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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -44.951007 0.0000000) to (31.785162 44.951007 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9859077 3.9662653 4.4508129 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -44.951007 0.0000000) to (31.785162 44.951007 4.4508129) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9859077 3.9662653 4.4508129 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -44.951007 0.0000000) to (31.785162 44.951007 4.4508129) create_atoms CPU = 0.001 seconds 410 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 29 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 818 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5226.2206 0 -5226.2206 110600.71 57 0 -5541.0082 0 -5541.0082 12790.018 Loop time of 0.390232 on 1 procs for 57 steps with 818 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 = -5226.22057443331 -5541.00290104292 -5541.00819830803 Force two-norm initial, final = 368.57983 0.32731775 Force max component initial, final = 67.999153 0.050602583 Final line search alpha, max atom move = 1.0000000 0.050602583 Iterations, force evaluations = 57 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38184 | 0.38184 | 0.38184 | 0.0 | 97.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043078 | 0.0043078 | 0.0043078 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004086 | | | 1.05 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4414.00 ave 4414 max 4414 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: 47904.0 ave 47904 max 47904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47904 Ave neighs/atom = 58.562347 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -5541.0082 0 -5541.0082 12790.018 12718.421 62 0 -5541.3558 0 -5541.3558 -17.290227 12773.652 Loop time of 0.0296809 on 1 procs for 5 steps with 818 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 = -5541.00819830803 -5541.35474727129 -5541.35576457026 Force two-norm initial, final = 193.84785 1.2447852 Force max component initial, final = 164.07331 0.71888830 Final line search alpha, max atom move = 0.00010120900 7.2757967e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028171 | 0.028171 | 0.028171 | 0.0 | 94.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027115 | 0.00027115 | 0.00027115 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001239 | | | 4.18 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4392.00 ave 4392 max 4392 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: 47904.0 ave 47904 max 47904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47904 Ave neighs/atom = 58.562347 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.674 | 4.674 | 4.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5541.3558 0 -5541.3558 -17.290227 Loop time of 1.759e-06 on 1 procs for 0 steps with 818 atoms 113.7% 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 | | 1.759e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4400.00 ave 4400 max 4400 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: 47824.0 ave 47824 max 47824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47824 Ave neighs/atom = 58.464548 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.674 | 4.674 | 4.674 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 -5541.3558 -5541.3558 31.762472 90.253207 4.4559277 -17.290227 -17.290227 -77.557162 -64.586023 90.272505 2.4061187 538.65526 Loop time of 1.647e-06 on 1 procs for 0 steps with 818 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 | | 1.647e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4400.00 ave 4400 max 4400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23912.0 ave 23912 max 23912 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47824.0 ave 47824 max 47824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47824 Ave neighs/atom = 58.464548 Neighbor list builds = 0 Dangerous builds = 0 818 -5541.35576457026 eV 2.40611868902673 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42