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 = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -51.395627 0.0000000) to (36.342196 51.395627 4.0380218) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9353600 4.7588543 4.0380218 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.395627 0.0000000) to (36.342196 51.395627 4.0380218) create_atoms CPU = 0.006 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9353600 4.7588543 4.0380218 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.395627 0.0000000) to (36.342196 51.395627 4.0380218) create_atoms CPU = 0.005 seconds 650 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.884 | 5.884 | 5.884 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4938.2208 0 -4938.2208 69618.328 60 0 -5193.4094 0 -5193.4094 4417.5405 Loop time of 4.37154 on 1 procs for 60 steps with 1298 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4938.2207971423 -5193.40491273792 -5193.40938586725 Force two-norm initial, final = 376.39858 0.27219124 Force max component initial, final = 95.290612 0.072349612 Final line search alpha, max atom move = 1.0000000 0.072349612 Iterations, force evaluations = 60 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3253 | 4.3253 | 4.3253 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.028145 | 0.028145 | 0.028145 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01809 | | | 0.41 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10917.0 ave 10917 max 10917 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: 295664.0 ave 295664 max 295664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295664 Ave neighs/atom = 227.78428 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.502 | 5.502 | 5.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -5193.4094 0 -5193.4094 4417.5405 15084.676 63 0 -5193.4924 0 -5193.4924 35.622826 15122.653 Loop time of 0.199558 on 1 procs for 3 steps with 1298 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 = -5193.40938586724 -5193.48829682132 -5193.49238775284 Force two-norm initial, final = 79.413482 1.1954225 Force max component initial, final = 68.298880 1.0604686 Final line search alpha, max atom move = 7.4437665e-05 7.8938806e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19508 | 0.19508 | 0.19508 | 0.0 | 97.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011467 | 0.0011467 | 0.0011467 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003332 | | | 1.67 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10900.0 ave 10900 max 10900 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: 293376.0 ave 293376 max 293376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293376 Ave neighs/atom = 226.02157 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.640 | 5.640 | 5.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5193.4924 0 -5193.4924 35.622826 Loop time of 6.375e-06 on 1 procs for 0 steps with 1298 atoms 203.9% 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 | | 6.375e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10884.0 ave 10884 max 10884 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: 291988.0 ave 291988 max 291988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291988 Ave neighs/atom = 224.95223 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.640 | 5.640 | 5.640 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 -5193.4924 -5193.4924 36.357923 103.0248 4.0372637 35.622826 35.622826 112.40046 33.724137 -39.256119 2.2406683 538.38468 Loop time of 7.077e-06 on 1 procs for 0 steps with 1298 atoms 254.3% 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 | | 7.077e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10884.0 ave 10884 max 10884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145994.0 ave 145994 max 145994 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 291988.0 ave 291988 max 291988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291988 Ave neighs/atom = 224.95223 Neighbor list builds = 0 Dangerous builds = 0 1298 -5193.49238775284 eV 2.24066834109662 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05