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 4.049999177455902*${_u_distance} variable lattice_constant_converted equal 4.049999177455902*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 77.37512564221541*${_u_distance} variable xmax_converted equal 77.37512564221541*1 variable ymin_converted equal -77.37917564139286*${_u_distance} variable ymin_converted equal -77.37917564139286*1 variable ymax_converted equal 77.37917564139286*${_u_distance} variable ymax_converted equal 77.37917564139286*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049999177455902*${_u_distance} variable zmax_converted equal 4.049999177455902*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0499991774559 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 77.3751256422154 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.3751256422154 -77.3791756413929 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.3751256422154 -77.3791756413929 77.3791756413929 ${zmin_converted} ${zmax_converted} units box region whole block 0 77.3751256422154 -77.3791756413929 77.3791756413929 0 ${zmax_converted} units box region whole block 0 77.3751256422154 -77.3791756413929 77.3791756413929 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -77.3792 0) to (77.3751 77.3792 4.05) 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 77.3791756413929 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72364 5.72364 4.05 create_atoms 1 region upper Created 1462 atoms create_atoms CPU = 0.00037694 secs group upper type 1 1462 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.59723792854426 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -77.3791756413929 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72364 5.72364 4.05 create_atoms 2 region lower Created 1462 atoms create_atoms CPU = 0.000258923 secs group lower type 2 1462 atoms in group lower displace_atoms lower move -8.59723792854426 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_656517352485_000-files/b'library.meam' Al Si Mg Cu Fe ./SM_656517352485_000-files/b'AlSiMgCuFe.meam' Al Al Reading potential file ./SM_656517352485_000-files/b'library.meam' with DATE: 2012-06-29 Reading potential file ./SM_656517352485_000-files/b'AlSiMgCuFe.meam' with DATE: 2012-06-29 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*4.0499991774559 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499958872795 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 23 45 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 32 atoms, new total = 2892 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 23 45 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 25.76 | 25.76 | 25.76 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9640.6549 0 -9640.6549 -197.76016 337 0 -9683.5426 0 -9683.5426 -6371.9249 Loop time of 25.2006 on 1 procs for 337 steps with 2892 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 = -9640.65492349 -9683.54258891 -9683.54258891 Force two-norm initial, final = 25.2979 2.12784e-05 Force max component initial, final = 4.67288 3.27592e-06 Final line search alpha, max atom move = 1 3.27592e-06 Iterations, force evaluations = 337 664 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.113 | 25.113 | 25.113 | 0.0 | 99.65 Neigh | 0.008265 | 0.008265 | 0.008265 | 0.0 | 0.03 Comm | 0.045779 | 0.045779 | 0.045779 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.034 | | | 0.13 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13760 ave 13760 max 13760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114370 ave 114370 max 114370 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 228740 ave 228740 max 228740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228740 Ave neighs/atom = 79.0941 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) = 25.81 | 25.81 | 25.81 Mbytes Step Temp E_pair E_mol TotEng Press Volume 337 0 -9683.5426 0 -9683.5426 -6371.9249 48496.5 1337 0 -9683.9621 0 -9683.9621 -2057.9321 48221.822 Loop time of 76.6058 on 1 procs for 1000 steps with 2892 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 = -9683.54258891 -9683.9620541 -9683.96205411 Force two-norm initial, final = 206.927 0.0153378 Force max component initial, final = 152.404 0.0106777 Final line search alpha, max atom move = 0.226918 0.00242297 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 76.028 | 76.028 | 76.028 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12779 | 0.12779 | 0.12779 | 0.0 | 0.17 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4495 | | | 0.59 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13678 ave 13678 max 13678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114446 ave 114446 max 114446 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 228892 ave 228892 max 228892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228892 Ave neighs/atom = 79.1466 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 23 45 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 23.62 | 23.62 | 23.62 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9683.9621 0 -9683.9621 -2057.9321 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 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: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13744 ave 13744 max 13744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117024 ave 117024 max 117024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 234048 ave 234048 max 234048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234048 Ave neighs/atom = 80.9295 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) = 23.62 | 23.62 | 23.62 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 -9683.9621 -9683.9621 77.196293 154.75835 4.0363896 -2057.9321 -2057.9321 -0.16383187 -6173.279 -0.35357671 2.4445504 241.92654 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 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: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13744 ave 13744 max 13744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117024 ave 117024 max 117024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 234048 ave 234048 max 234048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234048 Ave neighs/atom = 80.9295 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.7578/numatoms.out 2892 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9683.96205410909-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9683.96205410909-2892*${isolated_atom_energy} variable adjusted_pe_metal equal -9683.96205410909-2892*0 print "${adjusted_pe_metal} eV" file output/dump_085.7578/energy.out -9683.96205410909 eV print "${mindist_metal} Angstroms" file output/dump_085.7578/mindistance.out 2.44455035255225 Angstroms write_dump all cfg output/dump_085.7578/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_085.7578/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:42