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 = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -35.226425 0.0000000) to (17.613212 35.226425 3.5226425) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9316995 4.9316995 3.5226425 Created 199 atoms using lattice units in orthogonal box = (0.0000000 -35.226425 0.0000000) to (17.613212 35.226425 3.5226425) create_atoms CPU = 0.002 seconds 199 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9316995 4.9316995 3.5226425 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -35.226425 0.0000000) to (17.613212 35.226425 3.5226425) create_atoms CPU = 0.001 seconds 201 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 3 12 1 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 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 400 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_381861218831_004#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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.340 | 5.340 | 5.340 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1571.5493 0 -1571.5493 63083.217 71 0 -1685.131 0 -1685.131 8130.5193 Loop time of 4.55807 on 1 procs for 71 steps with 400 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 = -1571.54929214371 -1685.12954286155 -1685.13103557181 Force two-norm initial, final = 200.75011 0.16714316 Force max component initial, final = 73.401970 0.031078987 Final line search alpha, max atom move = 1.0000000 0.031078987 Iterations, force evaluations = 71 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4567 | 4.4567 | 4.4567 | 0.0 | 97.78 Neigh | 0.063171 | 0.063171 | 0.063171 | 0.0 | 1.39 Comm | 0.026479 | 0.026479 | 0.026479 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01173 | | | 0.26 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8968.00 ave 8968 max 8968 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: 249084.0 ave 249084 max 249084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249084 Ave neighs/atom = 622.71000 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.340 | 5.340 | 5.340 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -1685.131 0 -1685.131 8130.5193 4371.2506 80 0 -1685.3068 0 -1685.3068 287.03194 4389.4686 Loop time of 0.40135 on 1 procs for 9 steps with 400 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 = -1685.1310355718 -1685.30653701122 -1685.30682685156 Force two-norm initial, final = 51.029472 1.7904192 Force max component initial, final = 36.549273 1.6748839 Final line search alpha, max atom move = 0.00070365197 0.0011785353 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3936 | 0.3936 | 0.3936 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020882 | 0.0020882 | 0.0020882 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005658 | | | 1.41 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8968.00 ave 8968 max 8968 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: 249498.0 ave 249498 max 249498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249498 Ave neighs/atom = 623.74500 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.478 | 5.478 | 5.478 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1685.3068 0 -1685.3068 287.03194 Loop time of 6.415e-06 on 1 procs for 0 steps with 400 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 | | 6.415e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8968.00 ave 8968 max 8968 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: 248282.0 ave 248282 max 248282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248282 Ave neighs/atom = 620.70500 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.478 | 5.478 | 5.478 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 -1685.3068 -1685.3068 17.535401 70.492064 3.5510437 287.03194 287.03194 120.06989 124.7566 616.26933 2.2149724 124.01919 Loop time of 6.695e-06 on 1 procs for 0 steps with 400 atoms 298.7% 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 | | 6.695e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8968.00 ave 8968 max 8968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124141.0 ave 124141 max 124141 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248282.0 ave 248282 max 248282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248282 Ave neighs/atom = 620.70500 Neighbor list builds = 0 Dangerous builds = 0 400 -1685.30682685156 eV 2.21497244355678 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05