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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -40.858528 0.0000000) to (5.1068646 40.858528 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1068646 5.1068646 3.6110986 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -40.858528 0.0000000) to (5.1068646 40.858528 3.6110986) create_atoms CPU = 0.001 seconds 66 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1068646 5.1068646 3.6110986 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -40.858528 0.0000000) to (5.1068646 40.858528 3.6110986) create_atoms CPU = 0.001 seconds 66 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 = 2 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 124 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_162036141261_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 = 2 28 2 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) = 4.402 | 4.402 | 4.402 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -520.13059 0 -520.13059 -18450.515 37 0 -524.91121 0 -524.91121 -49420.084 Loop time of 0.751265 on 1 procs for 37 steps with 124 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -520.130588402088 -524.910834778421 -524.911212579907 Force two-norm initial, final = 3.3430208 0.033348938 Force max component initial, final = 1.0741210 0.0052613006 Final line search alpha, max atom move = 1.0000000 0.0052613006 Iterations, force evaluations = 37 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74614 | 0.74614 | 0.74614 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030572 | 0.0030572 | 0.0030572 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002072 | | | 0.28 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2067.00 ave 2067 max 2067 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: 9400.00 ave 9400 max 9400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9400 Ave neighs/atom = 75.806452 Neighbor list builds = 0 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 = 2 28 2 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.401 | 4.401 | 4.401 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -524.91121 0 -524.91121 -49420.084 1506.9762 228 0 -527.24201 0 -527.24201 41791.479 1425.8286 Loop time of 2.62474 on 1 procs for 191 steps with 124 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 = -524.911212579908 -527.241790869665 -527.242013760528 Force two-norm initial, final = 52.932785 0.052774827 Force max component initial, final = 45.590840 0.036129004 Final line search alpha, max atom move = 0.0037662129 0.00013606952 Iterations, force evaluations = 191 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5905 | 2.5905 | 2.5905 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0081966 | 0.0081966 | 0.0081966 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02604 | | | 0.99 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1892.00 ave 1892 max 1892 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: 9672.00 ave 9672 max 9672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9672 Ave neighs/atom = 78.000000 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 = 2 28 1 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) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -527.24201 0 -527.24201 41791.479 Loop time of 6.726e-06 on 1 procs for 0 steps with 124 atoms 163.5% 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 | | 6.726e-06 | | |100.00 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2036.00 ave 2036 max 2036 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: 7936.00 ave 7936 max 7936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7936 Ave neighs/atom = 64.000000 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 = 2 28 1 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) = 4.551 | 4.551 | 4.551 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 -527.24201 -527.24201 5.9066433 81.717055 2.9540231 41791.479 41791.479 46.955386 125344.19 -16.705758 2.4674735 0.00041501641 Loop time of 7.327e-06 on 1 procs for 0 steps with 124 atoms 177.4% 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 | | 7.327e-06 | | |100.00 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2036.00 ave 2036 max 2036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3968.00 ave 3968 max 3968 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7936.00 ave 7936 max 7936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7936 Ave neighs/atom = 64.000000 Neighbor list builds = 0 Dangerous builds = 0 124 -527.242013760528 eV 2.46747347989731 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03