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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -65.760007 0.0000000) to (23.248242 65.760007 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3404298 4.9815121 5.7233217 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.760007 0.0000000) to (23.248242 65.760007 5.7233217) create_atoms CPU = 0.001 seconds 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3404298 4.9815121 5.7233217 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.760007 0.0000000) to (23.248242 65.760007 5.7233217) 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 7 38 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1052 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 7 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3490.419 0 -3490.419 8872.1174 40 0 -3525.9034 0 -3525.9034 -702.06471 Loop time of 3.47163 on 1 procs for 40 steps with 1052 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3490.41900178024 -3525.90013915938 -3525.90341725485 Force two-norm initial, final = 30.248050 0.16005394 Force max component initial, final = 8.4184380 0.023568044 Final line search alpha, max atom move = 1.0000000 0.023568044 Iterations, force evaluations = 40 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4538 | 3.4538 | 3.4538 | 0.0 | 99.49 Neigh | 0.0069727 | 0.0069727 | 0.0069727 | 0.0 | 0.20 Comm | 0.0056492 | 0.0056492 | 0.0056492 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005161 | | | 0.15 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5549.00 ave 5549 max 5549 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: 89996.0 ave 89996 max 89996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89996 Ave neighs/atom = 85.547529 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 7 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -3525.9034 0 -3525.9034 -702.06471 17499.681 42 0 -3525.9075 0 -3525.9075 -50.612247 17485.15 Loop time of 0.249969 on 1 procs for 2 steps with 1052 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 = -3525.90341725485 -3525.90718407577 -3525.90754652749 Force two-norm initial, final = 11.782771 0.16545229 Force max component initial, final = 10.203697 0.027773676 Final line search alpha, max atom move = 0.00060853701 1.6901310e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24865 | 0.24865 | 0.24865 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022755 | 0.00022755 | 0.00022755 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001092 | | | 0.44 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5556.00 ave 5556 max 5556 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: 90112.0 ave 90112 max 90112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90112 Ave neighs/atom = 85.657795 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 7 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.772 | 4.772 | 4.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3525.9075 0 -3525.9075 -50.612247 Loop time of 2.216e-06 on 1 procs for 0 steps with 1052 atoms 135.4% 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 | | 2.216e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5556.00 ave 5556 max 5556 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: 90112.0 ave 90112 max 90112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90112 Ave neighs/atom = 85.657795 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 7 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.772 | 4.772 | 4.772 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 -3525.9075 -3525.9075 23.246971 131.52001 5.7188821 -50.612247 -50.612247 -1.9011812 -149.8951 -0.040456484 2.5268472 579.9602 Loop time of 2.367e-06 on 1 procs for 0 steps with 1052 atoms 211.2% 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 | | 2.367e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5556.00 ave 5556 max 5556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45056.0 ave 45056 max 45056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90112.0 ave 90112 max 90112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90112 Ave neighs/atom = 85.657795 Neighbor list builds = 0 Dangerous builds = 0 1052 -3525.90754652749 eV 2.52684718626321 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04