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 = 3.6150000 3.6150000 3.6150000 Created orthogonal box = (0.0000000 -65.470434 0.0000000) to (23.147294 65.470434 5.1123820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2102496 5.5889395 5.1123820 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.470434 0.0000000) to (23.147294 65.470434 5.1123820) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2102496 5.5889395 5.1123820 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.470434 0.0000000) to (23.147294 65.470434 5.1123820) create_atoms CPU = 0.002 seconds 658 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 33 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 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_128703483589_005#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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.525 | 5.525 | 5.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3678.1792 0 -3678.1792 161333.8 117 0 -4637.2877 0 -4637.2877 2027.9655 Loop time of 2.69311 on 1 procs for 117 steps with 1312 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 = -3678.17919119489 -4637.28322209344 -4637.28768407758 Force two-norm initial, final = 2431.7370 0.20373410 Force max component initial, final = 534.98479 0.038111576 Final line search alpha, max atom move = 1.0000000 0.038111576 Iterations, force evaluations = 117 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.615 | 2.615 | 2.615 | 0.0 | 97.10 Neigh | 0.042617 | 0.042617 | 0.042617 | 0.0 | 1.58 Comm | 0.019907 | 0.019907 | 0.019907 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01556 | | | 0.58 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8600.00 ave 8600 max 8600 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: 231624.0 ave 231624 max 231624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231624 Ave neighs/atom = 176.54268 Neighbor list builds = 3 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.520 | 5.520 | 5.520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -4637.2877 0 -4637.2877 2027.9655 15495.256 120 0 -4637.3173 0 -4637.3173 -43.760037 15518.349 Loop time of 0.0776825 on 1 procs for 3 steps with 1312 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 = -4637.28768407757 -4637.31713276762 -4637.31726082615 Force two-norm initial, final = 39.747423 0.79054563 Force max component initial, final = 33.466053 0.59524524 Final line search alpha, max atom move = 0.00064213752 0.00038222931 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075336 | 0.075336 | 0.075336 | 0.0 | 96.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044859 | 0.00044859 | 0.00044859 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001898 | | | 2.44 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8600.00 ave 8600 max 8600 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: 231556.0 ave 231556 max 231556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231556 Ave neighs/atom = 176.49085 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.658 | 5.658 | 5.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4637.3173 0 -4637.3173 -43.760037 Loop time of 2.33e-06 on 1 procs for 0 steps with 1312 atoms 171.7% 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 | | 2.33e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8592.00 ave 8592 max 8592 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: 231452.0 ave 231452 max 231452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231452 Ave neighs/atom = 176.41159 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.658 | 5.658 | 5.658 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 -4637.3173 -4637.3173 23.179839 131.04036 5.108931 -43.760037 -43.760037 -61.541908 -33.386712 -36.351491 2.3841713 518.2675 Loop time of 2.603e-06 on 1 procs for 0 steps with 1312 atoms 192.1% 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 | | 2.603e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8592.00 ave 8592 max 8592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115726.0 ave 115726 max 115726 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 231452.0 ave 231452 max 231452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231452 Ave neighs/atom = 176.41159 Neighbor list builds = 0 Dangerous builds = 0 1312 -4637.3169972053 eV 2.38417134605165 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03