LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.066269248723984*${_u_distance} variable lattice_constant_converted equal 4.066269248723984*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 34.742219690567225*${_u_distance} variable xmax_converted equal 34.742219690567225*1 variable ymin_converted equal -69.48850565038317*${_u_distance} variable ymin_converted equal -69.48850565038317*1 variable ymax_converted equal 69.48850565038317*${_u_distance} variable ymax_converted equal 69.48850565038317*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.066269248723984*${_u_distance} variable zmax_converted equal 4.066269248723984*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06626924872398 Lattice spacing in x,y,z = 4.06627 4.06627 4.06627 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.7422196905672 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.7422196905672 -69.4885056503832 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.7422196905672 -69.4885056503832 69.4885056503832 ${zmin_converted} ${zmax_converted} units box region whole block 0 34.7422196905672 -69.4885056503832 69.4885056503832 0 ${zmax_converted} units box region whole block 0 34.7422196905672 -69.4885056503832 69.4885056503832 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -69.4885 0) to (34.7422 69.4885 4.06627) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 69.4885056503832 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -3 0 orient y 3 8 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 8 -3 0 orient y 3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.23513 5.23513 4.06627 create_atoms 1 region upper Created 586 atoms create_atoms CPU = 0.000216007 secs group upper type 1 586 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.844801685392889 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -69.4885056503832 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 3 0 orient y -3 8 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 8 3 0 orient y -3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.23513 5.23513 4.06627 create_atoms 2 region lower Created 586 atoms create_atoms CPU = 0.00010705 secs group lower type 2 586 atoms in group lower displace_atoms lower move -3.844801685392889 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style bop pair_coeff * * ./SM_566399258279_000-files/b'AlCu.bop.table' Al Al Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 comm_modify cutoff 12.7 variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.06626924872398 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03313462436199 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 12 45 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 18 atoms, new total = 1154 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 12 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 13.14 | 13.14 | 13.14 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3852.3917 0 -3852.3917 -9698.494 289 0 -3864.066 0 -3864.066 -14174.167 Loop time of 39.4005 on 1 procs for 289 steps with 1154 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 = -3852.39170037 -3864.06603856 -3864.06603856 Force two-norm initial, final = 5.59912 6.85393e-06 Force max component initial, final = 1.05931 3.88946e-07 Final line search alpha, max atom move = 1 3.88946e-07 Iterations, force evaluations = 289 559 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 39.324 | 39.324 | 39.324 | 0.0 | 99.81 Neigh | 0.022891 | 0.022891 | 0.022891 | 0.0 | 0.06 Comm | 0.039431 | 0.039431 | 0.039431 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01372 | | | 0.03 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15458 ave 15458 max 15458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62336 ave 62336 max 62336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62336 Ave neighs/atom = 54.0173 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 13.55 | 13.55 | 13.55 Mbytes Step Temp E_pair E_mol TotEng Press Volume 289 0 -3864.066 0 -3864.066 -14174.167 19633.452 1289 0 -3865.3983 0 -3865.3983 -3689.6084 19363.836 Loop time of 140.228 on 1 procs for 1000 steps with 1154 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3864.06603856 -3865.39825892 -3865.39825924 Force two-norm initial, final = 215.454 0.0929296 Force max component initial, final = 190.3 0.0708658 Final line search alpha, max atom move = 0.0455824 0.00323023 Iterations, force evaluations = 1000 1987 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 139.72 | 139.72 | 139.72 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13797 | 0.13797 | 0.13797 | 0.0 | 0.10 Output | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3661 | | | 0.26 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15866 ave 15866 max 15866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62228 ave 62228 max 62228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62228 Ave neighs/atom = 53.9237 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 0.0 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 12.18 | 12.18 | 12.18 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3865.3983 0 -3865.3983 -3689.6084 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1154 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15936 ave 15936 max 15936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62340 ave 62340 max 62340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62340 Ave neighs/atom = 54.0208 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom 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 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 12.18 | 12.18 | 12.18 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 -3865.3983 -3865.3983 34.262277 138.97701 4.0666071 -3689.6084 -3689.6084 4.9035593 -11079.593 5.8639735 2.3403084 533.66394 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1154 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15936 ave 15936 max 15936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31170 ave 31170 max 31170 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62340 ave 62340 max 62340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62340 Ave neighs/atom = 54.0208 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_041.1121/numatoms.out 1154 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3865.39825924344-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3865.39825924344-1154*${isolated_atom_energy} variable adjusted_pe_metal equal -3865.39825924344-1154*0 print "${adjusted_pe_metal} eV" file output/dump_041.1121/energy.out -3865.39825924344 eV print "${mindist_metal} Angstroms" file output/dump_041.1121/mindistance.out 2.34030835945076 Angstroms write_dump all cfg output/dump_041.1121/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_041.1121/success.out This indicates that LAMMPS ran successfully Total wall time: 0:03:00