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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -49.042583 0.0000000) to (13.347700 49.042583 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7204430 5.4491758 5.8254140 Created 504 atoms using lattice units in orthogonal box = (0.0000000 -49.042583 0.0000000) to (13.347700 49.042583 8.7381210) create_atoms CPU = 0.001 seconds 504 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7204430 5.4491758 5.8254140 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -49.042583 0.0000000) to (13.347700 49.042583 8.7381210) create_atoms CPU = 0.001 seconds 508 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 36 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1004 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 36 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.529 | 4.529 | 4.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4103.0632 0 -4103.0632 30740.692 67 0 -4231.803 0 -4231.803 32804.042 Loop time of 3.25401 on 1 procs for 67 steps with 1004 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4103.06321704386 -4231.79875853992 -4231.80295280323 Force two-norm initial, final = 189.79307 0.24612912 Force max component initial, final = 40.209927 0.021210958 Final line search alpha, max atom move = 1.0000000 0.021210958 Iterations, force evaluations = 67 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2386 | 3.2386 | 3.2386 | 0.0 | 99.53 Neigh | 0.0053353 | 0.0053353 | 0.0053353 | 0.0 | 0.16 Comm | 0.004187 | 0.004187 | 0.004187 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005883 | | | 0.18 Nlocal: 1004.00 ave 1004 max 1004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3578.00 ave 3578 max 3578 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: 57120.0 ave 57120 max 57120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57120 Ave neighs/atom = 56.892430 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 36 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.529 | 4.529 | 4.529 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -4231.803 0 -4231.803 32804.042 11440.048 73 0 -4232.9514 0 -4232.9514 -641.04953 11547.669 Loop time of 0.206329 on 1 procs for 6 steps with 1004 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 = -4231.80295280324 -4232.94896769118 -4232.95141107044 Force two-norm initial, final = 410.55142 8.4715666 Force max component initial, final = 276.48572 6.4907061 Final line search alpha, max atom move = 0.00016759630 0.0010878183 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20483 | 0.20483 | 0.20483 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001282 | | | 0.62 Nlocal: 1004.00 ave 1004 max 1004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3584.00 ave 3584 max 3584 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: 57184.0 ave 57184 max 57184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57184 Ave neighs/atom = 56.956175 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.667 | 4.667 | 4.667 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4232.9514 0 -4232.9514 -641.04953 Loop time of 1.822e-06 on 1 procs for 0 steps with 1004 atoms 164.7% 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 | | 1.822e-06 | | |100.00 Nlocal: 1004.00 ave 1004 max 1004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3578.00 ave 3578 max 3578 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: 56280.0 ave 56280 max 56280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56280 Ave neighs/atom = 56.055777 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.667 | 4.667 | 4.667 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 -4232.9514 -4232.9514 13.357584 98.546613 8.7725276 -641.04953 -641.04953 -901.21707 -630.19868 -391.73283 2.3190657 572.2569 Loop time of 1.668e-06 on 1 procs for 0 steps with 1004 atoms 179.9% 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 | | 1.668e-06 | | |100.00 Nlocal: 1004.00 ave 1004 max 1004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3578.00 ave 3578 max 3578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28140.0 ave 28140 max 28140 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56280.0 ave 56280 max 56280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56280 Ave neighs/atom = 56.055777 Neighbor list builds = 0 Dangerous builds = 0 1004 -4232.95141107044 eV 2.31906566717662 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03