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 46.362602692314205*${_u_distance} variable xmax_converted equal 46.362602692314205*1 variable ymin_converted equal -46.36666896156293*${_u_distance} variable ymin_converted equal -46.36666896156293*1 variable ymax_converted equal 46.36666896156293*${_u_distance} variable ymax_converted equal 46.36666896156293*1 variable zmin_converted equal 0.0*${_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 46.3626026923142 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 46.3626026923142 -46.3666689615629 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 46.3626026923142 -46.3666689615629 46.3666689615629 ${zmin_converted} ${zmax_converted} units box region whole block 0 46.3626026923142 -46.3666689615629 46.3666689615629 0 ${zmax_converted} units box region whole block 0 46.3626026923142 -46.3666689615629 46.3666689615629 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -46.3667 0) to (46.3626 46.3667 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 46.3666689615629 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -7 0 orient y 7 9 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 9 -7 0 orient y 7 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70617 5.70617 4.06627 create_atoms 1 region upper Created 522 atoms create_atoms CPU = 0.00022912 secs group upper type 1 522 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.13078941294612 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -46.3666689615629 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 7 0 orient y -7 9 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 9 7 0 orient y -7 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70617 5.70617 4.06627 create_atoms 2 region lower Created 522 atoms create_atoms CPU = 0.000100851 secs group lower type 2 522 atoms in group lower displace_atoms lower move -5.13078941294612 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 15 30 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 24 atoms, new total = 1020 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 = 15 30 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) = 8.87 | 8.87 | 8.87 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3391.9205 0 -3391.9205 -11288.585 249 0 -3407.8109 0 -3407.8109 -16948.342 Loop time of 53.5741 on 1 procs for 249 steps with 1020 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 = -3391.92045766 -3407.81087096 -3407.81087096 Force two-norm initial, final = 7.03693 0.0058157 Force max component initial, final = 1.2752 0.0015449 Final line search alpha, max atom move = 0.03125 4.82782e-05 Iterations, force evaluations = 249 886 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.486 | 53.486 | 53.486 | 0.0 | 99.83 Neigh | 0.020392 | 0.020392 | 0.020392 | 0.0 | 0.04 Comm | 0.051804 | 0.051804 | 0.051804 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01637 | | | 0.03 Nlocal: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13029 ave 13029 max 13029 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: 54904 ave 54904 max 54904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54904 Ave neighs/atom = 53.8275 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) = 8.88 | 8.88 | 8.88 Mbytes Step Temp E_pair E_mol TotEng Press Volume 249 0 -3407.8109 0 -3407.8109 -16948.342 17482.351 1249 0 -3409.1752 0 -3409.1752 -5093.0704 17206.538 Loop time of 121.566 on 1 procs for 1000 steps with 1020 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 = -3407.81087096 -3409.17519182 -3409.1751929 Force two-norm initial, final = 216.245 0.13411 Force max component initial, final = 179.291 0.0771053 Final line search alpha, max atom move = 0.0189428 0.00146059 Iterations, force evaluations = 1000 1987 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 121.15 | 121.15 | 121.15 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11238 | 0.11238 | 0.11238 | 0.0 | 0.09 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3036 | | | 0.25 Nlocal: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12966 ave 12966 max 12966 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: 54976 ave 54976 max 54976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54976 Ave neighs/atom = 53.898 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 = 15 30 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) = 8.388 | 8.388 | 8.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3409.1752 0 -3409.1752 -5093.0704 Loop time of 0 on 1 procs for 0 steps with 1020 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 | | 0 | | | 0.00 Nlocal: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13071 ave 13071 max 13071 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: 55236 ave 55236 max 55236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55236 Ave neighs/atom = 54.1529 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) = 8.388 | 8.388 | 8.388 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 -3409.1752 -3409.1752 45.72559 92.733338 4.0578715 -5093.0704 -5093.0704 -6.6779809 -15265.368 -7.1647825 2.4645361 725.4386 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1020 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: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13071 ave 13071 max 13071 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27618 ave 27618 max 27618 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55236 ave 55236 max 55236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55236 Ave neighs/atom = 54.1529 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_075.7500/numatoms.out 1020 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3409.1751929005-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3409.1751929005-1020*${isolated_atom_energy} variable adjusted_pe_metal equal -3409.1751929005-1020*0 print "${adjusted_pe_metal} eV" file output/dump_075.7500/energy.out -3409.1751929005 eV print "${mindist_metal} Angstroms" file output/dump_075.7500/mindistance.out 2.46453606517906 Angstroms write_dump all cfg output/dump_075.7500/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_075.7500/success.out This indicates that LAMMPS ran successfully Total wall time: 0:02:55