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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -54.486084 0.0000000) to (38.527479 54.486084 5.1030893) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0832862 5.2574291 5.1030893 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.486084 0.0000000) to (38.527479 54.486084 5.1030893) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0832862 5.2574291 5.1030893 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.486084 0.0000000) to (38.527479 54.486084 5.1030893) create_atoms CPU = 0.002 seconds 916 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 = 13 37 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 12 atoms, new total = 1816 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_549900287421_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 = 13 37 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) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7457.4274 0 -7457.4274 44969.91 464 0 -7729.6044 0 -7729.6044 -5437.706 Loop time of 62.0681 on 1 procs for 464 steps with 1816 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 = -7457.42739285246 -7729.59712496865 -7729.60439892891 Force two-norm initial, final = 670.42104 0.27306958 Force max component initial, final = 155.80134 0.047372127 Final line search alpha, max atom move = 1.0000000 0.047372127 Iterations, force evaluations = 464 898 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 61.784 | 61.784 | 61.784 | 0.0 | 99.54 Neigh | 0.10204 | 0.10204 | 0.10204 | 0.0 | 0.16 Comm | 0.092493 | 0.092493 | 0.092493 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08983 | | | 0.14 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7415.00 ave 7415 max 7415 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: 133956.0 ave 133956 max 133956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133956 Ave neighs/atom = 73.764317 Neighbor list builds = 9 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 = 13 37 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 : 464 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press Volume 464 0 -7729.6044 0 -7729.6044 -5437.706 21424.927 482 0 -7733.4698 0 -7733.4698 5.9205844 21351.986 Loop time of 1.45513 on 1 procs for 18 steps with 1816 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 = -7729.60439892891 -7733.46951294364 -7733.46981456007 Force two-norm initial, final = 405.58160 1.0587394 Force max component initial, final = 386.78945 0.34863647 Final line search alpha, max atom move = 0.00044328112 0.00015454396 Iterations, force evaluations = 18 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4337 | 1.4337 | 1.4337 | 0.0 | 98.53 Neigh | 0.010901 | 0.010901 | 0.010901 | 0.0 | 0.75 Comm | 0.0016622 | 0.0016622 | 0.0016622 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00882 | | | 0.61 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7428.00 ave 7428 max 7428 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: 134034.0 ave 134034 max 134034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134034 Ave neighs/atom = 73.807269 Neighbor list builds = 1 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 = 13 37 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) = 5.293 | 5.293 | 5.293 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7733.4698 0 -7733.4698 5.9205844 Loop time of 2.235e-06 on 1 procs for 0 steps with 1816 atoms 179.0% 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 | | 2.235e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7428.00 ave 7428 max 7428 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: 134050.0 ave 134050 max 134050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134050 Ave neighs/atom = 73.816079 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 = 13 37 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) = 5.293 | 5.293 | 5.293 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 -7733.4698 -7733.4698 37.883161 109.93484 5.1269222 5.9205844 5.9205844 0.43601222 -8.9568668 26.282608 2.3286593 5560.4107 Loop time of 2.217e-06 on 1 procs for 0 steps with 1816 atoms 270.6% 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 | | 2.217e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7428.00 ave 7428 max 7428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67025.0 ave 67025 max 67025 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134050.0 ave 134050 max 134050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134050 Ave neighs/atom = 73.816079 Neighbor list builds = 0 Dangerous builds = 0 1816 -7733.46981456007 eV 2.3286592985356 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:04