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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -57.193230 0.0000000) to (20.220860 57.193230 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5147801 6.0659486 4.9780317 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.193230 0.0000000) to (20.220860 57.193230 4.9780317) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5147801 6.0659486 4.9780317 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.193230 0.0000000) to (20.220860 57.193230 4.9780317) create_atoms CPU = 0.001 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 27 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.480 | 5.480 | 5.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4655.167 0 -4655.167 4289.4443 48 0 -4689.0019 0 -4689.0019 4411.7743 Loop time of 1.42566 on 1 procs for 48 steps with 1056 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 = -4655.16700813291 -4688.99791750835 -4689.00193180678 Force two-norm initial, final = 22.162102 0.20779268 Force max component initial, final = 4.7468541 0.029022914 Final line search alpha, max atom move = 1.0000000 0.029022914 Iterations, force evaluations = 48 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3784 | 1.3784 | 1.3784 | 0.0 | 96.68 Neigh | 0.033351 | 0.033351 | 0.033351 | 0.0 | 2.34 Comm | 0.0082716 | 0.0082716 | 0.0082716 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005658 | | | 0.40 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9123.00 ave 9123 max 9123 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: 261640.0 ave 261640 max 261640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261640 Ave neighs/atom = 247.76515 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -4689.0019 0 -4689.0019 4411.7743 11514.151 53 0 -4689.204 0 -4689.204 93.524837 11541.987 Loop time of 0.108247 on 1 procs for 5 steps with 1056 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 = -4689.00193180679 -4689.20248174481 -4689.20401005319 Force two-norm initial, final = 92.060027 1.5223429 Force max component initial, final = 90.183398 1.4214423 Final line search alpha, max atom move = 0.00017668968 0.00025115418 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10589 | 0.10589 | 0.10589 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047179 | 0.00047179 | 0.00047179 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001884 | | | 1.74 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9123.00 ave 9123 max 9123 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: 261592.0 ave 261592 max 261592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261592 Ave neighs/atom = 247.71970 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.617 | 5.617 | 5.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4689.204 0 -4689.204 93.524837 Loop time of 1.823e-06 on 1 procs for 0 steps with 1056 atoms 109.7% 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 | | 1.823e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9123.00 ave 9123 max 9123 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: 261412.0 ave 261412 max 261412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261412 Ave neighs/atom = 247.54924 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.617 | 5.617 | 5.617 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 -4689.204 -4689.204 20.179336 114.86874 4.9793407 93.524837 93.524837 62.193338 21.014781 197.36639 2.2975418 345.67064 Loop time of 2.27e-06 on 1 procs for 0 steps with 1056 atoms 176.2% 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 | | 2.27e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9123.00 ave 9123 max 9123 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130706.0 ave 130706 max 130706 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261412.0 ave 261412 max 261412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261412 Ave neighs/atom = 247.54924 Neighbor list builds = 0 Dangerous builds = 0 1056 -4689.20401005319 eV 2.29754184592807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01