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 -39.099282 0.0000000) to (13.033094 39.099282 3.6147299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0127284 5.0127284 3.6147299 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -39.099282 0.0000000) to (13.033094 39.099282 3.6147299) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0127284 5.0127284 3.6147299 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.099282 0.0000000) to (13.033094 39.099282 3.6147299) create_atoms CPU = 0.001 seconds 158 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 = 5 29 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 314 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 = 5 29 2 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) = 4.420 | 4.420 | 4.420 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1042.5438 0 -1042.5438 62421.742 42 0 -1111.6587 0 -1111.6587 12898.731 Loop time of 0.639939 on 1 procs for 42 steps with 314 atoms 35.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1042.54383010065 -1111.65787957889 -1111.65870598283 Force two-norm initial, final = 165.33046 0.079156961 Force max component initial, final = 76.311822 0.019009452 Final line search alpha, max atom move = 1.0000000 0.019009452 Iterations, force evaluations = 42 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6257 | 0.6257 | 0.6257 | 0.0 | 97.78 Neigh | 0.0035954 | 0.0035954 | 0.0035954 | 0.0 | 0.56 Comm | 0.0056991 | 0.0056991 | 0.0056991 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004943 | | | 0.77 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2646.00 ave 2646 max 2646 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: 17208.0 ave 17208 max 17208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17208 Ave neighs/atom = 54.802548 Neighbor list builds = 1 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 = 5 29 2 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.421 | 4.421 | 4.421 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1111.6587 0 -1111.6587 12898.731 3684.0214 46 0 -1111.7862 0 -1111.7862 6776.244 3699.8735 Loop time of 0.161076 on 1 procs for 4 steps with 314 atoms 35.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1111.65870598283 -1111.78546234211 -1111.78617430784 Force two-norm initial, final = 56.960043 34.203247 Force max component initial, final = 40.843564 25.737360 Final line search alpha, max atom move = 6.0467814e-07 1.5562819e-05 Iterations, force evaluations = 4 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15629 | 0.15629 | 0.15629 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011677 | 0.0011677 | 0.0011677 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003619 | | | 2.25 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2669.00 ave 2669 max 2669 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: 17232.0 ave 17232 max 17232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17232 Ave neighs/atom = 54.878981 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 = 5 29 2 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) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1111.7862 0 -1111.7862 6776.244 Loop time of 6.034e-06 on 1 procs for 0 steps with 314 atoms 99.4% 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 | | 6.034e-06 | | |100.00 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2669.00 ave 2669 max 2669 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: 17228.0 ave 17228 max 17228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17228 Ave neighs/atom = 54.866242 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 = 5 29 2 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) = 4.559 | 4.559 | 4.559 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 -1111.7862 -1111.7862 13.037657 78.347196 3.6221288 6776.244 6776.244 -594.43333 9755.1623 11168.003 2.2867008 138.06706 Loop time of 7.588e-06 on 1 procs for 0 steps with 314 atoms 237.2% 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 | | 7.588e-06 | | |100.00 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2669.00 ave 2669 max 2669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8614.00 ave 8614 max 8614 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17228.0 ave 17228 max 17228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17228 Ave neighs/atom = 54.866242 Neighbor list builds = 0 Dangerous builds = 0 314 -1111.78617430784 eV 2.28670076339344 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01