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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -36.863156 0.0000000) to (31.924430 36.863156 6.2608958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7300259 5.6712548 6.2608958 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -36.863156 0.0000000) to (31.924430 36.863156 6.2608958) create_atoms CPU = 0.004 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7300259 5.6712548 6.2608958 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -36.863156 0.0000000) to (31.924430 36.863156 6.2608958) create_atoms CPU = 0.004 seconds 630 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1252 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_887933271505_003#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4020.1027 0 -4020.1027 74663.896 40 0 -4428.55 0 -4428.55 10096.766 Loop time of 1.83444 on 1 procs for 40 steps with 1252 atoms 55.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4020.10273904435 -4428.55001160452 -4428.55001160452 Force two-norm initial, final = 548.47813 0.80573169 Force max component initial, final = 130.17428 0.10386523 Final line search alpha, max atom move = 1.0835060e-08 1.1253861e-09 Iterations, force evaluations = 40 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7783 | 1.7783 | 1.7783 | 0.0 | 96.94 Neigh | 0.026343 | 0.026343 | 0.026343 | 0.0 | 1.44 Comm | 0.014272 | 0.014272 | 0.014272 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01554 | | | 0.85 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4016.00 ave 4016 max 4016 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: 68708.0 ave 68708 max 68708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68708 Ave neighs/atom = 54.878594 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -4428.55 0 -4428.55 10096.766 14736.086 44 0 -4428.5947 0 -4428.5947 9541.7825 14741.839 Loop time of 0.378618 on 1 procs for 4 steps with 1252 atoms 55.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4428.55001160453 -4428.59396072037 -4428.59472240998 Force two-norm initial, final = 180.56663 172.05891 Force max component initial, final = 158.16871 151.90873 Final line search alpha, max atom move = 2.5696010e-08 3.9034482e-06 Iterations, force evaluations = 4 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36518 | 0.36518 | 0.36518 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026199 | 0.0026199 | 0.0026199 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01082 | | | 2.86 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4005.00 ave 4005 max 4005 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: 68860.0 ave 68860 max 68860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68860 Ave neighs/atom = 55.000000 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.717 | 4.717 | 4.717 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4428.5947 0 -4428.5947 9541.7825 Loop time of 6.294e-06 on 1 procs for 0 steps with 1252 atoms 143.0% 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 | | 6.294e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4005.00 ave 4005 max 4005 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: 68856.0 ave 68856 max 68856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68856 Ave neighs/atom = 54.996805 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.717 | 4.717 | 4.717 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 -4428.5947 -4428.5947 31.927691 73.742728 6.2613063 9541.7825 9541.7825 7428.0518 16513.461 4683.8344 2.2847258 1011.8616 Loop time of 6.575e-06 on 1 procs for 0 steps with 1252 atoms 197.7% 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 | | 6.575e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4005.00 ave 4005 max 4005 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34428.0 ave 34428 max 34428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68856.0 ave 68856 max 68856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68856 Ave neighs/atom = 54.996805 Neighbor list builds = 0 Dangerous builds = 0 1252 -4428.59472240998 eV 2.28472575088455 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02