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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -58.227214 0.0000000) to (29.113607 58.227214 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0311148 4.0311148 3.6110985 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.227214 0.0000000) to (29.113607 58.227214 3.6110985) create_atoms CPU = 0.003 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0311148 4.0311148 3.6110985 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.227214 0.0000000) to (29.113607 58.227214 3.6110985) create_atoms CPU = 0.002 seconds 522 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1036 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4022.1015 0 -4022.1015 52543.612 70 0 -4384.4046 0 -4384.4046 -1872.8714 Loop time of 19.5975 on 1 procs for 70 steps with 1036 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 = -4022.10149923319 -4384.40055136003 -4384.40464570781 Force two-norm initial, final = 689.57852 0.19738382 Force max component initial, final = 235.65939 0.039105093 Final line search alpha, max atom move = 1.0000000 0.039105093 Iterations, force evaluations = 70 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.543 | 19.543 | 19.543 | 0.0 | 99.72 Neigh | 0.016422 | 0.016422 | 0.016422 | 0.0 | 0.08 Comm | 0.020692 | 0.020692 | 0.020692 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01689 | | | 0.09 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 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: 126104.0 ave 126104 max 126104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126104 Ave neighs/atom = 121.72201 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -4384.4046 0 -4384.4046 -1872.8714 12243.099 83 0 -4384.8511 0 -4384.8511 -15.015915 12229.378 Loop time of 2.25859 on 1 procs for 13 steps with 1036 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 = -4384.40464570781 -4384.84687144199 -4384.85114954654 Force two-norm initial, final = 55.939957 1.4693499 Force max component initial, final = 43.372256 1.1064394 Final line search alpha, max atom move = 0.00026077722 0.00028853417 Iterations, force evaluations = 13 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2315 | 2.2315 | 2.2315 | 0.0 | 98.80 Neigh | 0.016516 | 0.016516 | 0.016516 | 0.0 | 0.73 Comm | 0.0025562 | 0.0025562 | 0.0025562 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008059 | | | 0.36 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 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: 130000.0 ave 130000 max 130000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130000 Ave neighs/atom = 125.48263 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.151 | 5.151 | 5.151 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4384.8511 0 -4384.8511 -15.015915 Loop time of 6.635e-06 on 1 procs for 0 steps with 1036 atoms 180.9% 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 | | 6.635e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 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: 127696.0 ave 127696 max 127696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127696 Ave neighs/atom = 123.25869 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.151 | 5.151 | 5.151 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 -4384.8511 -4384.8511 29.011565 115.28269 3.6565297 -15.015915 -15.015915 67.503484 -143.49663 30.945399 2.2861116 211.07455 Loop time of 6.826e-06 on 1 procs for 0 steps with 1036 atoms 263.7% 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 | | 6.826e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63848.0 ave 63848 max 63848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127696.0 ave 127696 max 127696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127696 Ave neighs/atom = 123.25869 Neighbor list builds = 0 Dangerous builds = 0 1036 -4384.85114954654 eV 2.28611157625352 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23