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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -53.853577 0.0000000) to (43.971262 53.853577 8.9139075) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4211144 5.1640416 5.9426050 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -53.853577 0.0000000) to (43.971262 53.853577 8.9139075) create_atoms CPU = 0.002 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4211144 5.1640416 5.9426050 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -53.853577 0.0000000) to (43.971262 53.853577 8.9139075) create_atoms CPU = 0.002 seconds 1760 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 27 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3504 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_945691923444_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.438 | 7.438 | 7.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8295.9074 0 -8295.9074 184642.36 64 0 -11455.758 0 -11455.758 6148.0921 Loop time of 3.19412 on 1 procs for 64 steps with 3504 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 = -8295.90743828857 -11455.7465128834 -11455.7575063647 Force two-norm initial, final = 3725.4743 0.27192742 Force max component initial, final = 535.67230 0.0088275286 Final line search alpha, max atom move = 1.0000000 0.0088275286 Iterations, force evaluations = 64 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0843 | 3.0843 | 3.0843 | 0.0 | 96.56 Neigh | 0.076845 | 0.076845 | 0.076845 | 0.0 | 2.41 Comm | 0.013951 | 0.013951 | 0.013951 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01901 | | | 0.60 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12026.0 ave 12026 max 12026 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: 616096.0 ave 616096 max 616096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 616096 Ave neighs/atom = 175.82648 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.438 | 7.438 | 7.438 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -11455.758 0 -11455.758 6148.0921 42216.439 71 0 -11456.609 0 -11456.609 165.67435 42392.24 Loop time of 0.260501 on 1 procs for 7 steps with 3504 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 = -11455.7575063647 -11456.6077879712 -11456.6090343545 Force two-norm initial, final = 333.21090 8.7005763 Force max component initial, final = 306.53693 6.9523489 Final line search alpha, max atom move = 9.5030493e-05 0.00066068514 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25457 | 0.25457 | 0.25457 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084317 | 0.00084317 | 0.00084317 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005093 | | | 1.95 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12037.0 ave 12037 max 12037 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: 614752.0 ave 614752 max 614752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614752 Ave neighs/atom = 175.44292 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.576 | 7.576 | 7.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11456.609 0 -11456.609 165.67435 Loop time of 1.897e-06 on 1 procs for 0 steps with 3504 atoms 158.1% 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 | | 1.897e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11968.0 ave 11968 max 11968 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: 614080.0 ave 614080 max 614080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614080 Ave neighs/atom = 175.25114 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.576 | 7.576 | 7.576 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 -11456.609 -11456.609 43.932099 108.35867 8.9051397 165.67435 165.67435 40.052256 264.34717 192.62361 2.2393884 1595.0547 Loop time of 2.077e-06 on 1 procs for 0 steps with 3504 atoms 337.0% 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 | | 2.077e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11968.0 ave 11968 max 11968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307040.0 ave 307040 max 307040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 614080.0 ave 614080 max 614080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614080 Ave neighs/atom = 175.25114 Neighbor list builds = 0 Dangerous builds = 0 3504 -11456.6090343545 eV 2.23938844568004 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04