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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -36.541763 0.0000000) to (25.838928 36.541763 4.9727041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7419841 4.7368952 4.9727041 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -36.541763 0.0000000) to (25.838928 36.541763 4.9727041) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7419841 4.7368952 4.9727041 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -36.541763 0.0000000) to (25.838928 36.541763 4.9727041) create_atoms CPU = 0.001 seconds 440 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 17 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 864 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_047308317761_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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4127.0503 0 -4127.0503 56349.233 32 0 -4195.2356 0 -4195.2356 8717.1643 Loop time of 0.793435 on 1 procs for 32 steps with 864 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 = -4127.05034195327 -4195.23284736359 -4195.23563353543 Force two-norm initial, final = 128.32756 0.18033464 Force max component initial, final = 16.271862 0.015879745 Final line search alpha, max atom move = 1.0000000 0.015879745 Iterations, force evaluations = 32 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78586 | 0.78586 | 0.78586 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004242 | 0.004242 | 0.004242 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003336 | | | 0.42 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7371.00 ave 7371 max 7371 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: 216160.0 ave 216160 max 216160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216160 Ave neighs/atom = 250.18519 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.397 | 5.397 | 5.397 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -4195.2356 0 -4195.2356 8717.1643 9390.4544 35 0 -4195.3636 0 -4195.3636 6.737181 9434.9761 Loop time of 0.082578 on 1 procs for 3 steps with 864 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 = -4195.23563353542 -4195.36083489886 -4195.36361417324 Force two-norm initial, final = 89.265738 2.3643635 Force max component initial, final = 59.478852 1.9363613 Final line search alpha, max atom move = 0.00018249051 0.00035336756 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.080597 | 0.080597 | 0.080597 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037356 | 0.00037356 | 0.00037356 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001607 | | | 1.95 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7326.00 ave 7326 max 7326 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: 218400.0 ave 218400 max 218400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218400 Ave neighs/atom = 252.77778 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.535 | 5.535 | 5.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4195.3636 0 -4195.3636 6.737181 Loop time of 2.169e-06 on 1 procs for 0 steps with 864 atoms 184.4% 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 | | 2.169e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7326.00 ave 7326 max 7326 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: 218176.0 ave 218176 max 218176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218176 Ave neighs/atom = 252.51852 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.535 | 5.535 | 5.535 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 -4195.3636 -4195.3636 25.902494 73.12599 4.9811253 6.737181 6.737181 -201.01352 -108.15007 329.37513 2.3315455 409.8372 Loop time of 2.56e-06 on 1 procs for 0 steps with 864 atoms 273.4% 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 | | 2.56e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7326.00 ave 7326 max 7326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109088.0 ave 109088 max 109088 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 218176.0 ave 218176 max 218176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218176 Ave neighs/atom = 252.51852 Neighbor list builds = 0 Dangerous builds = 0 864 -4195.36361417324 eV 2.33154550029519 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01