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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -46.612974 0.0000000) to (16.480175 46.612974 4.0571386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4945932 4.9438003 4.0571386 Created 263 atoms using lattice units in orthogonal box = (0.0000000 -46.612974 0.0000000) to (16.480175 46.612974 4.0571386) create_atoms CPU = 0.001 seconds 263 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4945932 4.9438003 4.0571386 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -46.612974 0.0000000) to (16.480175 46.612974 4.0571386) create_atoms CPU = 0.001 seconds 265 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 528 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.352 | 5.352 | 5.352 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2042.1828 0 -2042.1828 52701.108 91 0 -2171.4142 0 -2171.4142 5024.4889 Loop time of 1.25799 on 1 procs for 91 steps with 528 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2042.18279352226 -2171.41206489097 -2171.4142247251 Force two-norm initial, final = 180.71170 0.20927179 Force max component initial, final = 53.967570 0.051266771 Final line search alpha, max atom move = 1.0000000 0.051266771 Iterations, force evaluations = 91 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2113 | 1.2113 | 1.2113 | 0.0 | 96.29 Neigh | 0.029686 | 0.029686 | 0.029686 | 0.0 | 2.36 Comm | 0.011322 | 0.011322 | 0.011322 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005713 | | | 0.45 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8427.00 ave 8427 max 8427 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: 203974.0 ave 203974 max 203974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203974 Ave neighs/atom = 386.31439 Neighbor list builds = 3 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.362 | 5.362 | 5.362 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -2171.4142 0 -2171.4142 5024.4889 6233.3064 98 0 -2171.7383 0 -2171.7383 -22.188539 6251.3526 Loop time of 0.0720032 on 1 procs for 7 steps with 528 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 = -2171.41422472511 -2171.73767350613 -2171.73830063123 Force two-norm initial, final = 77.740446 0.61092305 Force max component initial, final = 51.841199 0.22973841 Final line search alpha, max atom move = 0.00045050215 0.00010349765 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069347 | 0.069347 | 0.069347 | 0.0 | 96.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056064 | 0.00056064 | 0.00056064 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002095 | | | 2.91 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8946.00 ave 8946 max 8946 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: 204434.0 ave 204434 max 204434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204434 Ave neighs/atom = 387.18561 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.500 | 5.500 | 5.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2171.7383 0 -2171.7383 -22.188539 Loop time of 2.168e-06 on 1 procs for 0 steps with 528 atoms 138.4% 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 | | 2.168e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8972.00 ave 8972 max 8972 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: 203930.0 ave 203930 max 203930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203930 Ave neighs/atom = 386.23106 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.500 | 5.500 | 5.500 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 -2171.7383 -2171.7383 16.381679 93.597402 4.077104 -22.188539 -22.188539 -19.841787 12.446219 -59.170048 2.3042311 501.2865 Loop time of 2.196e-06 on 1 procs for 0 steps with 528 atoms 182.1% 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 | | 2.196e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8972.00 ave 8972 max 8972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101965.0 ave 101965 max 101965 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203930.0 ave 203930 max 203930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203930 Ave neighs/atom = 386.23106 Neighbor list builds = 0 Dangerous builds = 0 528 -2171.73830063123 eV 2.30423110407732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01