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 53.80677778918555*${_u_distance} variable xmax_converted equal 53.80677778918555*1 variable ymin_converted equal -53.81081077768913*${_u_distance} variable ymin_converted equal -53.81081077768913*1 variable ymax_converted equal 53.81081077768913*${_u_distance} variable ymax_converted equal 53.81081077768913*1 variable zmin_converted equal 0.0*${_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 53.8067777891856 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.8067777891856 -53.8108107776891 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.8067777891856 -53.8108107776891 53.8108107776891 ${zmin_converted} ${zmax_converted} units box region whole block 0 53.8067777891856 -53.8108107776891 53.8108107776891 0 ${zmax_converted} units box region whole block 0 53.8067777891856 -53.8108107776891 53.8108107776891 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -53.8108 0) to (53.8068 53.8108 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 53.8108107776891 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -3 0 orient y 3 13 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 13 -3 0 orient y 3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.83656 4.83656 4.03299 create_atoms 1 region upper Created 714 atoms create_atoms CPU = 0.000237942 secs group upper type 1 714 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.003748828856851 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -53.8108107776891 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 3 0 orient y -3 13 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 13 3 0 orient y -3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.83656 4.83656 4.03299 create_atoms 2 region lower Created 714 atoms create_atoms CPU = 0.000115871 secs group lower type 2 714 atoms in group lower displace_atoms lower move -6.003748828856851 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 8 16 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 20 atoms, new total = 1408 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 = 8 16 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) = 12.23 | 12.23 | 12.23 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4048.0264 0 -4048.0264 1540.852 388 0 -4086.6622 0 -4086.6622 -4815.1785 Loop time of 14.1713 on 1 procs for 388 steps with 1408 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4048.02644063 -4086.6622296 -4086.6622296 Force two-norm initial, final = 30.2362 7.08851e-06 Force max component initial, final = 5.53062 8.20447e-07 Final line search alpha, max atom move = 1 8.20447e-07 Iterations, force evaluations = 388 766 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.049 | 14.049 | 14.049 | 0.0 | 99.14 Neigh | 0.028173 | 0.028173 | 0.028173 | 0.0 | 0.20 Comm | 0.071397 | 0.071397 | 0.071397 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02223 | | | 0.16 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19944 ave 19944 max 19944 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: 931624 ave 931624 max 931624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 931624 Ave neighs/atom = 661.665 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) = 12.23 | 12.23 | 12.23 Mbytes Step Temp E_pair E_mol TotEng Press Volume 388 0 -4086.6622 0 -4086.6622 -4815.1785 23354.12 1388 0 -4086.9198 0 -4086.9198 -757.42887 23224.642 Loop time of 38.5409 on 1 procs for 1000 steps with 1408 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 = -4086.6622296 -4086.91979271 -4086.91979299 Force two-norm initial, final = 93.7734 0.0546296 Force max component initial, final = 80.0118 0.0467744 Final line search alpha, max atom move = 0.0714789 0.00334338 Iterations, force evaluations = 1000 1994 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.893 | 37.893 | 37.893 | 0.0 | 98.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.17858 | 0.17858 | 0.17858 | 0.0 | 0.46 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4692 | | | 1.22 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19920 ave 19920 max 19920 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: 930384 ave 930384 max 930384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 930384 Ave neighs/atom = 660.784 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 = 8 16 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) = 11.74 | 11.74 | 11.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4086.9198 0 -4086.9198 -757.42887 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1408 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: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19984 ave 19984 max 19984 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: 932992 ave 932992 max 932992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 932992 Ave neighs/atom = 662.636 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) = 11.74 | 11.74 | 11.74 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 -4086.9198 -4086.9198 53.389417 107.62162 4.0419815 -757.42887 -757.42887 -1.1455083 -2267.9071 -3.2339748 2.5500451 803.90117 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1408 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 | | 2.146e-06 | | |100.00 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19984 ave 19984 max 19984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 466496 ave 466496 max 466496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 932992 ave 932992 max 932992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 932992 Ave neighs/atom = 662.636 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.9892/numatoms.out 1408 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4086.91979298869-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4086.91979298869-1408*${isolated_atom_energy} variable adjusted_pe_metal equal -4086.91979298869-1408*0 print "${adjusted_pe_metal} eV" file output/dump_025.9892/energy.out -4086.91979298869 eV print "${mindist_metal} Angstroms" file output/dump_025.9892/mindistance.out 2.55004514713477 Angstroms write_dump all cfg output/dump_025.9892/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_025.9892/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:52