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 = 3.6135806 3.6135806 3.6135806 Created orthogonal box = (0.0000000 -63.828560 0.0000000) to (36.851436 63.828560 6.2589052) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6694517 5.7282041 6.2589052 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -63.828560 0.0000000) to (36.851436 63.828560 6.2589052) create_atoms CPU = 0.008 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6694517 5.7282041 6.2589052 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.828560 0.0000000) to (36.851436 63.828560 6.2589052) create_atoms CPU = 0.007 seconds 1249 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 35 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2494 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_426403318662_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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.127 | 6.127 | 6.127 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8039.155 0 -8039.155 78806.94 90 0 -8804.3548 0 -8804.3548 3473.8092 Loop time of 5.51205 on 1 procs for 90 steps with 2494 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 = -8039.15498281463 -8804.34735577643 -8804.35477025994 Force two-norm initial, final = 1557.3325 0.26632787 Force max component initial, final = 414.59130 0.058788602 Final line search alpha, max atom move = 0.52839409 0.031063550 Iterations, force evaluations = 90 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1045 | 5.1045 | 5.1045 | 0.0 | 92.61 Neigh | 0.32324 | 0.32324 | 0.32324 | 0.0 | 5.86 Comm | 0.042252 | 0.042252 | 0.042252 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04204 | | | 0.76 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10625.0 ave 10625 max 10625 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: 350794.0 ave 350794 max 350794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350794 Ave neighs/atom = 140.65517 Neighbor list builds = 6 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.128 | 6.128 | 6.128 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -8804.3548 0 -8804.3548 3473.8092 29444.069 94 0 -8804.5377 0 -8804.5377 -81.816559 29519.229 Loop time of 0.210641 on 1 procs for 4 steps with 2494 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8804.35477025994 -8804.5367160386 -8804.53772530052 Force two-norm initial, final = 131.15240 4.6892270 Force max component initial, final = 120.36763 4.3532240 Final line search alpha, max atom move = 0.00010740330 0.00046755062 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2041 | 0.2041 | 0.2041 | 0.0 | 96.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001395 | 0.001395 | 0.001395 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005141 | | | 2.44 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10625.0 ave 10625 max 10625 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: 350742.0 ave 350742 max 350742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350742 Ave neighs/atom = 140.63432 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.266 | 6.266 | 6.266 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8804.5377 0 -8804.5377 -81.816559 Loop time of 6.425e-06 on 1 procs for 0 steps with 2494 atoms 186.8% 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 | | 6.425e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10625.0 ave 10625 max 10625 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: 350616.0 ave 350616 max 350616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350616 Ave neighs/atom = 140.58380 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.266 | 6.266 | 6.266 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 -8804.5377 -8804.5377 36.848347 128.06011 6.2556599 -81.816559 -81.816559 -236.25443 61.085722 -70.280973 2.3046781 988.42163 Loop time of 6.876e-06 on 1 procs for 0 steps with 2494 atoms 261.8% 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 | | 6.876e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10625.0 ave 10625 max 10625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 175308.0 ave 175308 max 175308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 350616.0 ave 350616 max 350616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350616 Ave neighs/atom = 140.58380 Neighbor list builds = 0 Dangerous builds = 0 2494 -8804.55019530052 eV 2.30467806859722 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06