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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5169606 4.3345336 4.9800000 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5169606 4.3345336 4.9800000 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) create_atoms CPU = 0.001 seconds 530 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 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_876687166519_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4234.278 0 -4234.278 92566.516 75 0 -4691.8481 0 -4691.8481 11033.502 Loop time of 6.94683 on 1 procs for 75 steps with 1058 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 = -4234.27798449085 -4691.84357719381 -4691.84807868781 Force two-norm initial, final = 569.44085 0.26045441 Force max component initial, final = 144.27574 0.036930983 Final line search alpha, max atom move = 1.0000000 0.036930983 Iterations, force evaluations = 75 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9197 | 6.9197 | 6.9197 | 0.0 | 99.61 Neigh | 0.0075117 | 0.0075117 | 0.0075117 | 0.0 | 0.11 Comm | 0.010201 | 0.010201 | 0.010201 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009416 | | | 0.14 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5676.00 ave 5676 max 5676 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: 94348.0 ave 94348 max 94348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94348 Ave neighs/atom = 89.175803 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4691.8481 0 -4691.8481 11033.502 11527.814 81 0 -4692.1707 0 -4692.1707 -226.89542 11596.817 Loop time of 0.446714 on 1 procs for 6 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 = -4691.84807868781 -4692.16851436525 -4692.17072120134 Force two-norm initial, final = 143.48449 4.1047616 Force max component initial, final = 112.64088 2.9973297 Final line search alpha, max atom move = 8.4926905e-05 0.00025455394 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44419 | 0.44419 | 0.44419 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040657 | 0.00040657 | 0.00040657 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002122 | | | 0.47 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5676.00 ave 5676 max 5676 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: 93288.0 ave 93288 max 93288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93288 Ave neighs/atom = 88.173913 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.775 | 4.775 | 4.775 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4692.1707 0 -4692.1707 -226.89542 Loop time of 2.86e-06 on 1 procs for 0 steps with 1058 atoms 174.8% 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 | | 2.86e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5676.00 ave 5676 max 5676 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: 92980.0 ave 92980 max 92980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92980 Ave neighs/atom = 87.882798 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.775 | 4.775 | 4.775 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 -4692.1707 -4692.1707 20.231573 115.05094 4.9821754 -226.89542 -226.89542 -370.53038 104.12582 -414.28169 2.3287263 399.43116 Loop time of 2.445e-06 on 1 procs for 0 steps with 1058 atoms 245.4% 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 | | 2.445e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5676.00 ave 5676 max 5676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46490.0 ave 46490 max 46490 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92980.0 ave 92980 max 92980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92980 Ave neighs/atom = 87.882798 Neighbor list builds = 0 Dangerous builds = 0 1058 -4692.17072120134 eV 2.32872634606887 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07