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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -41.726897 0.0000000) to (29.502823 41.726897 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7244284 6.2273571 5.0973115 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.726897 0.0000000) to (29.502823 41.726897 5.0973115) create_atoms CPU = 0.001 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7244284 6.2273571 5.0973115 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.726897 0.0000000) to (29.502823 41.726897 5.0973115) create_atoms CPU = 0.001 seconds 538 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 28 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1058 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4454.9547 0 -4454.9547 -3203.658 88 0 -4487.823 0 -4487.823 -19462.345 Loop time of 5.05118 on 1 procs for 88 steps with 1058 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 = -4454.95469881149 -4487.81939180384 -4487.82299720624 Force two-norm initial, final = 22.425616 0.16176134 Force max component initial, final = 7.8840473 0.020002769 Final line search alpha, max atom move = 1.0000000 0.020002769 Iterations, force evaluations = 88 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0292 | 5.0292 | 5.0292 | 0.0 | 99.57 Neigh | 0.0060237 | 0.0060237 | 0.0060237 | 0.0 | 0.12 Comm | 0.0079087 | 0.0079087 | 0.0079087 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008037 | | | 0.16 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4976.00 ave 4976 max 4976 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: 82152.0 ave 82152 max 82152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82152 Ave neighs/atom = 77.648393 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4487.823 0 -4487.823 -19462.345 12550.205 102 0 -4489.5641 0 -4489.5641 2785.1376 12373.782 Loop time of 0.543128 on 1 procs for 14 steps with 1058 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 = -4487.82299720624 -4489.56401137176 -4489.56411169724 Force two-norm initial, final = 291.68749 0.50311355 Force max component initial, final = 252.53886 0.37513537 Final line search alpha, max atom move = 0.00049158558 0.00018441114 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53921 | 0.53921 | 0.53921 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063914 | 0.00063914 | 0.00063914 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00328 | | | 0.60 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4941.00 ave 4941 max 4941 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: 81976.0 ave 81976 max 81976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81976 Ave neighs/atom = 77.482042 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.746 | 4.746 | 4.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4489.5641 0 -4489.5641 2785.1376 Loop time of 2.029e-06 on 1 procs for 0 steps with 1058 atoms 197.1% 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 | | 2.029e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4962.00 ave 4962 max 4962 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: 82452.0 ave 82452 max 82452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82452 Ave neighs/atom = 77.931947 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.746 | 4.746 | 4.746 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 -4489.5641 -4489.5641 29.121823 83.453794 5.0914068 2785.1376 2785.1376 -23.770252 8330.6661 48.516846 2.3498288 1174.8758 Loop time of 2.28e-06 on 1 procs for 0 steps with 1058 atoms 175.4% 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 | | 2.28e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4962.00 ave 4962 max 4962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41226.0 ave 41226 max 41226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82452.0 ave 82452 max 82452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82452 Ave neighs/atom = 77.931947 Neighbor list builds = 0 Dangerous builds = 0 1058 -4489.56411169724 eV 2.34982876865726 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05