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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -53.733184 0.0000000) to (32.902240 53.733184 9.9203987) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9822255 6.1055834 6.6135992 Created 1067 atoms using lattice units in orthogonal box = (0.0000000 -53.733184 0.0000000) to (32.902240 53.733184 9.9203987) create_atoms CPU = 0.005 seconds 1067 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9822255 6.1055834 6.6135992 Created 1067 atoms using lattice units in orthogonal box = (0.0000000 -53.733184 0.0000000) to (32.902240 53.733184 9.9203987) create_atoms CPU = 0.004 seconds 1067 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 ghost atom cutoff = 6 binsize = 3, bins = 11 36 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 70 atoms, new total = 2064 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_022920256108_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 ghost atom cutoff = 6 binsize = 3, bins = 11 36 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.036 | 5.036 | 5.036 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6858.1024 0 -6858.1024 -1052.2786 73 0 -6907.8714 0 -6907.8714 -12754.363 Loop time of 7.93781 on 1 procs for 73 steps with 2064 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 = -6858.10236989773 -6907.86538478742 -6907.87139020779 Force two-norm initial, final = 12.216118 0.21736559 Force max component initial, final = 1.5533246 0.010456728 Final line search alpha, max atom move = 1.0000000 0.010456728 Iterations, force evaluations = 73 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8565 | 7.8565 | 7.8565 | 0.0 | 98.98 Neigh | 0.040153 | 0.040153 | 0.040153 | 0.0 | 0.51 Comm | 0.01498 | 0.01498 | 0.01498 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02614 | | | 0.33 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5030.00 ave 5030 max 5030 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: 111028.0 ave 111028 max 111028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111028 Ave neighs/atom = 53.792636 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 36 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -6907.8714 0 -6907.8714 -12754.363 35077.382 83 0 -6909.7121 0 -6909.7121 -3294.546 34548.632 Loop time of 0.862803 on 1 procs for 10 steps with 2064 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6907.87139020776 -6909.71096623135 -6909.71214414377 Force two-norm initial, final = 335.95176 0.50853722 Force max component initial, final = 253.62027 0.049823289 Final line search alpha, max atom move = 0.00019176977 9.5546003e-06 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85391 | 0.85391 | 0.85391 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013184 | 0.0013184 | 0.0013184 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007576 | | | 0.88 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5000.00 ave 5000 max 5000 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: 111168.0 ave 111168 max 111168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111168 Ave neighs/atom = 53.860465 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 ghost atom cutoff = 6 binsize = 3, bins = 11 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.175 | 5.175 | 5.175 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6909.7121 0 -6909.7121 -3294.546 Loop time of 6.214e-06 on 1 procs for 0 steps with 2064 atoms 177.0% 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 | | 6.214e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5046.00 ave 5046 max 5046 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: 111168.0 ave 111168 max 111168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111168 Ave neighs/atom = 53.860465 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 ghost atom cutoff = 6 binsize = 3, bins = 11 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.175 | 5.175 | 5.175 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 -6909.7121 -6909.7121 32.607431 107.46637 9.8592005 -3294.546 -3294.546 1.1604929 -9882.8296 -1.9687804 2.7450266 796.02212 Loop time of 6.525e-06 on 1 procs for 0 steps with 2064 atoms 306.5% 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 | | 6.525e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5046.00 ave 5046 max 5046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55584.0 ave 55584 max 55584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111168.0 ave 111168 max 111168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111168 Ave neighs/atom = 53.860465 Neighbor list builds = 0 Dangerous builds = 0 2064 -6909.71214414377 eV 2.74502664649254 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09