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 4.081654928624631*${_u_distance} variable lattice_constant_converted equal 4.081654928624631*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 28.861658784939703*${_u_distance} variable xmax_converted equal 28.861658784939703*1 variable ymin_converted equal -57.72739922480803*${_u_distance} variable ymin_converted equal -57.72739922480803*1 variable ymax_converted equal 57.72739922480803*${_u_distance} variable ymax_converted equal 57.72739922480803*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.081654928624631*${_u_distance} variable zmax_converted equal 4.081654928624631*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.08165492862463 Lattice spacing in x,y,z = 4.08165 4.08165 4.08165 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 28.8616587849397 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.8616587849397 -57.727399224808 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.8616587849397 -57.727399224808 57.727399224808 ${zmin_converted} ${zmax_converted} units box region whole block 0 28.8616587849397 -57.727399224808 57.727399224808 0 ${zmax_converted} units box region whole block 0 28.8616587849397 -57.727399224808 57.727399224808 0 4.08165492862463 units box create_box 2 whole Created orthogonal box = (0 -57.7274 0) to (28.8617 57.7274 4.08165) 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 57.727399224808 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.61787 4.61787 4.08165 create_atoms 1 region upper Created 402 atoms create_atoms CPU = 0.000251055 secs group upper type 1 402 atoms in group upper mass 1 26.981538*${_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 -57.727399224808 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.61787 4.61787 4.08165 create_atoms 2 region lower Created 402 atoms create_atoms CPU = 0.000102997 secs group lower type 2 402 atoms in group lower displace_atoms lower move -3.181980515339464 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_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*4.08165492862463 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.04082746431231 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 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 12.1025 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.827 | 5.827 | 5.827 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2824.5932 0 -2824.5932 -1054.3165 242 0 -2829.4364 0 -2829.4364 -4576.5628 Loop time of 4.78319 on 1 procs for 242 steps with 792 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2824.59320983 -2829.43635619 -2829.43635619 Force two-norm initial, final = 7.76807 1.44887e-05 Force max component initial, final = 2.30522 1.88658e-06 Final line search alpha, max atom move = 1 1.88658e-06 Iterations, force evaluations = 242 477 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7324 | 4.7324 | 4.7324 | 0.0 | 98.94 Neigh | 0.007983 | 0.007983 | 0.007983 | 0.0 | 0.17 Comm | 0.031342 | 0.031342 | 0.031342 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01147 | | | 0.24 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11549 ave 11549 max 11549 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: 337084 ave 337084 max 337084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337084 Ave neighs/atom = 425.611 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) = 5.828 | 5.828 | 5.828 Mbytes Step Temp E_pair E_mol TotEng Press Volume 242 0 -2829.4364 0 -2829.4364 -4576.5628 13600.96 1242 0 -2829.502 0 -2829.502 -979.19703 13547.395 Loop time of 19.5136 on 1 procs for 1000 steps with 792 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 = -2829.43635619 -2829.50204618 -2829.50204621 Force two-norm initial, final = 46.8604 0.0112039 Force max component initial, final = 34.3655 0.00767666 Final line search alpha, max atom move = 0.251718 0.00193235 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.052 | 19.052 | 19.052 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11778 | 0.11778 | 0.11778 | 0.0 | 0.60 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3442 | | | 1.76 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11570 ave 11570 max 11570 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: 337024 ave 337024 max 337024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337024 Ave neighs/atom = 425.535 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 2.2204e-16 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 5.966 | 5.966 | 5.966 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2829.502 0 -2829.502 -979.19703 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: 11598 ave 11598 max 11598 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: 337336 ave 337336 max 337336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337336 Ave neighs/atom = 425.929 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) = 5.966 | 5.966 | 5.966 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 -2829.502 -2829.502 28.795487 115.4548 4.0749227 -979.19703 -979.19703 -0.90579559 -2936.2002 -0.48513775 2.5193328 287.80149 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: 11598 ave 11598 max 11598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 168668 ave 168668 max 168668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 337336 ave 337336 max 337336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337336 Ave neighs/atom = 425.929 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -2829.50204620549-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2829.50204620549-792*${isolated_atom_energy} variable adjusted_pe_metal equal -2829.50204620549-792*2.2204e-16 print "${adjusted_pe_metal} eV" file output/dump_016.2602/energy.out -2829.50204620549 eV print "${mindist_metal} Angstroms" file output/dump_016.2602/mindistance.out 2.51933282094679 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: 0:00:24