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 = 3.6150000 3.6150000 3.6150000 Created orthogonal box = (0.0000000 -65.070000 0.0000000) to (46.011438 65.070000 5.1123820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2484669 6.0250000 5.1123820 Created 1295 atoms using lattice units in orthogonal box = (0.0000000 -65.070000 0.0000000) to (46.011438 65.070000 5.1123820) create_atoms CPU = 0.004 seconds 1295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2484669 6.0250000 5.1123820 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -65.070000 0.0000000) to (46.011438 65.070000 5.1123820) create_atoms CPU = 0.003 seconds 1299 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 12 33 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 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2594 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_128703483589_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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 6.542 | 6.542 | 6.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8708.2232 0 -8708.2232 56255.804 139 0 -9162.9378 0 -9162.9378 3861.7621 Loop time of 6.38235 on 1 procs for 139 steps with 2594 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 = -8708.22320499702 -9162.92878302304 -9162.93781324007 Force two-norm initial, final = 390.76781 0.30611576 Force max component initial, final = 66.367991 0.058114693 Final line search alpha, max atom move = 1.0000000 0.058114693 Iterations, force evaluations = 139 257 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1983 | 6.1983 | 6.1983 | 0.0 | 97.12 Neigh | 0.1098 | 0.1098 | 0.1098 | 0.0 | 1.72 Comm | 0.039978 | 0.039978 | 0.039978 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03423 | | | 0.54 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13070.0 ave 13070 max 13070 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: 458268.0 ave 458268 max 458268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458268 Ave neighs/atom = 176.66461 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 139 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.541 | 6.541 | 6.541 Mbytes Step Temp E_pair E_mol TotEng Press Volume 139 0 -9162.9378 0 -9162.9378 3861.7621 30612.578 141 0 -9163.0473 0 -9163.0473 -230.0806 30702.736 Loop time of 0.0940111 on 1 procs for 2 steps with 2594 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 = -9162.93781324007 -9163.04378090308 -9163.04730574888 Force two-norm initial, final = 129.21885 8.0402340 Force max component initial, final = 82.553272 6.3279919 Final line search alpha, max atom move = 0.00011059161 0.00069982282 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091952 | 0.091952 | 0.091952 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039943 | 0.00039943 | 0.00039943 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00166 | | | 1.77 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13046.0 ave 13046 max 13046 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: 457530.0 ave 457530 max 457530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457530 Ave neighs/atom = 176.38011 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 6.679 | 6.679 | 6.679 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9163.0473 0 -9163.0473 -230.0806 Loop time of 1.686e-06 on 1 procs for 0 steps with 2594 atoms 177.9% 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 | | 1.686e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13038.0 ave 13038 max 13038 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: 457186.0 ave 457186 max 457186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457186 Ave neighs/atom = 176.24749 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 6.679 | 6.679 | 6.679 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 -9163.0473 -9163.0473 46.067494 130.31101 5.1144787 -230.0806 -230.0806 -212.71057 -147.17899 -330.35224 2.3642939 1347.5118 Loop time of 2.436e-06 on 1 procs for 0 steps with 2594 atoms 0.0% 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 | | 2.436e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13038.0 ave 13038 max 13038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228593.0 ave 228593 max 228593 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 457186.0 ave 457186 max 457186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457186 Ave neighs/atom = 176.24749 Neighbor list builds = 0 Dangerous builds = 0 2594 -9163.0467845351 eV 2.36429386641063 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07