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 = 3.1706996 3.1706996 3.1706996 Created orthogonal box = (0.0000000 -63.572329 0.0000000) to (36.703501 63.572329 5.4918128) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9303211 5.0604839 5.4918128 Created 803 atoms using lattice units in orthogonal box = (0.0000000 -63.572329 0.0000000) to (36.703501 63.572329 5.4918128) create_atoms CPU = 0.002 seconds 803 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9303211 5.0604839 5.4918128 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -63.572329 0.0000000) to (36.703501 63.572329 5.4918128) create_atoms CPU = 0.002 seconds 806 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 39 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1609 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_468686727341_000#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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17326.251 0 -17326.251 10543.99 56 0 -17404.578 0 -17404.578 7177.1548 Loop time of 60.4152 on 1 procs for 56 steps with 1609 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 = -17326.251136511 -17404.5623924487 -17404.5776123064 Force two-norm initial, final = 53.534530 0.38891195 Force max component initial, final = 12.893783 0.067008421 Final line search alpha, max atom move = 1.0000000 0.067008421 Iterations, force evaluations = 56 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 60.385 | 60.385 | 60.385 | 0.0 | 99.95 Neigh | 0.0083317 | 0.0083317 | 0.0083317 | 0.0 | 0.01 Comm | 0.011738 | 0.011738 | 0.011738 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01053 | | | 0.02 Nlocal: 1609.00 ave 1609 max 1609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6822.00 ave 6822 max 6822 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: 103536.0 ave 103536 max 103536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103536 Ave neighs/atom = 64.348042 Neighbor list builds = 1 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -17404.578 0 -17404.578 7177.1548 25628.391 59 0 -17404.785 0 -17404.785 -0.56034743 25697.805 Loop time of 3.79336 on 1 procs for 3 steps with 1609 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 = -17404.5776123064 -17404.7736134902 -17404.7845691356 Force two-norm initial, final = 208.63097 2.0105673 Force max component initial, final = 165.39373 1.5027611 Final line search alpha, max atom move = 3.5869482e-05 5.3903261e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7911 | 3.7911 | 3.7911 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037699 | 0.00037699 | 0.00037699 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001884 | | | 0.05 Nlocal: 1609.00 ave 1609 max 1609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6831.00 ave 6831 max 6831 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: 103466.0 ave 103466 max 103466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103466 Ave neighs/atom = 64.304537 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.252 | 5.252 | 5.252 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17404.785 0 -17404.785 -0.56034743 Loop time of 2.142e-06 on 1 procs for 0 steps with 1609 atoms 140.1% 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 | | 2.142e-06 | | |100.00 Nlocal: 1609.00 ave 1609 max 1609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6824.00 ave 6824 max 6824 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: 103452.0 ave 103452 max 103452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103452 Ave neighs/atom = 64.295836 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.252 | 5.252 | 5.252 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 -17404.785 -17404.785 36.705349 127.42742 5.4941914 -0.56034743 -0.56034743 77.450962 14.600954 -93.732959 2.3653074 650.90012 Loop time of 2.544e-06 on 1 procs for 0 steps with 1609 atoms 196.5% 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 | | 2.544e-06 | | |100.00 Nlocal: 1609.00 ave 1609 max 1609 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6824.00 ave 6824 max 6824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51726.0 ave 51726 max 51726 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103452.0 ave 103452 max 103452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103452 Ave neighs/atom = 64.295836 Neighbor list builds = 0 Dangerous builds = 0 1609 -4976.5135231223 eV 2.36530735140042 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:06