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 -58.031500 0.0000000) to (29.015750 58.031500 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4377030 4.4377030 3.1472000 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -58.031500 0.0000000) to (29.015750 58.031500 3.1472000) create_atoms CPU = 0.002 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4377030 4.4377030 3.1472000 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.031500 0.0000000) to (29.015750 58.031500 3.1472000) create_atoms CPU = 0.001 seconds 341 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 = 10 38 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 = 681 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 = 10 38 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) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4393.2513 0 -4393.2513 70522.294 35 0 -4629.9736 0 -4629.9736 4859.8358 Loop time of 0.459819 on 1 procs for 35 steps with 681 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 = -4393.25134648407 -4629.9690029103 -4629.97362245383 Force two-norm initial, final = 395.16218 0.30315784 Force max component initial, final = 126.32926 0.037270684 Final line search alpha, max atom move = 1.0000000 0.037270684 Iterations, force evaluations = 35 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44757 | 0.44757 | 0.44757 | 0.0 | 97.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0063539 | 0.0063539 | 0.0063539 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005899 | | | 1.28 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4689.00 ave 4689 max 4689 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: 39852.0 ave 39852 max 39852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39852 Ave neighs/atom = 58.519824 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 = 10 38 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -4629.9736 0 -4629.9736 4859.8358 10598.684 39 0 -4630.1064 0 -4630.1064 -57.304056 10615.399 Loop time of 0.0532161 on 1 procs for 4 steps with 681 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 = -4629.97362245383 -4630.10536383685 -4630.10640357552 Force two-norm initial, final = 86.832155 2.0278614 Force max component initial, final = 79.299072 1.9008064 Final line search alpha, max atom move = 9.4925405e-05 0.00018043482 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.050208 | 0.050208 | 0.050208 | 0.0 | 94.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069796 | 0.00069796 | 0.00069796 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00231 | | | 4.34 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4697.00 ave 4697 max 4697 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: 39874.0 ave 39874 max 39874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39874 Ave neighs/atom = 58.552129 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 = 10 38 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) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4630.1064 0 -4630.1064 -57.304056 Loop time of 6.575e-06 on 1 procs for 0 steps with 681 atoms 182.5% 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 | | 6.575e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4689.00 ave 4689 max 4689 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: 39814.0 ave 39814 max 39814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39814 Ave neighs/atom = 58.464023 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 = 10 38 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) = 4.650 | 4.650 | 4.650 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 -4630.1064 -4630.1064 29.026358 116.39931 3.1419074 -57.304056 -57.304056 -286.99258 32.407018 82.673394 2.5238233 217.26967 Loop time of 7.467e-06 on 1 procs for 0 steps with 681 atoms 187.5% 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 | | 7.467e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4689.00 ave 4689 max 4689 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19907.0 ave 19907 max 19907 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39814.0 ave 39814 max 39814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39814 Ave neighs/atom = 58.464023 Neighbor list builds = 0 Dangerous builds = 0 681 -4630.10640357552 eV 2.52382328392951 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