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 4.03203821182251*${_u_distance} variable lattice_constant_converted equal 4.03203821182251*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 28.510815615829777*${_u_distance} variable xmax_converted equal 28.510815615829777*1 variable ymin_converted equal -57.02566326987138*${_u_distance} variable ymin_converted equal -57.02566326987138*1 variable ymax_converted equal 57.02566326987138*${_u_distance} variable ymax_converted equal 57.02566326987138*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.03203821182251*${_u_distance} variable zmax_converted equal 4.03203821182251*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03203821182251 Lattice spacing in x,y,z = 4.03204 4.03204 4.03204 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 28.5108156158298 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.5108156158298 -57.0256632698714 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.5108156158298 -57.0256632698714 57.0256632698714 ${zmin_converted} ${zmax_converted} units box region whole block 0 28.5108156158298 -57.0256632698714 57.0256632698714 0 ${zmax_converted} units box region whole block 0 28.5108156158298 -57.0256632698714 57.0256632698714 0 4.03203821182251 units box create_box 2 whole Created orthogonal box = (0 -57.0257 0) to (28.5108 57.0257 4.03204) 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 57.0256632698714 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.56173 4.56173 4.03204 create_atoms 1 region upper Created 402 atoms create_atoms CPU = 0.000221014 secs group upper type 1 402 atoms in group upper mass 1 26.981538*${_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 -57.0256632698714 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.56173 4.56173 4.03204 create_atoms 2 region lower Created 402 atoms create_atoms CPU = 9.29832e-05 secs group lower type 2 402 atoms in group lower displace_atoms lower move -3.181980515339464 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_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*4.03203821182251 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01601910591125 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 27 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 8.68 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.969 | 4.969 | 4.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2643.6623 0 -2643.6623 2459.5909 260 0 -2653.1287 0 -2653.1287 -2738.3497 Loop time of 1.62887 on 1 procs for 260 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 = -2643.66225512 -2653.1286806 -2653.1286806 Force two-norm initial, final = 18.8734 3.24593e-05 Force max component initial, final = 5.59155 6.73215e-06 Final line search alpha, max atom move = 1 6.73215e-06 Iterations, force evaluations = 260 518 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6006 | 1.6006 | 1.6006 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018437 | 0.018437 | 0.018437 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009808 | | | 0.60 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6533 ave 6533 max 6533 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: 137596 ave 137596 max 137596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137596 Ave neighs/atom = 173.732 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) = 4.969 | 4.969 | 4.969 Mbytes Step Temp E_pair E_mol TotEng Press Volume 260 0 -2653.1287 0 -2653.1287 -2738.3497 13110.964 1260 0 -2653.1388 0 -2653.1388 -1543.4591 13091.417 Loop time of 5.93649 on 1 procs for 1000 steps with 792 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2653.1286806 -2653.13878076 -2653.13878076 Force two-norm initial, final = 16.1175 0.00142242 Force max component initial, final = 13.8785 0.00076286 Final line search alpha, max atom move = 1 0.00076286 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6652 | 5.6652 | 5.6652 | 0.0 | 95.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.063782 | 0.063782 | 0.063782 | 0.0 | 1.07 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2075 | | | 3.50 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6533 ave 6533 max 6533 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: 137344 ave 137344 max 137344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137344 Ave neighs/atom = 173.414 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.107 | 5.107 | 5.107 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2653.1388 0 -2653.1388 -1543.4591 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6533 ave 6533 max 6533 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: 137376 ave 137376 max 137376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137376 Ave neighs/atom = 173.455 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) = 5.107 | 5.107 | 5.107 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 -2653.1388 -2653.1388 28.470787 114.05133 4.0316873 -1543.4591 -1543.4591 0.093230632 -4630.3902 -0.080363309 2.5216124 411.1537 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6533 ave 6533 max 6533 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68688 ave 68688 max 68688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137376 ave 137376 max 137376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137376 Ave neighs/atom = 173.455 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -2653.1387807617-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2653.1387807617-792*${isolated_atom_energy} variable adjusted_pe_metal equal -2653.1387807617-792*0 print "${adjusted_pe_metal} eV" file output/dump_016.2602/energy.out -2653.1387807617 eV print "${mindist_metal} Angstroms" file output/dump_016.2602/mindistance.out 2.52161239603185 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: 0:00:07