LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 45.98314381483932*${_u_distance} variable xmax_converted equal 45.98314381483932*1 variable ymin_converted equal -45.9871768033429*${_u_distance} variable ymin_converted equal -45.9871768033429*1 variable ymax_converted equal 45.9871768033429*${_u_distance} variable ymax_converted equal 45.9871768033429*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 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 45.9831438148393 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.9831438148393 -45.9871768033429 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.9831438148393 -45.9871768033429 45.9871768033429 ${zmin_converted} ${zmax_converted} units box region whole block 0 45.9831438148393 -45.9871768033429 45.9871768033429 0 ${zmax_converted} units box region whole block 0 45.9831438148393 -45.9871768033429 45.9871768033429 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -45.9872 0) to (45.9831 45.9872 4.03299) 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 45.9871768033429 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -3 0 orient y 3 11 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 11 -3 0 orient y 3 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95203 4.95203 4.03299 create_atoms 1 region upper Created 522 atoms create_atoms CPU = 0.00019908 secs group upper type 1 522 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.13078941294612 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.9871768033429 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 3 0 orient y -3 11 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 11 3 0 orient y -3 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95203 4.95203 4.03299 create_atoms 2 region lower Created 522 atoms create_atoms CPU = 9.17912e-05 secs group lower type 2 522 atoms in group lower displace_atoms lower move -5.13078941294612 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 7 14 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1026 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 7 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2937.2504 0 -2937.2504 2417.4303 230 0 -2974.3985 0 -2974.3985 -5778.1816 Loop time of 6.47628 on 1 procs for 230 steps with 1026 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 = -2937.25040164 -2974.39847454 -2974.39847454 Force two-norm initial, final = 30.7744 5.10314e-06 Force max component initial, final = 5.70133 6.6487e-07 Final line search alpha, max atom move = 1 6.6487e-07 Iterations, force evaluations = 230 439 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4117 | 6.4117 | 6.4117 | 0.0 | 99.00 Neigh | 0.020331 | 0.020331 | 0.020331 | 0.0 | 0.31 Comm | 0.033939 | 0.033939 | 0.033939 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01033 | | | 0.16 Nlocal: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15966 ave 15966 max 15966 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: 678664 ave 678664 max 678664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 678664 Ave neighs/atom = 661.466 Neighbor list builds = 2 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 230 0 -2974.3985 0 -2974.3985 -5778.1816 17056.597 1230 0 -2974.6638 0 -2974.6638 -713.44962 16937.858 Loop time of 28.4162 on 1 procs for 1000 steps with 1026 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 = -2974.39847454 -2974.66376681 -2974.66376682 Force two-norm initial, final = 85.1568 0.0108337 Force max component initial, final = 70.5604 0.010138 Final line search alpha, max atom move = 0.0494075 0.000500891 Iterations, force evaluations = 1000 1994 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.897 | 27.897 | 27.897 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.14389 | 0.14389 | 0.14389 | 0.0 | 0.51 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3751 | | | 1.32 Nlocal: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16022 ave 16022 max 16022 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: 677172 ave 677172 max 677172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 677172 Ave neighs/atom = 660.012 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 7 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 10.46 | 10.46 | 10.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2974.6638 0 -2974.6638 -713.44962 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1026 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: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16054 ave 16054 max 16054 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: 678884 ave 678884 max 678884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 678884 Ave neighs/atom = 661.68 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:52) Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 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 -2974.6638 -2974.6638 45.587934 91.974354 4.0396323 -713.44962 -713.44962 -0.95072143 -2139.5117 0.11357897 2.5491952 712.09177 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1026 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: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16054 ave 16054 max 16054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 339442 ave 339442 max 339442 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 678884 ave 678884 max 678884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 678884 Ave neighs/atom = 661.68 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_030.5102/numatoms.out 1026 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2974.66376682138-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2974.66376682138-1026*${isolated_atom_energy} variable adjusted_pe_metal equal -2974.66376682138-1026*0 print "${adjusted_pe_metal} eV" file output/dump_030.5102/energy.out -2974.66376682138 eV print "${mindist_metal} Angstroms" file output/dump_030.5102/mindistance.out 2.54919519087297 Angstroms write_dump all cfg output/dump_030.5102/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_030.5102/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:35