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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5169606 6.0683471 4.9800000 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5169606 6.0683471 4.9800000 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) create_atoms CPU = 0.002 seconds 530 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_008996216289_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.640 | 4.640 | 4.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4541.7652 0 -4541.7652 45392.587 60 0 -4695.6956 0 -4695.6956 8982.4859 Loop time of 5.70418 on 1 procs for 60 steps with 1058 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 = -4541.76520056118 -4695.69119662154 -4695.69555710813 Force two-norm initial, final = 251.07462 0.24426333 Force max component initial, final = 81.067592 0.063894642 Final line search alpha, max atom move = 1.0000000 0.063894642 Iterations, force evaluations = 60 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6892 | 5.6892 | 5.6892 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.007852 | 0.007852 | 0.007852 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007085 | | | 0.12 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5746.00 ave 5746 max 5746 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: 92256.0 ave 92256 max 92256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92256 Ave neighs/atom = 87.198488 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -4695.6956 0 -4695.6956 8982.4859 11527.814 67 0 -4696.0977 0 -4696.0977 -85.32057 11582.926 Loop time of 0.541524 on 1 procs for 7 steps with 1058 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 = -4695.69555710814 -4696.09757806833 -4696.09771317846 Force two-norm initial, final = 147.41821 1.3443611 Force max component initial, final = 142.77390 1.0212803 Final line search alpha, max atom move = 0.00043089598 0.00044006556 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53816 | 0.53816 | 0.53816 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054815 | 0.00054815 | 0.00054815 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002813 | | | 0.52 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6164.00 ave 6164 max 6164 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: 93388.0 ave 93388 max 93388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93388 Ave neighs/atom = 88.268431 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.781 | 4.781 | 4.781 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4696.0977 0 -4696.0977 -85.32057 Loop time of 2.243e-06 on 1 procs for 0 steps with 1058 atoms 178.3% 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 | | 2.243e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6164.00 ave 6164 max 6164 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: 92976.0 ave 92976 max 92976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92976 Ave neighs/atom = 87.879017 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.781 | 4.781 | 4.781 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 -4696.0977 -4696.0977 20.207025 115.10069 4.9800991 -85.32057 -85.32057 -141.11334 -111.18632 -3.6620551 2.3055895 349.84443 Loop time of 2.428e-06 on 1 procs for 0 steps with 1058 atoms 205.9% 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 | | 2.428e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6164.00 ave 6164 max 6164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46488.0 ave 46488 max 46488 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92976.0 ave 92976 max 92976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92976 Ave neighs/atom = 87.879017 Neighbor list builds = 0 Dangerous builds = 0 1058 -4696.09771317846 eV 2.30558947206142 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06