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 = 3.6150000 3.6150000 3.6150000 Created orthogonal box = (0.0000000 -39.600341 0.0000000) to (8.0833857 39.600341 8.8549054) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8500314 5.2800454 5.9032703 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.600341 0.0000000) to (8.0833857 39.600341 8.8549054) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8500314 5.2800454 5.9032703 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.600341 0.0000000) to (8.0833857 39.600341 8.8549054) create_atoms CPU = 0.001 seconds 242 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 3 20 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 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_128703483589_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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 3 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1618.3952 0 -1618.3952 51032.9 45 0 -1691.3675 0 -1691.3675 7888.1311 Loop time of 0.423603 on 1 procs for 45 steps with 480 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 = -1618.39522470472 -1691.36599286906 -1691.36748525683 Force two-norm initial, final = 176.29865 0.12091136 Force max component initial, final = 55.024599 0.026049804 Final line search alpha, max atom move = 1.0000000 0.026049804 Iterations, force evaluations = 45 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41804 | 0.41804 | 0.41804 | 0.0 | 98.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0031134 | 0.0031134 | 0.0031134 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002449 | | | 0.58 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4434.00 ave 4434 max 4434 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: 84708.0 ave 84708 max 84708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84708 Ave neighs/atom = 176.47500 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 3 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -1691.3675 0 -1691.3675 7888.1311 5668.996 54 0 -1691.5608 0 -1691.5608 108.00179 5700.3976 Loop time of 0.0558907 on 1 procs for 9 steps with 480 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 = -1691.36748525683 -1691.55961271152 -1691.56081431337 Force two-norm initial, final = 56.067104 0.76474830 Force max component initial, final = 50.798047 0.50100062 Final line search alpha, max atom move = 0.00050395530 0.00025248192 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053845 | 0.053845 | 0.053845 | 0.0 | 96.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036269 | 0.00036269 | 0.00036269 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001683 | | | 3.01 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4132.00 ave 4132 max 4132 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: 84684.0 ave 84684 max 84684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84684 Ave neighs/atom = 176.42500 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 3 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 4.699 | 4.699 | 4.699 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1691.5608 0 -1691.5608 108.00179 Loop time of 2.233e-06 on 1 procs for 0 steps with 480 atoms 179.1% 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 | | 2.233e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4132.00 ave 4132 max 4132 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: 84424.0 ave 84424 max 84424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84424 Ave neighs/atom = 175.88333 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 3 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 4.699 | 4.699 | 4.699 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 -1691.5608 -1691.5608 8.0707945 79.885628 8.841383 108.00179 108.00179 85.434993 97.972174 140.5982 2.2850554 293.0661 Loop time of 2.926e-06 on 1 procs for 0 steps with 480 atoms 205.1% 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 | | 2.926e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4132.00 ave 4132 max 4132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42212.0 ave 42212 max 42212 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84424.0 ave 84424 max 84424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84424 Ave neighs/atom = 175.88333 Neighbor list builds = 0 Dangerous builds = 0 480 -1691.56071786672 eV 2.28505541723134 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00