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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -53.729323 0.0000000) to (32.902356 53.729323 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9822466 6.1056048 6.6136224 Created 1052 atoms using lattice units in orthogonal box = (0.0000000 -53.729323 0.0000000) to (32.902356 53.729323 9.9204336) create_atoms CPU = 0.005 seconds 1052 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9822466 6.1056048 6.6136224 Created 1076 atoms using lattice units in orthogonal box = (0.0000000 -53.729323 0.0000000) to (32.902356 53.729323 9.9204336) create_atoms CPU = 0.004 seconds 1076 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 29 3 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2112 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.524 | 5.524 | 5.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7088.4221 0 -7088.4221 2065.8981 11 0 -7093.1492 0 -7093.1492 2093.8982 Loop time of 0.545937 on 1 procs for 11 steps with 2112 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 = -7088.42211131609 -7093.14334551598 -7093.14918179739 Force two-norm initial, final = 9.6604045 0.11793396 Force max component initial, final = 0.99236835 0.0099448027 Final line search alpha, max atom move = 1.0000000 0.0099448027 Iterations, force evaluations = 11 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53736 | 0.53736 | 0.53736 | 0.0 | 98.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037485 | 0.0037485 | 0.0037485 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004824 | | | 0.88 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6788.00 ave 6788 max 6788 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: 280800.0 ave 280800 max 280800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280800 Ave neighs/atom = 132.95455 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 11 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.524 | 5.524 | 5.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 11 0 -7093.1492 0 -7093.1492 2093.8982 35075.108 15 0 -7093.2431 0 -7093.2431 -0.22501249 35169.583 Loop time of 0.180049 on 1 procs for 4 steps with 2112 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 = -7093.14918179742 -7093.24293712461 -7093.24311555309 Force two-norm initial, final = 84.206939 0.27202281 Force max component initial, final = 68.615237 0.16893219 Final line search alpha, max atom move = 0.00021403032 3.6156611e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17343 | 0.17343 | 0.17343 | 0.0 | 96.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011581 | 0.0011581 | 0.0011581 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00546 | | | 3.03 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6788.00 ave 6788 max 6788 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: 280704.0 ave 280704 max 280704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280704 Ave neighs/atom = 132.90909 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.662 | 5.662 | 5.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7093.2431 0 -7093.2431 -0.22501249 Loop time of 6.566e-06 on 1 procs for 0 steps with 2112 atoms 137.1% 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 | | 6.566e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6788.00 ave 6788 max 6788 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: 280704.0 ave 280704 max 280704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280704 Ave neighs/atom = 132.90909 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.662 | 5.662 | 5.662 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 -7093.2431 -7093.2431 32.905787 107.75892 9.9184018 -0.22501249 -0.22501249 -7.608345 -0.76094784 7.6942554 2.6842024 828.69607 Loop time of 7.758e-06 on 1 procs for 0 steps with 2112 atoms 219.1% 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 | | 7.758e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6788.00 ave 6788 max 6788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140352.0 ave 140352 max 140352 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280704.0 ave 280704 max 280704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280704 Ave neighs/atom = 132.90909 Neighbor list builds = 0 Dangerous builds = 0 2112 -7093.24311555309 eV 2.68420238082424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01