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 = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -34.500873 0.0000000) to (42.254768 34.500873 6.9940589) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0518270 4.2535323 4.6627059 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -34.500873 0.0000000) to (42.254768 34.500873 6.9940589) create_atoms CPU = 0.002 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0518270 4.2535323 4.6627059 Created 882 atoms using lattice units in orthogonal box = (0.0000000 -34.500873 0.0000000) to (42.254768 34.500873 6.9940589) create_atoms CPU = 0.001 seconds 882 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 17 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1740 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.971 | 5.971 | 5.971 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5692.1113 0 -5692.1113 157843.78 84 0 -6938.5935 0 -6938.5935 -690.06149 Loop time of 3.36605 on 1 procs for 84 steps with 1740 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5692.11133412651 -6938.58728873701 -6938.59353714757 Force two-norm initial, final = 1945.6211 0.29108555 Force max component initial, final = 356.43982 0.029492554 Final line search alpha, max atom move = 1.0000000 0.029492554 Iterations, force evaluations = 84 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2875 | 3.2875 | 3.2875 | 0.0 | 97.67 Neigh | 0.047156 | 0.047156 | 0.047156 | 0.0 | 1.40 Comm | 0.016601 | 0.016601 | 0.016601 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01477 | | | 0.44 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8455.00 ave 8455 max 8455 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: 386052.0 ave 386052 max 386052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 386052 Ave neighs/atom = 221.86897 Neighbor list builds = 2 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.968 | 5.968 | 5.968 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -6938.5935 0 -6938.5935 -690.06149 20392.247 88 0 -6938.7362 0 -6938.7362 -3.5874551 20385.219 Loop time of 0.153979 on 1 procs for 4 steps with 1740 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6938.59353714755 -6938.73561325758 -6938.73621990565 Force two-norm initial, final = 74.419865 0.67401337 Force max component initial, final = 49.602970 0.29581776 Final line search alpha, max atom move = 0.00012690404 3.7540469e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15067 | 0.15067 | 0.15067 | 0.0 | 97.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050767 | 0.00050767 | 0.00050767 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002798 | | | 1.82 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8343.00 ave 8343 max 8343 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: 390132.0 ave 390132 max 390132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390132 Ave neighs/atom = 224.21379 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.106 | 6.106 | 6.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6938.7362 0 -6938.7362 -3.5874551 Loop time of 2.265e-06 on 1 procs for 0 steps with 1740 atoms 176.6% 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 | | 2.265e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8361.00 ave 8361 max 8361 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: 390072.0 ave 390072 max 390072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390072 Ave neighs/atom = 224.17931 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.106 | 6.106 | 6.106 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 -6938.7362 -6938.7362 42.15481 69.204939 6.9876503 -3.5874551 -3.5874551 -21.186522 -12.804339 23.228496 2.2431737 1579.7739 Loop time of 2.943e-06 on 1 procs for 0 steps with 1740 atoms 203.9% 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 | | 2.943e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8361.00 ave 8361 max 8361 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195036.0 ave 195036 max 195036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 390072.0 ave 390072 max 390072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390072 Ave neighs/atom = 224.17931 Neighbor list builds = 0 Dangerous builds = 0 1740 -6938.73621990565 eV 2.24317370996071 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04