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 = 3.6147282 3.6147282 3.6147282 Created orthogonal box = (0.0000000 -39.099263 0.0000000) to (13.033088 39.099263 3.6147282) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0127260 5.0127260 3.6147282 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -39.099263 0.0000000) to (13.033088 39.099263 3.6147282) create_atoms CPU = 0.001 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0127260 5.0127260 3.6147282 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.099263 0.0000000) to (13.033088 39.099263 3.6147282) create_atoms CPU = 0.000 seconds 158 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 4 19 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_942551040047_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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1061.245 0 -1061.245 35274.674 17 0 -1095.0949 0 -1095.0949 7857.4451 Loop time of 0.11334 on 1 procs for 17 steps with 312 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 = -1061.24497833268 -1095.09383613463 -1095.09487083962 Force two-norm initial, final = 93.192153 0.12031608 Force max component initial, final = 32.731676 0.017329567 Final line search alpha, max atom move = 1.0000000 0.017329567 Iterations, force evaluations = 17 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11157 | 0.11157 | 0.11157 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011478 | 0.0011478 | 0.0011478 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006203 | | | 0.55 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5070.00 ave 5070 max 5070 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: 70056.0 ave 70056 max 70056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70056 Ave neighs/atom = 224.53846 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1095.0949 0 -1095.0949 7857.4451 3684.0162 24 0 -1095.1871 0 -1095.1871 222.35047 3703.9627 Loop time of 0.0382184 on 1 procs for 7 steps with 312 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 = -1095.09487083962 -1095.18677300254 -1095.1871239631 Force two-norm initial, final = 35.618897 0.92617357 Force max component initial, final = 29.650223 0.66489292 Final line search alpha, max atom move = 0.0022330345 0.0014847288 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036478 | 0.036478 | 0.036478 | 0.0 | 95.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036937 | 0.00036937 | 0.00036937 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001371 | | | 3.59 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5070.00 ave 5070 max 5070 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: 69832.0 ave 69832 max 69832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69832 Ave neighs/atom = 223.82051 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 3 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.617 | 4.617 | 4.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1095.1871 0 -1095.1871 222.35047 Loop time of 1.54e-06 on 1 procs for 0 steps with 312 atoms 129.9% 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 | | 1.54e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5070.00 ave 5070 max 5070 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: 69784.0 ave 69784 max 69784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69784 Ave neighs/atom = 223.66667 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 3 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.617 | 4.617 | 4.617 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 -1095.1871 -1095.1871 13.000026 78.602765 3.6248043 222.35047 222.35047 218.50702 160.13831 288.40607 2.2993984 153.34056 Loop time of 1.823e-06 on 1 procs for 0 steps with 312 atoms 219.4% 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 | | 1.823e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5070.00 ave 5070 max 5070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34892.0 ave 34892 max 34892 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69784.0 ave 69784 max 69784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69784 Ave neighs/atom = 223.66667 Neighbor list builds = 0 Dangerous builds = 0 312 -1095.1871239631 eV 2.29939836219569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00