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 65.92929997034666*${_u_distance} variable xmax_converted equal 65.92929997034666*1 variable ymin_converted equal -65.93334997504947*${_u_distance} variable ymin_converted equal -65.93334997504947*1 variable ymax_converted equal 65.93334997504947*${_u_distance} variable ymax_converted equal 65.93334997504947*1 variable zmin_converted equal 0.0*${_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 65.9292999703467 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.9292999703467 -65.9333499750495 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.9292999703467 -65.9333499750495 65.9333499750495 ${zmin_converted} ${zmax_converted} units box region whole block 0 65.9292999703467 -65.9333499750495 65.9333499750495 0 ${zmax_converted} units box region whole block 0 65.9292999703467 -65.9333499750495 65.9333499750495 0 4.05000470280647 units box create_box 2 whole Created orthogonal box = (0 -65.9333 0) to (65.9293 65.9333 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 65.9333499750495 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72217 5.72217 4.05 create_atoms 1 region upper Created 1062 atoms create_atoms CPU = 0.0004251 secs group upper type 1 1062 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.325469268244868 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -65.9333499750495 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72217 5.72217 4.05 create_atoms 2 region lower Created 1062 atoms create_atoms CPU = 0.000337124 secs group lower type 2 1062 atoms in group lower displace_atoms lower move -7.325469268244868 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2092 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 = 16 32 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) = 5.655 | 5.655 | 5.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6991.6142 0 -6991.6142 -2205.1098 316 0 -7015.7162 0 -7015.7162 -8716.839 Loop time of 4.20949 on 1 procs for 316 steps with 2092 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6991.61415856 -7015.71622653 -7015.71622653 Force two-norm initial, final = 12.6302 3.07656e-06 Force max component initial, final = 2.12962 3.79701e-07 Final line search alpha, max atom move = 1 3.79701e-07 Iterations, force evaluations = 316 616 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1278 | 4.1278 | 4.1278 | 0.0 | 98.06 Neigh | 0.0084481 | 0.0084481 | 0.0084481 | 0.0 | 0.20 Comm | 0.045244 | 0.045244 | 0.045244 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02805 | | | 0.67 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12607 ave 12607 max 12607 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: 291676 ave 291676 max 291676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291676 Ave neighs/atom = 139.424 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) = 5.655 | 5.655 | 5.655 Mbytes Step Temp E_pair E_mol TotEng Press Volume 316 0 -7015.7162 0 -7015.7162 -8716.839 35210.252 1316 0 -7016.2515 0 -7016.2515 -2929.6598 34949.66 Loop time of 13.1192 on 1 procs for 1000 steps with 2092 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 = -7015.71622653 -7016.25153921 -7016.25153921 Force two-norm initial, final = 203.599 0.00148301 Force max component initial, final = 144.768 0.00147395 Final line search alpha, max atom move = 0.384088 0.000566126 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.524 | 12.524 | 12.524 | 0.0 | 95.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13175 | 0.13175 | 0.13175 | 0.0 | 1.00 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4635 | | | 3.53 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12631 ave 12631 max 12631 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: 292344 ave 292344 max 292344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292344 Ave neighs/atom = 139.744 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 = 16 32 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) = 5.793 | 5.793 | 5.793 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7016.2515 0 -7016.2515 -2929.6598 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12649 ave 12649 max 12649 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: 292516 ave 292516 max 292516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292516 Ave neighs/atom = 139.826 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) = 5.793 | 5.793 | 5.793 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 -7016.2515 -7016.2515 65.698643 131.8667 4.0341441 -2929.6598 -2929.6598 -0.0054958971 -8788.9067 -0.067304747 2.6194315 277.56411 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12649 ave 12649 max 12649 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146258 ave 146258 max 146258 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 292516 ave 292516 max 292516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292516 Ave neighs/atom = 139.826 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.0209/numatoms.out 2092 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7016.2515392124-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7016.2515392124-2092*${isolated_atom_energy} variable adjusted_pe_metal equal -7016.2515392124-2092*1.04222210722815e-10 print "${adjusted_pe_metal} eV" file output/dump_085.0209/energy.out -7016.25153943043 eV print "${mindist_metal} Angstroms" file output/dump_085.0209/mindistance.out 2.61943145584873 Angstroms write_dump all cfg output/dump_085.0209/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_085.0209/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:17