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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -71.488312 0.0000000) to (41.271459 71.488312 7.0096089) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3494553 6.4152545 7.0096089 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.488312 0.0000000) to (41.271459 71.488312 7.0096089) create_atoms CPU = 0.002 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3494553 6.4152545 7.0096089 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.488312 0.0000000) to (41.271459 71.488312 7.0096089) create_atoms CPU = 0.002 seconds 1251 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 41 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 2471 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.701 | 5.701 | 5.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8237.5033 0 -8237.5033 1728.3362 97 0 -8281.6114 0 -8281.6114 -4445.0647 Loop time of 19.4432 on 1 procs for 97 steps with 2471 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8237.50329172442 -8281.60506034204 -8281.61136242806 Force two-norm initial, final = 31.879664 0.23340423 Force max component initial, final = 5.7809993 0.066390358 Final line search alpha, max atom move = 0.98737499 0.065552180 Iterations, force evaluations = 97 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.349 | 19.349 | 19.349 | 0.0 | 99.52 Neigh | 0.046039 | 0.046039 | 0.046039 | 0.0 | 0.24 Comm | 0.019834 | 0.019834 | 0.019834 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.028 | | | 0.14 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8458.00 ave 8458 max 8458 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: 211474.0 ave 211474 max 211474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211474 Ave neighs/atom = 85.582355 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.702 | 5.702 | 5.702 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -8281.6114 0 -8281.6114 -4445.0647 41362.678 100 0 -8281.8465 0 -8281.8465 -901.38299 41173.752 Loop time of 0.509228 on 1 procs for 3 steps with 2471 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8281.61136242804 -8281.83994457847 -8281.84646531928 Force two-norm initial, final = 144.84808 2.8517125 Force max component initial, final = 106.14389 2.2819248 Final line search alpha, max atom move = 5.1043411e-05 0.00011647723 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50674 | 0.50674 | 0.50674 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003399 | 0.0003399 | 0.0003399 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002153 | | | 0.42 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8455.00 ave 8455 max 8455 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: 211486.0 ave 211486 max 211486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211486 Ave neighs/atom = 85.587212 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.840 | 5.840 | 5.840 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8281.8465 0 -8281.8465 -901.38299 Loop time of 1.748e-06 on 1 procs for 0 steps with 2471 atoms 171.6% 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 | | 1.748e-06 | | |100.00 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8469.00 ave 8469 max 8469 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: 211562.0 ave 211562 max 211562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211562 Ave neighs/atom = 85.617968 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.840 | 5.840 | 5.840 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 -8281.8465 -8281.8465 41.183444 142.97662 6.9925044 -901.38299 -901.38299 88.606194 -2727.1719 -65.583239 2.4408092 1619.6642 Loop time of 1.891e-06 on 1 procs for 0 steps with 2471 atoms 211.5% 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 | | 1.891e-06 | | |100.00 Nlocal: 2471.00 ave 2471 max 2471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8469.00 ave 8469 max 8469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105781.0 ave 105781 max 105781 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 211562.0 ave 211562 max 211562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211562 Ave neighs/atom = 85.617968 Neighbor list builds = 0 Dangerous builds = 0 2471 -8281.84646531928 eV 2.44080916250278 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20