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 12.90732619730583*${_u_distance} variable xmax_converted equal 12.90732619730583*1 variable ymin_converted equal -51.633386444151945*${_u_distance} variable ymin_converted equal -51.633386444151945*1 variable ymax_converted equal 51.633386444151945*${_u_distance} variable ymax_converted equal 51.633386444151945*1 variable zmin_converted equal 0.0*${_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 12.9073261973058 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.9073261973058 -51.6333864441519 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.9073261973058 -51.6333864441519 51.6333864441519 ${zmin_converted} ${zmax_converted} units box region whole block 0 12.9073261973058 -51.6333864441519 51.6333864441519 0 ${zmax_converted} units box region whole block 0 12.9073261973058 -51.6333864441519 51.6333864441519 0 4.08165492862463 units box create_box 2 whole Created orthogonal box = (0 -51.6334 0) to (12.9073 51.6334 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 51.6333864441519 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.16293 5.16293 4.08165 create_atoms 1 region upper Created 162 atoms create_atoms CPU = 0.000218153 secs group upper type 1 162 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.4230249470757705 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.6333864441519 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.16293 5.16293 4.08165 create_atoms 2 region lower Created 162 atoms create_atoms CPU = 6.50883e-05 secs group lower type 2 162 atoms in group lower displace_atoms lower move -1.4230249470757705 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 3 18 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 6 atoms, new total = 318 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 = 3 18 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) = 4.925 | 4.925 | 4.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1129.2743 0 -1129.2743 3814.7898 333 0 -1135.8623 0 -1135.8623 -365.92162 Loop time of 2.75831 on 1 procs for 333 steps with 318 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 = -1129.27430196 -1135.86227834 -1135.86227834 Force two-norm initial, final = 11.6701 4.54633e-06 Force max component initial, final = 2.94872 1.20667e-06 Final line search alpha, max atom move = 1 1.20667e-06 Iterations, force evaluations = 333 657 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7175 | 2.7175 | 2.7175 | 0.0 | 98.52 Neigh | 0.003222 | 0.003222 | 0.003222 | 0.0 | 0.12 Comm | 0.028835 | 0.028835 | 0.028835 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008712 | | | 0.32 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7634 ave 7634 max 7634 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: 135320 ave 135320 max 135320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135320 Ave neighs/atom = 425.535 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) = 4.925 | 4.925 | 4.925 Mbytes Step Temp E_pair E_mol TotEng Press Volume 333 0 -1135.8623 0 -1135.8623 -365.92162 5440.4294 1333 0 -1135.8643 0 -1135.8643 629.22129 5434.6028 Loop time of 8.65229 on 1 procs for 1000 steps with 318 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1135.86227834 -1135.86430759 -1135.86430759 Force two-norm initial, final = 5.24461 0.001676 Force max component initial, final = 3.9775 0.00122414 Final line search alpha, max atom move = 0.428197 0.000524173 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3457 | 8.3457 | 8.3457 | 0.0 | 96.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.079443 | 0.079443 | 0.079443 | 0.0 | 0.92 Output | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2271 | | | 2.62 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7538 ave 7538 max 7538 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: 135328 ave 135328 max 135328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135328 Ave neighs/atom = 425.56 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 = 3 18 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) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1135.8643 0 -1135.8643 629.22129 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7545 ave 7545 max 7545 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: 135360 ave 135360 max 135360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135360 Ave neighs/atom = 425.66 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) = 5.063 | 5.063 | 5.063 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 -1135.8643 -1135.8643 12.898335 103.26677 4.0801259 629.22129 629.22129 -0.36063753 1888.0918 -0.067292849 2.5646185 208.62222 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7545 ave 7545 max 7545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67680 ave 67680 max 67680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135360 ave 135360 max 135360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135360 Ave neighs/atom = 425.66 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_036.8699/numatoms.out 318 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1135.86430758791-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1135.86430758791-318*${isolated_atom_energy} variable adjusted_pe_metal equal -1135.86430758791-318*2.2204e-16 print "${adjusted_pe_metal} eV" file output/dump_036.8699/energy.out -1135.86430758791 eV print "${mindist_metal} Angstroms" file output/dump_036.8699/mindistance.out 2.56461851116244 Angstroms write_dump all cfg output/dump_036.8699/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_036.8699/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11