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 4.032082033157349*${_u_distance} variable lattice_constant_converted equal 4.032082033157349*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 28.51112547946003*${_u_distance} variable xmax_converted equal 28.51112547946003*1 variable ymin_converted equal -57.02628304095322*${_u_distance} variable ymin_converted equal -57.02628304095322*1 variable ymax_converted equal 57.02628304095322*${_u_distance} variable ymax_converted equal 57.02628304095322*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082033157349*${_u_distance} variable zmax_converted equal 4.032082033157349*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03208203315735 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 28.51112547946 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.51112547946 -57.0262830409532 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.51112547946 -57.0262830409532 57.0262830409532 ${zmin_converted} ${zmax_converted} units box region whole block 0 28.51112547946 -57.0262830409532 57.0262830409532 0 ${zmax_converted} units box region whole block 0 28.51112547946 -57.0262830409532 57.0262830409532 0 4.03208203315735 units box create_box 2 whole Created orthogonal box = (0 -57.0263 0) to (28.5111 57.0263 4.03208) 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 57.0262830409532 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 lattice fcc 4.03208203315735 orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.56178 4.56178 4.03208 create_atoms 1 region upper Created 402 atoms create_atoms CPU = 0.000222921 secs group upper type 1 402 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.181980515339464 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -57.0262830409532 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 lattice fcc 4.03208203315735 orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.56178 4.56178 4.03208 create_atoms 2 region lower Created 402 atoms create_atoms CPU = 9.29832e-05 secs group lower type 2 402 atoms in group lower displace_atoms lower move -3.181980515339464 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 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*4.03208203315735 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604101657867 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 31 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 792 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2643.6509 0 -2643.6509 1992.2976 304 0 -2653.5418 0 -2653.5418 -3454.8279 Loop time of 1.26581 on 1 procs for 304 steps with 792 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2643.65094577 -2653.54177217 -2653.54177217 Force two-norm initial, final = 18.6461 1.27083e-05 Force max component initial, final = 5.54008 2.36156e-06 Final line search alpha, max atom move = 1 2.36156e-06 Iterations, force evaluations = 304 605 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2345 | 1.2345 | 1.2345 | 0.0 | 97.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020086 | 0.020086 | 0.020086 | 0.0 | 1.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01125 | | | 0.89 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6053 ave 6053 max 6053 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: 103816 ave 103816 max 103816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103816 Ave neighs/atom = 131.081 Neighbor list builds = 0 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) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press Volume 304 0 -2653.5418 0 -2653.5418 -3454.8279 13111.391 1147 0 -2653.5671 0 -2653.5671 -1654.7683 13081.492 Loop time of 3.48362 on 1 procs for 843 steps with 792 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 = -2653.54177217 -2653.56713211 -2653.56713211 Force two-norm initial, final = 24.5806 4.96098e-05 Force max component initial, final = 21.772 4.38466e-05 Final line search alpha, max atom move = 1 4.38466e-05 Iterations, force evaluations = 843 1685 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2478 | 3.2478 | 3.2478 | 0.0 | 93.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.053701 | 0.053701 | 0.053701 | 0.0 | 1.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1822 | | | 5.23 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6008 ave 6008 max 6008 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: 89584 ave 89584 max 89584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89584 Ave neighs/atom = 113.111 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 4.699 | 4.699 | 4.699 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2653.5671 0 -2653.5671 -1654.7683 Loop time of 1.19209e-06 on 1 procs for 0 steps with 792 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: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6008 ave 6008 max 6008 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: 91768 ave 91768 max 91768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91768 Ave neighs/atom = 115.869 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) = 4.699 | 4.699 | 4.699 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 -2653.5671 -2653.5671 28.443065 114.05257 4.0325135 -1654.7683 -1654.7683 0.0053573673 -4964.3108 0.00036496624 2.5965884 308.46274 Loop time of 1.90735e-06 on 1 procs for 0 steps with 792 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: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6008 ave 6008 max 6008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45884 ave 45884 max 45884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91768 ave 91768 max 91768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91768 Ave neighs/atom = 115.869 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_016.2602/numatoms.out 792 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2653.56713211425-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2653.56713211425-792*${isolated_atom_energy} variable adjusted_pe_metal equal -2653.56713211425-792*0 print "${adjusted_pe_metal} eV" file output/dump_016.2602/energy.out -2653.56713211425 eV print "${mindist_metal} Angstroms" file output/dump_016.2602/mindistance.out 2.59658838853513 Angstroms write_dump all cfg output/dump_016.2602/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_016.2602/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:04