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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -35.911291 0.0000000) to (31.100090 35.911291 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -35.911291 0.0000000) to (31.100090 35.911291 6.0992294) create_atoms CPU = 0.002 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -35.911291 0.0000000) to (31.100090 35.911291 6.0992294) create_atoms CPU = 0.001 seconds 630 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 ghost atom cutoff = 6 binsize = 3, bins = 11 24 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1254 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_700541006254_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 ghost atom cutoff = 6 binsize = 3, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.021 | 5.021 | 5.021 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4694.1572 0 -4694.1572 205439.12 131 0 -5543.8946 0 -5543.8946 23416.908 Loop time of 12.0361 on 1 procs for 131 steps with 1254 atoms 91.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4694.15724019378 -5543.8891283502 -5543.89455348742 Force two-norm initial, final = 1551.2694 0.28668805 Force max component initial, final = 539.99758 0.063859370 Final line search alpha, max atom move = 1.0000000 0.063859370 Iterations, force evaluations = 131 242 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.956 | 11.956 | 11.956 | 0.0 | 99.33 Neigh | 0.045823 | 0.045823 | 0.045823 | 0.0 | 0.38 Comm | 0.015332 | 0.015332 | 0.015332 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0191 | | | 0.16 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836.00 ave 4836 max 4836 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: 97780.0 ave 97780 max 97780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97780 Ave neighs/atom = 77.974482 Neighbor list builds = 4 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 ghost atom cutoff = 6 binsize = 3, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 131 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 131 0 -5543.8946 0 -5543.8946 23416.908 13623.78 145 0 -5546.4338 0 -5546.4338 10.518411 13792.285 Loop time of 0.73661 on 1 procs for 14 steps with 1254 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 = -5543.89455348742 -5546.42961469936 -5546.43380767671 Force two-norm initial, final = 417.24530 1.4718199 Force max component initial, final = 385.53391 0.81691946 Final line search alpha, max atom move = 0.00010154763 8.2956235e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7229 | 0.7229 | 0.7229 | 0.0 | 98.14 Neigh | 0.0081369 | 0.0081369 | 0.0081369 | 0.0 | 1.10 Comm | 0.00086177 | 0.00086177 | 0.00086177 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004709 | | | 0.64 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4782.00 ave 4782 max 4782 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: 97412.0 ave 97412 max 97412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97412 Ave neighs/atom = 77.681021 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5546.4338 0 -5546.4338 10.518411 Loop time of 2.316e-06 on 1 procs for 0 steps with 1254 atoms 172.7% 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 | | 2.316e-06 | | |100.00 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4782.00 ave 4782 max 4782 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: 97412.0 ave 97412 max 97412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97412 Ave neighs/atom = 77.681021 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 ghost atom cutoff = 6 binsize = 3, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.777 | 4.777 | 4.777 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 -5546.4338 -5546.4338 31.114869 72.796005 6.0892065 10.518411 10.518411 -46.680318 -16.505697 94.741248 2.2360434 865.77398 Loop time of 2.488e-06 on 1 procs for 0 steps with 1254 atoms 442.1% 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 | | 2.488e-06 | | |100.00 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4782.00 ave 4782 max 4782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48706.0 ave 48706 max 48706 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97412.0 ave 97412 max 97412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97412 Ave neighs/atom = 77.681021 Neighbor list builds = 0 Dangerous builds = 0 1254 -5546.43380767671 eV 2.23604343276034 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13