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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -60.939166 0.0000000) to (24.876874 60.939166 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9704497 5.2810894 5.7450679 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -60.939166 0.0000000) to (24.876874 60.939166 8.6176019) create_atoms CPU = 0.002 seconds 1203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9704497 5.2810894 5.7450679 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -60.939166 0.0000000) to (24.876874 60.939166 8.6176019) create_atoms CPU = 0.002 seconds 1203 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 29 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2384 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.996 | 6.996 | 6.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10393.887 0 -10393.887 4376.7352 22 0 -10428.724 0 -10428.724 -6128.1979 Loop time of 1.17811 on 1 procs for 22 steps with 2384 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 = -10393.8871589294 -10428.7157048708 -10428.7235064336 Force two-norm initial, final = 48.734380 0.26531664 Force max component initial, final = 9.5073932 0.035743278 Final line search alpha, max atom move = 1.0000000 0.035743278 Iterations, force evaluations = 22 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1321 | 1.1321 | 1.1321 | 0.0 | 96.10 Neigh | 0.036247 | 0.036247 | 0.036247 | 0.0 | 3.08 Comm | 0.0050252 | 0.0050252 | 0.0050252 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004705 | | | 0.40 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11816.0 ave 11816 max 11816 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: 588672.0 ave 588672 max 588672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 588672 Ave neighs/atom = 246.92617 Neighbor list builds = 1 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.996 | 6.996 | 6.996 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -10428.724 0 -10428.724 -6128.1979 26128.154 24 0 -10428.788 0 -10428.788 -2730.1451 26076.438 Loop time of 0.163144 on 1 procs for 2 steps with 2384 atoms 84.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10428.7235064335 -10428.7874948601 -10428.7877960046 Force two-norm initial, final = 92.360953 1.6084892 Force max component initial, final = 69.052989 1.5580990 Final line search alpha, max atom move = 0.00019535816 0.00030438735 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16071 | 0.16071 | 0.16071 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040215 | 0.00040215 | 0.00040215 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002036 | | | 1.25 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11801.0 ave 11801 max 11801 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: 588578.0 ave 588578 max 588578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 588578 Ave neighs/atom = 246.88674 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 7.134 | 7.134 | 7.134 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10428.788 0 -10428.788 -2730.1451 Loop time of 2.267e-06 on 1 procs for 0 steps with 2384 atoms 176.4% 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 | | 2.267e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11871.0 ave 11871 max 11871 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: 588776.0 ave 588776 max 588776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 588776 Ave neighs/atom = 246.96980 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 7.134 | 7.134 | 7.134 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 -10428.788 -10428.788 24.8553 121.87833 8.6080097 -2730.1451 -2730.1451 95.64898 -8303.8972 17.812946 2.303949 642.65581 Loop time of 2.811e-06 on 1 procs for 0 steps with 2384 atoms 284.6% 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 | | 2.811e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11871.0 ave 11871 max 11871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 294388.0 ave 294388 max 294388 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 588776.0 ave 588776 max 588776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 588776 Ave neighs/atom = 246.96980 Neighbor list builds = 0 Dangerous builds = 0 2384 -10428.7877960046 eV 2.30394896388119 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02