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 = 2.6534432 2.6534432 2.6534432 Created orthogonal box = (0.0000000 -50.065066 0.0000000) to (25.032533 50.065066 2.6534432) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6564374 3.6564374 2.6534432 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -50.065066 0.0000000) to (25.032533 50.065066 2.6534432) create_atoms CPU = 0.001 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6564374 3.6564374 2.6534432 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -50.065066 0.0000000) to (25.032533 50.065066 2.6534432) create_atoms CPU = 0.000 seconds 357 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 27 1 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 709 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_201919462778_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4960.8369 0 -4960.8369 407220.17 106 0 -5911.5981 0 -5911.5981 28186.896 Loop time of 4.91762 on 1 procs for 106 steps with 709 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 = -4960.83691086965 -5911.59277633635 -5911.59807844494 Force two-norm initial, final = 4347.3964 0.50522461 Force max component initial, final = 2070.9464 0.047543049 Final line search alpha, max atom move = 0.95343449 0.045329182 Iterations, force evaluations = 106 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8802 | 4.8802 | 4.8802 | 0.0 | 99.24 Neigh | 0.015608 | 0.015608 | 0.015608 | 0.0 | 0.32 Comm | 0.013424 | 0.013424 | 0.013424 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008347 | | | 0.17 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7749.00 ave 7749 max 7749 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: 126480.0 ave 126480 max 126480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126480 Ave neighs/atom = 178.39210 Neighbor list builds = 2 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -5911.5981 0 -5911.5981 28186.896 6650.8842 115 0 -5912.7323 0 -5912.7323 333.48817 6678.4583 Loop time of 0.279503 on 1 procs for 9 steps with 709 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 = -5911.59807844494 -5912.73214304415 -5912.73230395679 Force two-norm initial, final = 295.96753 2.8306088 Force max component initial, final = 285.64004 1.8385245 Final line search alpha, max atom move = 0.00037141289 0.00068285169 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27618 | 0.27618 | 0.27618 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063646 | 0.00063646 | 0.00063646 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002691 | | | 0.96 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7751.00 ave 7751 max 7751 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: 126552.0 ave 126552 max 126552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126552 Ave neighs/atom = 178.49365 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.095 | 5.095 | 5.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5912.7323 0 -5912.7323 333.48817 Loop time of 2.083e-06 on 1 procs for 0 steps with 709 atoms 144.0% 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 | | 2.083e-06 | | |100.00 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7751.00 ave 7751 max 7751 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: 126362.0 ave 126362 max 126362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126362 Ave neighs/atom = 178.22567 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.095 | 5.095 | 5.095 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 -5912.7323 -5912.7323 25.078154 100.85611 2.6404529 333.48817 333.48817 366.38738 444.26387 189.81325 2.168561 364.70675 Loop time of 1.898e-06 on 1 procs for 0 steps with 709 atoms 210.7% 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 | | 1.898e-06 | | |100.00 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7751.00 ave 7751 max 7751 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63181.0 ave 63181 max 63181 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126362.0 ave 126362 max 126362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126362 Ave neighs/atom = 178.22567 Neighbor list builds = 0 Dangerous builds = 0 709 -5912.73230395679 eV 2.16856099396834 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05