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 4.061213478446007*${_u_distance} variable lattice_constant_converted equal 4.061213478446007*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 77.58937456180261*${_u_distance} variable xmax_converted equal 77.58937456180261*1 variable ymin_converted equal -77.59343577528107*${_u_distance} variable ymin_converted equal -77.59343577528107*1 variable ymax_converted equal 77.59343577528107*${_u_distance} variable ymax_converted equal 77.59343577528107*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.061213478446007*${_u_distance} variable zmax_converted equal 4.061213478446007*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06121347844601 Lattice spacing in x,y,z = 4.06121 4.06121 4.06121 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 77.5893745618026 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.5893745618026 -77.5934357752811 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.5893745618026 -77.5934357752811 77.5934357752811 ${zmin_converted} ${zmax_converted} units box region whole block 0 77.5893745618026 -77.5934357752811 77.5934357752811 0 ${zmax_converted} units box region whole block 0 77.5893745618026 -77.5934357752811 77.5934357752811 0 4.06121347844601 units box create_box 2 whole Created orthogonal box = (0 -77.5934 0) to (77.5894 77.5934 4.06121) 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 77.5934357752811 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.73949 5.73949 4.06121 create_atoms 1 region upper Created 1462 atoms create_atoms CPU = 0.000346184 secs group upper type 1 1462 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.59723792854426 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -77.5934357752811 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.73949 5.73949 4.06121 create_atoms 2 region lower Created 1462 atoms create_atoms CPU = 0.000303984 secs group lower type 2 1462 atoms in group lower displace_atoms lower move -8.59723792854426 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Al__MO_411898953661_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.06121347844601 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03060673922301 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 16 32 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2892 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 16 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7718.6067 0 -7718.6067 979.70099 456 0 -7797.6603 0 -7797.6603 -6123.534 Loop time of 13.9762 on 1 procs for 456 steps with 2892 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 = -7718.6067057 -7797.66030044 -7797.66030044 Force two-norm initial, final = 33.8458 4.31579e-06 Force max component initial, final = 5.65983 5.35362e-07 Final line search alpha, max atom move = 1 5.35362e-07 Iterations, force evaluations = 456 878 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.743 | 13.743 | 13.743 | 0.0 | 98.33 Neigh | 0.055365 | 0.055365 | 0.055365 | 0.0 | 0.40 Comm | 0.12037 | 0.12037 | 0.12037 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05708 | | | 0.41 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21498 ave 21498 max 21498 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: 647984 ave 647984 max 647984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 647984 Ave neighs/atom = 224.061 Neighbor list builds = 4 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) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 456 0 -7797.6603 0 -7797.6603 -6123.534 48900.472 1456 0 -7798.0816 0 -7798.0816 -2682.5856 48671.277 Loop time of 31.7948 on 1 procs for 1000 steps with 2892 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 = -7797.66030044 -7798.08163682 -7798.08163783 Force two-norm initial, final = 155.815 0.106459 Force max component initial, final = 146.553 0.100611 Final line search alpha, max atom move = 0.0136075 0.00136906 Iterations, force evaluations = 1000 1994 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.817 | 30.817 | 30.817 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.23021 | 0.23021 | 0.23021 | 0.0 | 0.72 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.7477 | | | 2.35 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21504 ave 21504 max 21504 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: 648120 ave 648120 max 648120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 648120 Ave neighs/atom = 224.108 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 16 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7798.0816 0 -7798.0816 -2682.5856 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 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: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21504 ave 21504 max 21504 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: 648392 ave 648392 max 648392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 648392 Ave neighs/atom = 224.202 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) = 10.83 | 10.83 | 10.83 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 -7798.0816 -7798.0816 77.716443 155.18687 4.0355697 -2682.5856 -2682.5856 -1.1333927 -8043.3323 -3.2910293 2.5862356 183.53161 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 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: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21504 ave 21504 max 21504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 324196 ave 324196 max 324196 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 648392 ave 648392 max 648392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 648392 Ave neighs/atom = 224.202 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.7578/numatoms.out 2892 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7798.08163782915-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7798.08163782915-2892*${isolated_atom_energy} variable adjusted_pe_metal equal -7798.08163782915-2892*0 print "${adjusted_pe_metal} eV" file output/dump_085.7578/energy.out -7798.08163782915 eV print "${mindist_metal} Angstroms" file output/dump_085.7578/mindistance.out 2.58623557094793 Angstroms write_dump all cfg output/dump_085.7578/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_085.7578/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:46