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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -43.676947 0.0000000) to (53.493117 43.676947 8.8542437) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1294770 5.3848291 5.9028292 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -43.676947 0.0000000) to (53.493117 43.676947 8.8542437) create_atoms CPU = 0.003 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1294770 5.3848291 5.9028292 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -43.676947 0.0000000) to (53.493117 43.676947 8.8542437) create_atoms CPU = 0.002 seconds 1758 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 42 atoms, new total = 3468 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11808.821 0 -11808.821 22859.277 22 0 -12222.257 0 -12222.257 1325.1477 Loop time of 0.870511 on 1 procs for 22 steps with 3468 atoms 46.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11808.820647657 -12222.2536539709 -12222.2571941942 Force two-norm initial, final = 468.87922 0.44152510 Force max component initial, final = 90.110665 0.057955787 Final line search alpha, max atom move = 0.015625000 0.00090555917 Iterations, force evaluations = 22 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85939 | 0.85939 | 0.85939 | 0.0 | 98.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037033 | 0.0037033 | 0.0037033 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00742 | | | 0.85 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7072.00 ave 7072 max 7072 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: 186168.0 ave 186168 max 186168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186168 Ave neighs/atom = 53.681661 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -12222.257 0 -12222.257 1325.1477 41374.394 23 0 -12222.26 0 -12222.26 1269.2342 41376.087 Loop time of 0.115306 on 1 procs for 1 steps with 3468 atoms 50.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12222.2571941941 -12222.2571941941 -12222.2598725526 Force two-norm initial, final = 82.535056 80.352784 Force max component initial, final = 78.423982 76.536825 Final line search alpha, max atom move = 3.9847505e-07 3.0498015e-05 Iterations, force evaluations = 1 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11228 | 0.11228 | 0.11228 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041098 | 0.00041098 | 0.00041098 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00261 | | | 2.26 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7072.00 ave 7072 max 7072 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: 187128.0 ave 187128 max 187128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187128 Ave neighs/atom = 53.958478 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.373 | 5.373 | 5.373 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 12263.933 0 12263.933 1269.2342 Loop time of 2.166e-06 on 1 procs for 0 steps with 3468 atoms 184.7% 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 | | 2.166e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7072.00 ave 7072 max 7072 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: 187128.0 ave 187128 max 187128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187128 Ave neighs/atom = 53.958478 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.373 | 5.373 | 5.373 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 12263.933 -12222.26 53.493086 87.356624 8.8543343 1269.2342 1269.2342 -98.272591 2963.7731 942.20218 2.2472643 958.51072 Loop time of 2.359e-06 on 1 procs for 0 steps with 3468 atoms 254.3% 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 | | 2.359e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7072.00 ave 7072 max 7072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93564.0 ave 93564 max 93564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187128.0 ave 187128 max 187128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187128 Ave neighs/atom = 53.958478 Neighbor list builds = 0 Dangerous builds = 0 3468 12263.9328289284 eV 2.24726433649712 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01