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 44.73376406380368*${_u_distance} variable xmax_converted equal 44.73376406380368*1 variable ymin_converted equal -44.73781406850649*${_u_distance} variable ymin_converted equal -44.73781406850649*1 variable ymax_converted equal 44.73781406850649*${_u_distance} variable ymax_converted equal 44.73781406850649*1 variable zmin_converted equal 0.0*${_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 44.7337640638037 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 44.7337640638037 -44.7378140685065 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 44.7337640638037 -44.7378140685065 44.7378140685065 ${zmin_converted} ${zmax_converted} units box region whole block 0 44.7337640638037 -44.7378140685065 44.7378140685065 0 ${zmax_converted} units box region whole block 0 44.7337640638037 -44.7378140685065 44.7378140685065 0 4.05000470280647 units box create_box 2 whole Created orthogonal box = (0 -44.7378 0) to (44.7338 44.7378 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 44.7378140685065 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -1 0 orient y 1 11 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 11 -1 0 orient y 1 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.40004 4.40004 4.05 create_atoms 1 region upper Created 490 atoms create_atoms CPU = 0.000212908 secs group upper type 1 490 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.970412457734268 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -44.7378140685065 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 1 0 orient y -1 11 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 11 1 0 orient y -1 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.40004 4.40004 4.05 create_atoms 2 region lower Created 490 atoms create_atoms CPU = 6.81877e-05 secs group lower type 2 490 atoms in group lower displace_atoms lower move -4.970412457734268 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 11 22 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 18 atoms, new total = 962 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 = 11 22 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 | 5 | 5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3208.2759 0 -3208.2759 -661.17161 182 0 -3222.1257 0 -3222.1257 -8109.5679 Loop time of 1.04603 on 1 procs for 182 steps with 962 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3208.27594897 -3222.125707 -3222.125707 Force two-norm initial, final = 12.6031 2.83912e-06 Force max component initial, final = 3.61005 4.0804e-07 Final line search alpha, max atom move = 1 4.0804e-07 Iterations, force evaluations = 182 356 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0215 | 1.0215 | 1.0215 | 0.0 | 97.66 Neigh | 0.003623 | 0.003623 | 0.003623 | 0.0 | 0.35 Comm | 0.013237 | 0.013237 | 0.013237 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007619 | | | 0.73 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6858 ave 6858 max 6858 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: 134192 ave 134192 max 134192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134192 Ave neighs/atom = 139.493 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) = 5 | 5 | 5 Mbytes Step Temp E_pair E_mol TotEng Press Volume 182 0 -3222.1257 0 -3222.1257 -8109.5679 16210.474 1182 0 -3222.3917 0 -3222.3917 -2137.3788 16086.481 Loop time of 6.14791 on 1 procs for 1000 steps with 962 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3222.125707 -3222.39170432 -3222.39170438 Force two-norm initial, final = 95.4999 0.0193006 Force max component initial, final = 73.7734 0.0130376 Final line search alpha, max atom move = 0.0928262 0.00121023 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8336 | 5.8336 | 5.8336 | 0.0 | 94.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.070846 | 0.070846 | 0.070846 | 0.0 | 1.15 Output | 4.8876e-05 | 4.8876e-05 | 4.8876e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2434 | | | 3.96 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6853 ave 6853 max 6853 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: 134140 ave 134140 max 134140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134140 Ave neighs/atom = 139.439 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 = 11 22 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) = 5.138 | 5.138 | 5.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3222.3917 0 -3222.3917 -2137.3788 Loop time of 1.19209e-06 on 1 procs for 0 steps with 962 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: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6868 ave 6868 max 6868 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: 134224 ave 134224 max 134224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134224 Ave neighs/atom = 139.526 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) = 5.138 | 5.138 | 5.138 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 -3222.3917 -3222.3917 44.613765 89.475628 4.0298365 -2137.3788 -2137.3788 1.2203509 -6414.6487 1.292052 2.5762685 395.51094 Loop time of 1.90735e-06 on 1 procs for 0 steps with 962 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 | | 1.907e-06 | | |100.00 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6868 ave 6868 max 6868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67112 ave 67112 max 67112 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134224 ave 134224 max 134224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134224 Ave neighs/atom = 139.526 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_010.3889/numatoms.out 962 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3222.39170437786-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3222.39170437786-962*${isolated_atom_energy} variable adjusted_pe_metal equal -3222.39170437786-962*1.04222210722815e-10 print "${adjusted_pe_metal} eV" file output/dump_010.3889/energy.out -3222.39170447812 eV print "${mindist_metal} Angstroms" file output/dump_010.3889/mindistance.out 2.57626850947344 Angstroms write_dump all cfg output/dump_010.3889/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_010.3889/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:07