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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -40.901207 0.0000000) to (28.921521 40.901207 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5367092 3.6089301 4.0498230 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.901207 0.0000000) to (28.921521 40.901207 4.0498230) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5367092 3.6089301 4.0498230 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.901207 0.0000000) to (28.921521 40.901207 4.0498230) create_atoms CPU = 0.001 seconds 410 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 = 10 28 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 814 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_179158257180_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 = 10 28 2 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) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2949.6552 0 -2949.6552 92071.811 113 0 -3473.8777 0 -3473.8777 4588.0058 Loop time of 4.5249 on 1 procs for 113 steps with 814 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 = -2949.65520751227 -3473.87465734273 -3473.87773647925 Force two-norm initial, final = 950.44965 0.16888014 Force max component initial, final = 323.16080 0.032011194 Final line search alpha, max atom move = 1.0000000 0.032011194 Iterations, force evaluations = 113 195 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4929 | 4.4929 | 4.4929 | 0.0 | 99.29 Neigh | 0.013614 | 0.013614 | 0.013614 | 0.0 | 0.30 Comm | 0.0086067 | 0.0086067 | 0.0086067 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009736 | | | 0.22 Nlocal: 814.000 ave 814 max 814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3791.00 ave 3791 max 3791 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: 52412.0 ave 52412 max 52412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52412 Ave neighs/atom = 64.388206 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 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 : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -3473.8777 0 -3473.8777 4588.0058 9581.2749 119 0 -3474.0004 0 -3474.0004 -0.68729211 9606.6634 Loop time of 0.212052 on 1 procs for 6 steps with 814 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 = -3473.87773647926 -3473.99980873789 -3474.0004154736 Force two-norm initial, final = 58.600673 0.26144622 Force max component initial, final = 55.422672 0.036703117 Final line search alpha, max atom move = 0.00021058275 7.7290432e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21006 | 0.21006 | 0.21006 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029654 | 0.00029654 | 0.00029654 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001692 | | | 0.80 Nlocal: 814.000 ave 814 max 814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3810.00 ave 3810 max 3810 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: 52288.0 ave 52288 max 52288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52288 Ave neighs/atom = 64.235872 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 = 10 28 2 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) = 4.671 | 4.671 | 4.671 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3474.0004 0 -3474.0004 -0.68729211 Loop time of 2.265e-06 on 1 procs for 0 steps with 814 atoms 176.6% 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 | | 2.265e-06 | | |100.00 Nlocal: 814.000 ave 814 max 814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3810.00 ave 3810 max 3810 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: 52292.0 ave 52292 max 52292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52292 Ave neighs/atom = 64.240786 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 = 10 28 2 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) = 4.671 | 4.671 | 4.671 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 -3474.0004 -3474.0004 28.8898 82.213401 4.0446917 -0.68729211 -0.68729211 0.61093472 -1.4798043 -1.1930067 2.314005 475.94945 Loop time of 3.658e-06 on 1 procs for 0 steps with 814 atoms 218.7% 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 | | 3.658e-06 | | |100.00 Nlocal: 814.000 ave 814 max 814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3810.00 ave 3810 max 3810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26146.0 ave 26146 max 26146 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52292.0 ave 52292 max 52292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52292 Ave neighs/atom = 64.240786 Neighbor list builds = 0 Dangerous builds = 0 814 -3474.0004154736 eV 2.3140050486544 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05