 5062 max 5062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45888.0 ave 45888 max 45888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91776.0 ave 91776 max 91776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91776 Ave neighs/atom = 112.47059 Neighbor list builds = 0 Dangerous builds = 0 816 -3485.46093442209 eV 2.35559506835217 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:11