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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -59.029536 0.0000000) to (12.049353 59.029536 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4769789 5.3663214 5.9326915 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.029536 0.0000000) to (12.049353 59.029536 8.8990373) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4769789 5.3663214 5.9326915 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.029536 0.0000000) to (12.049353 59.029536 8.8990373) create_atoms CPU = 0.001 seconds 530 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 31 3 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4293.6385 0 -4293.6385 57466.174 69 0 -4507.2771 0 -4507.2771 9055.0761 Loop time of 1.08589 on 1 procs for 69 steps with 1058 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 = -4293.63848286941 -4507.27266220388 -4507.27706222157 Force two-norm initial, final = 294.60883 0.28771446 Force max component initial, final = 71.674990 0.052461675 Final line search alpha, max atom move = 1.0000000 0.052461675 Iterations, force evaluations = 69 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0602 | 1.0602 | 1.0602 | 0.0 | 97.63 Neigh | 0.01091 | 0.01091 | 0.01091 | 0.0 | 1.00 Comm | 0.0079123 | 0.0079123 | 0.0079123 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006895 | | | 0.63 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6386.00 ave 6386 max 6386 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: 177144.0 ave 177144 max 177144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177144 Ave neighs/atom = 167.43289 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4507.2771 0 -4507.2771 9055.0761 12659.196 76 0 -4507.6911 0 -4507.6911 34.994526 12732.408 Loop time of 0.0736263 on 1 procs for 7 steps with 1058 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4507.27706222157 -4507.69034214092 -4507.69113254415 Force two-norm initial, final = 148.07526 0.71831176 Force max component initial, final = 137.16688 0.32143944 Final line search alpha, max atom move = 0.00027078976 8.7042508e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.070736 | 0.070736 | 0.070736 | 0.0 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046451 | 0.00046451 | 0.00046451 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002426 | | | 3.29 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6418.00 ave 6418 max 6418 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: 177996.0 ave 177996 max 177996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177996 Ave neighs/atom = 168.23819 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.222 | 5.222 | 5.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4507.6911 0 -4507.6911 34.994526 Loop time of 1.923e-06 on 1 procs for 0 steps with 1058 atoms 104.0% 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 | | 1.923e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6396.00 ave 6396 max 6396 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: 171576.0 ave 171576 max 171576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171576 Ave neighs/atom = 162.17013 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.222 | 5.222 | 5.222 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 -4507.6911 -4507.6911 12.045994 118.78931 8.8979618 34.994526 34.994526 40.436904 39.021918 25.524755 2.3037095 391.35783 Loop time of 2.207e-06 on 1 procs for 0 steps with 1058 atoms 226.6% 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 | | 2.207e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6396.00 ave 6396 max 6396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85788.0 ave 85788 max 85788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171576.0 ave 171576 max 171576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171576 Ave neighs/atom = 162.17013 Neighbor list builds = 0 Dangerous builds = 0 1058 -4507.69113254415 eV 2.30370946060479 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01