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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -47.726184 0.0000000) to (33.747508 47.726184 5.1464468) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2786062 6.1045119 5.1464468 Created 684 atoms using lattice units in orthogonal box = (0.0000000 -47.726184 0.0000000) to (33.747508 47.726184 5.1464468) create_atoms CPU = 0.006 seconds 684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2786062 6.1045119 5.1464468 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.726184 0.0000000) to (33.747508 47.726184 5.1464468) create_atoms CPU = 0.005 seconds 692 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 0 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_609260676108_000#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 -4036.4973 0 -4036.4973 114836.35 114 0 -4501.53 0 -4501.53 4909.7099 Loop time of 10.9039 on 1 procs for 114 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 = -4036.49727964687 -4501.52567143629 -4501.52997080025 Force two-norm initial, final = 650.66342 0.17387363 Force max component initial, final = 166.81533 0.010484527 Final line search alpha, max atom move = 1.0000000 0.010484527 Iterations, force evaluations = 114 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.618 | 10.618 | 10.618 | 0.0 | 97.38 Neigh | 0.19852 | 0.19852 | 0.19852 | 0.0 | 1.82 Comm | 0.051154 | 0.051154 | 0.051154 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03634 | | | 0.33 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10834.0 ave 10834 max 10834 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: 437156.0 ave 437156 max 437156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437156 Ave neighs/atom = 317.70058 Neighbor list builds = 4 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 : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -4501.53 0 -4501.53 4909.7099 16578.144 118 0 -4501.6433 0 -4501.6433 -19.139395 16634.656 Loop time of 0.416536 on 1 procs for 4 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 = -4501.52997080026 -4501.64333983341 -4501.64334340724 Force two-norm initial, final = 92.330640 0.41680347 Force max component initial, final = 67.844408 0.29301847 Final line search alpha, max atom move = 0.0074653435 0.0021874835 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40905 | 0.40905 | 0.40905 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017589 | 0.0017589 | 0.0017589 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005725 | | | 1.37 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10536.0 ave 10536 max 10536 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: 436996.0 ave 436996 max 436996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436996 Ave neighs/atom = 317.58430 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) = 6.447 | 6.447 | 6.447 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4501.6433 0 -4501.6433 -19.139395 Loop time of 6.535e-06 on 1 procs for 0 steps with 1376 atoms 0.0% 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 | | 6.535e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10539.0 ave 10539 max 10539 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: 436706.0 ave 436706 max 436706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436706 Ave neighs/atom = 317.37355 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) = 6.447 | 6.447 | 6.447 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 -4501.6433 -4501.6433 33.798538 95.671294 5.1443945 -19.139395 -19.139395 -28.264918 -17.306809 -11.846459 2.3447694 999.66173 Loop time of 7.157e-06 on 1 procs for 0 steps with 1376 atoms 265.5% 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 | | 7.157e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10539.0 ave 10539 max 10539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218353.0 ave 218353 max 218353 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 436706.0 ave 436706 max 436706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436706 Ave neighs/atom = 317.37355 Neighbor list builds = 0 Dangerous builds = 0 1376 -4501.64334340724 eV 2.34476943613916 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12