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 4.050199627876282*${_u_distance} variable lattice_constant_converted equal 4.050199627876282*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 42.285325537303834*${_u_distance} variable xmax_converted equal 42.285325537303834*1 variable ymin_converted equal -42.28937573693171*${_u_distance} variable ymin_converted equal -42.28937573693171*1 variable ymax_converted equal 42.28937573693171*${_u_distance} variable ymax_converted equal 42.28937573693171*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050199627876282*${_u_distance} variable zmax_converted equal 4.050199627876282*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05019962787628 Lattice spacing in x,y,z = 4.0502 4.0502 4.0502 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 42.2853255373038 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2853255373038 -42.2893757369317 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2853255373038 -42.2893757369317 42.2893757369317 ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2853255373038 -42.2893757369317 42.2893757369317 0 ${zmax_converted} units box region whole block 0 42.2853255373038 -42.2893757369317 42.2893757369317 0 4.05019962787628 units box create_box 2 whole Created orthogonal box = (0 -42.2894 0) to (42.2853 42.2894 4.0502) 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 42.2893757369317 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.0432 5.0432 4.0502 create_atoms 1 region upper Created 438 atoms create_atoms CPU = 0.000246048 secs group upper type 1 438 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.698137929009748 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.2893757369317 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.0432 5.0432 4.0502 create_atoms 2 region lower Created 438 atoms create_atoms CPU = 0.00011611 secs group lower type 2 438 atoms in group lower displace_atoms lower move -4.698137929009748 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Al__MO_060567868558_000 pair_coeff * * Al Al 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*4.05019962787628 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02509981393814 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 11 21 1 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 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 856 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3046.7824 0 -3046.7824 -2605.4889 107 0 -3056.8189 0 -3056.8189 -4870.1265 Loop time of 0.664604 on 1 procs for 107 steps with 856 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3046.78236264 -3056.81894253 -3056.81894253 Force two-norm initial, final = 10.1584 0.00667299 Force max component initial, final = 2.61388 0.00134141 Final line search alpha, max atom move = 0.000244141 3.27493e-07 Iterations, force evaluations = 107 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64868 | 0.64868 | 0.64868 | 0.0 | 97.60 Neigh | 0.0032508 | 0.0032508 | 0.0032508 | 0.0 | 0.49 Comm | 0.0080678 | 0.0080678 | 0.0080678 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00461 | | | 0.69 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6299 ave 6299 max 6299 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: 119084 ave 119084 max 119084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119084 Ave neighs/atom = 139.117 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) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -3056.8189 0 -3056.8189 -4870.1265 14485.296 115 0 -3056.9391 0 -3056.9391 -683.88476 14404.826 Loop time of 0.147461 on 1 procs for 8 steps with 856 atoms 94.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3056.81894253 -3056.93905309 -3056.93905309 Force two-norm initial, final = 59.1308 0.374002 Force max component initial, final = 43.7002 0.277923 Final line search alpha, max atom move = 8.5929e-08 2.38816e-08 Iterations, force evaluations = 8 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14076 | 0.14076 | 0.14076 | 0.0 | 95.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015333 | 0.0015333 | 0.0015333 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00517 | | | 3.51 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6345 ave 6345 max 6345 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: 119224 ave 119224 max 119224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119224 Ave neighs/atom = 139.28 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3056.9391 0 -3056.9391 -683.88476 Loop time of 1.90735e-06 on 1 procs for 0 steps with 856 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 | | 1.907e-06 | | |100.00 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6363 ave 6363 max 6363 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: 119292 ave 119292 max 119292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119292 Ave neighs/atom = 139.36 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) = 5.105 | 5.105 | 5.105 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 -3056.9391 -3056.9391 42.19142 84.578751 4.0366639 -683.88476 -683.88476 30.84332 -2109.278 26.780432 2.5103879 716.28433 Loop time of 1.19209e-06 on 1 procs for 0 steps with 856 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 | | 1.192e-06 | | |100.00 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6363 ave 6363 max 6363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59646 ave 59646 max 59646 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119292 ave 119292 max 119292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119292 Ave neighs/atom = 139.36 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_033.3985/numatoms.out 856 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3056.93905309243-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3056.93905309243-856*${isolated_atom_energy} variable adjusted_pe_metal equal -3056.93905309243-856*0 print "${adjusted_pe_metal} eV" file output/dump_033.3985/energy.out -3056.93905309243 eV print "${mindist_metal} Angstroms" file output/dump_033.3985/mindistance.out 2.51038786982348 Angstroms write_dump all cfg output/dump_033.3985/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_033.3985/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00