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 = 4.0496966 4.0496966 4.0496966 Created orthogonal box = (0.0000000 -77.475257 0.0000000) to (44.730361 77.475257 7.0142802) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5995614 5.9270689 7.0142802 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -77.475257 0.0000000) to (44.730361 77.475257 7.0142802) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5995614 5.9270689 7.0142802 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.475257 0.0000000) to (44.730361 77.475257 7.0142802) create_atoms CPU = 0.008 seconds 1466 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_284963179498_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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.199 | 6.199 | 6.199 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9067.1442 0 -9067.1442 36709.62 186 0 -9842.5333 0 -9842.5333 2728.3589 Loop time of 12.4456 on 1 procs for 186 steps with 2926 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9067.14419692693 -9842.52373287345 -9842.53334261088 Force two-norm initial, final = 820.23533 0.25129792 Force max component initial, final = 209.44234 0.054709646 Final line search alpha, max atom move = 0.50905735 0.027850347 Iterations, force evaluations = 186 349 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.825 | 11.825 | 11.825 | 0.0 | 95.01 Neigh | 0.40956 | 0.40956 | 0.40956 | 0.0 | 3.29 Comm | 0.1071 | 0.1071 | 0.1071 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.104 | | | 0.84 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11416.0 ave 11416 max 11416 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: 378908.0 ave 378908 max 378908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 378908 Ave neighs/atom = 129.49692 Neighbor list builds = 8 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 186 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.199 | 6.199 | 6.199 Mbytes Step Temp E_pair E_mol TotEng Press Volume 186 0 -9842.5333 0 -9842.5333 2728.3589 48615.923 191 0 -9842.8554 0 -9842.8554 -94.576371 48810.924 Loop time of 0.242793 on 1 procs for 5 steps with 2926 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9842.53334261084 -9842.84986987038 -9842.85539444363 Force two-norm initial, final = 162.73208 8.5237637 Force max component initial, final = 144.93557 6.1228930 Final line search alpha, max atom move = 3.9407333e-05 0.00024128688 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23408 | 0.23408 | 0.23408 | 0.0 | 96.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001786 | 0.001786 | 0.001786 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00693 | | | 2.85 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11416.0 ave 11416 max 11416 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: 379052.0 ave 379052 max 379052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379052 Ave neighs/atom = 129.54614 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.337 | 6.337 | 6.337 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9842.8554 0 -9842.8554 -94.576371 Loop time of 6.144e-06 on 1 procs for 0 steps with 2926 atoms 211.6% 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 | | 6.144e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11398.0 ave 11398 max 11398 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: 375404.0 ave 375404 max 375404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375404 Ave neighs/atom = 128.29938 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.337 | 6.337 | 6.337 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 -9842.8554 -9842.8554 44.734671 155.64106 7.0104936 -94.576371 -94.576371 -200.99805 89.808335 -172.5394 2.6321162 1239.2574 Loop time of 6.475e-06 on 1 procs for 0 steps with 2926 atoms 308.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11398.0 ave 11398 max 11398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 187702.0 ave 187702 max 187702 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 375404.0 ave 375404 max 375404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375404 Ave neighs/atom = 128.29938 Neighbor list builds = 0 Dangerous builds = 0 2926 -9842.85539444363 eV 2.63211620164334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13