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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -47.726154 0.0000000) to (33.747487 47.726154 5.1464435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2786022 6.1045080 5.1464435 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -47.726154 0.0000000) to (33.747487 47.726154 5.1464435) create_atoms CPU = 0.005 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2786022 6.1045080 5.1464435 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -47.726154 0.0000000) to (33.747487 47.726154 5.1464435) create_atoms CPU = 0.005 seconds 694 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 20 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1376 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_600021860456_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.312 | 6.312 | 6.312 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3204.5032 0 -3204.5032 195927.1 109 0 -4501.5289 0 -4501.5289 4710.9913 Loop time of 10.5464 on 1 procs for 109 steps with 1376 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 = -3204.50318788009 -4501.52499974751 -4501.52885176901 Force two-norm initial, final = 1901.5271 0.14716131 Force max component initial, final = 332.93543 0.0081132704 Final line search alpha, max atom move = 1.0000000 0.0081132704 Iterations, force evaluations = 109 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.415 | 10.415 | 10.415 | 0.0 | 98.75 Neigh | 0.047662 | 0.047662 | 0.047662 | 0.0 | 0.45 Comm | 0.048934 | 0.048934 | 0.048934 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03512 | | | 0.33 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10324.0 ave 10324 max 10324 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: 436458.0 ave 436458 max 436458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436458 Ave neighs/atom = 317.19331 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.307 | 6.307 | 6.307 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -4501.5289 0 -4501.5289 4710.9913 16578.112 114 0 -4501.6994 0 -4501.6994 -9.0016483 16632.853 Loop time of 0.410234 on 1 procs for 5 steps with 1376 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4501.528851769 -4501.69856274732 -4501.69938071676 Force two-norm initial, final = 99.507559 0.78783741 Force max component initial, final = 86.075616 0.49803093 Final line search alpha, max atom move = 0.00015257205 7.5985601e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40298 | 0.40298 | 0.40298 | 0.0 | 98.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018377 | 0.0018377 | 0.0018377 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00542 | | | 1.32 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10315.0 ave 10315 max 10315 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: 436416.0 ave 436416 max 436416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436416 Ave neighs/atom = 317.16279 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.445 | 6.445 | 6.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4501.6994 0 -4501.6994 -9.0016483 Loop time of 6.094e-06 on 1 procs for 0 steps with 1376 atoms 180.5% 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 | | 6.094e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10297.0 ave 10297 max 10297 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: 436082.0 ave 436082 max 436082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436082 Ave neighs/atom = 316.92006 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.445 | 6.445 | 6.445 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 -4501.6994 -4501.6994 33.863385 95.579104 5.1389386 -9.0016483 -9.0016483 -48.13809 47.724433 -26.591288 2.3664468 1346.7075 Loop time of 6.425e-06 on 1 procs for 0 steps with 1376 atoms 311.3% 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 | | 6.425e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10297.0 ave 10297 max 10297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218041.0 ave 218041 max 218041 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 436082.0 ave 436082 max 436082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436082 Ave neighs/atom = 316.92006 Neighbor list builds = 0 Dangerous builds = 0 1376 -4501.69938071676 eV 2.36644678485715 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12