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 4.050004702806472*${_u_distance} variable lattice_constant_converted equal 4.050004702806472*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 38.207667951016774*${_u_distance} variable xmax_converted equal 38.207667951016774*1 variable ymin_converted equal -76.41938590673635*${_u_distance} variable ymin_converted equal -76.41938590673635*1 variable ymax_converted equal 76.41938590673635*${_u_distance} variable ymax_converted equal 76.41938590673635*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050004702806472*${_u_distance} variable zmax_converted equal 4.050004702806472*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000470280647 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 38.2076679510168 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 38.2076679510168 -76.4193859067364 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 38.2076679510168 -76.4193859067364 76.4193859067364 ${zmin_converted} ${zmax_converted} units box region whole block 0 38.2076679510168 -76.4193859067364 76.4193859067364 0 ${zmax_converted} units box region whole block 0 38.2076679510168 -76.4193859067364 76.4193859067364 0 4.05000470280647 units box create_box 2 whole Created orthogonal box = (0 -76.4194 0) to (38.2077 76.4194 4.05) 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 76.4193859067364 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -5 0 orient y 5 8 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 8 -5 0 orient y 5 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.5809 5.5809 4.05 create_atoms 1 region upper Created 714 atoms create_atoms CPU = 0.000249147 secs group upper type 1 714 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.245291509425472 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -76.4193859067364 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 5 0 orient y -5 8 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 8 5 0 orient y -5 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.5809 5.5809 4.05 create_atoms 2 region lower Created 714 atoms create_atoms CPU = 0.000135183 secs group lower type 2 714 atoms in group lower displace_atoms lower move -4.245291509425472 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005 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*4.05000470280647 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500235140324 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 10 37 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1412 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 10 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.524 | 5.524 | 5.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4718.1177 0 -4718.1177 -435.27952 482 0 -4733.7933 0 -4733.7933 -3741.6914 Loop time of 3.99594 on 1 procs for 482 steps with 1412 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4718.11771472 -4733.79330806 -4733.79330806 Force two-norm initial, final = 14.2642 3.11501e-07 Force max component initial, final = 3.1729 7.22001e-08 Final line search alpha, max atom move = 1 7.22001e-08 Iterations, force evaluations = 482 947 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8961 | 3.8961 | 3.8961 | 0.0 | 97.50 Neigh | 0.020249 | 0.020249 | 0.020249 | 0.0 | 0.51 Comm | 0.050811 | 0.050811 | 0.050811 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02875 | | | 0.72 Nlocal: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9808 ave 9808 max 9808 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: 196892 ave 196892 max 196892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196892 Ave neighs/atom = 139.442 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) = 5.524 | 5.524 | 5.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 482 0 -4733.7933 0 -4733.7933 -3741.6914 23650.46 1482 0 -4733.9046 0 -4733.9046 -509.52409 23552.955 Loop time of 9.06191 on 1 procs for 1000 steps with 1412 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 = -4733.79330806 -4733.90461666 -4733.90461668 Force two-norm initial, final = 75.8795 0.0167416 Force max component initial, final = 55.3233 0.0109326 Final line search alpha, max atom move = 0.306043 0.00334584 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.6034 | 8.6034 | 8.6034 | 0.0 | 94.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10219 | 0.10219 | 0.10219 | 0.0 | 1.13 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3563 | | | 3.93 Nlocal: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9813 ave 9813 max 9813 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: 196892 ave 196892 max 196892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196892 Ave neighs/atom = 139.442 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 1.04222210722815e-10 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 10 37 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.662 | 5.662 | 5.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4733.9046 0 -4733.9046 -509.52409 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1412 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: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9818 ave 9818 max 9818 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: 196944 ave 196944 max 196944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196944 Ave neighs/atom = 139.479 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) = 5.662 | 5.662 | 5.662 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 -4733.9046 -4733.9046 38.139394 152.83877 4.0405275 -509.52409 -509.52409 -0.5308298 -1527.2995 -0.7419421 2.4803459 649.70833 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1412 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: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9818 ave 9818 max 9818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98472 ave 98472 max 98472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 196944 ave 196944 max 196944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196944 Ave neighs/atom = 139.479 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_064.0108/numatoms.out 1412 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4733.90461668278-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4733.90461668278-1412*${isolated_atom_energy} variable adjusted_pe_metal equal -4733.90461668278-1412*1.04222210722815e-10 print "${adjusted_pe_metal} eV" file output/dump_064.0108/energy.out -4733.90461682994 eV print "${mindist_metal} Angstroms" file output/dump_064.0108/mindistance.out 2.48034591132157 Angstroms write_dump all cfg output/dump_064.0108/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_064.0108/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:13