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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -62.608237 0.0000000) to (31.304119 62.608237 3.6390299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0763436 5.0763436 3.6390299 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.608237 0.0000000) to (31.304119 62.608237 3.6390299) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0763436 5.0763436 3.6390299 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.608237 0.0000000) to (31.304119 62.608237 3.6390299) create_atoms CPU = 0.001 seconds 594 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 32 1 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_748636486270_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.467 | 5.467 | 5.467 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3865.1132 0 -3865.1132 61958.64 48 0 -4048.3765 0 -4048.3765 5679.9239 Loop time of 1.00431 on 1 procs for 48 steps with 1186 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 = -3865.11321354486 -4048.37361408804 -4048.37650674494 Force two-norm initial, final = 292.33549 0.13103123 Force max component initial, final = 62.765008 0.0087760756 Final line search alpha, max atom move = 1.0000000 0.0087760756 Iterations, force evaluations = 48 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99063 | 0.99063 | 0.99063 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0080055 | 0.0080055 | 0.0080055 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005675 | | | 0.57 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9890.00 ave 9890 max 9890 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: 209148.0 ave 209148 max 209148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209148 Ave neighs/atom = 176.34739 Neighbor list builds = 0 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.467 | 5.467 | 5.467 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -4048.3765 0 -4048.3765 5679.9239 14264.238 54 0 -4048.5937 0 -4048.5937 -271.87916 14322.978 Loop time of 0.116225 on 1 procs for 6 steps with 1186 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 = -4048.37650674497 -4048.59278479722 -4048.59374952933 Force two-norm initial, final = 103.92821 5.2537609 Force max component initial, final = 93.564524 4.3097029 Final line search alpha, max atom move = 0.00025918807 0.0011170236 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11201 | 0.11201 | 0.11201 | 0.0 | 96.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073017 | 0.00073017 | 0.00073017 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003481 | | | 3.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900.00 ave 9900 max 9900 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: 208724.0 ave 208724 max 208724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208724 Ave neighs/atom = 175.98988 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.605 | 5.605 | 5.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4048.5937 0 -4048.5937 -271.87916 Loop time of 2.104e-06 on 1 procs for 0 steps with 1186 atoms 142.6% 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 | | 2.104e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9887.00 ave 9887 max 9887 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: 208504.0 ave 208504 max 208504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208504 Ave neighs/atom = 175.80438 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.605 | 5.605 | 5.605 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 -4048.5937 -4048.5937 31.277774 125.84115 3.6389391 -271.87916 -271.87916 3.343837 -336.9075 -482.0738 2.2427355 307.94598 Loop time of 2.377e-06 on 1 procs for 0 steps with 1186 atoms 168.3% 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 | | 2.377e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9887.00 ave 9887 max 9887 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104252.0 ave 104252 max 104252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 208504.0 ave 208504 max 208504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208504 Ave neighs/atom = 175.80438 Neighbor list builds = 0 Dangerous builds = 0 1186 -4048.59374952933 eV 2.24273548969309 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01