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 4.032082033157349*${_u_distance} variable lattice_constant_converted equal 4.032082033157349*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 80.03454314051814*${_u_distance} variable xmax_converted equal 80.03454314051814*1 variable ymin_converted equal -80.0385752225513*${_u_distance} variable ymin_converted equal -80.0385752225513*1 variable ymax_converted equal 80.0385752225513*${_u_distance} variable ymax_converted equal 80.0385752225513*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082033157349*${_u_distance} variable zmax_converted equal 4.032082033157349*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03208203315735 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 80.0345431405181 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 80.0345431405181 -80.0385752225513 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 80.0345431405181 -80.0385752225513 80.0385752225513 ${zmin_converted} ${zmax_converted} units box region whole block 0 80.0345431405181 -80.0385752225513 80.0385752225513 0 ${zmax_converted} units box region whole block 0 80.0345431405181 -80.0385752225513 80.0385752225513 0 4.03208203315735 units box create_box 2 whole Created orthogonal box = (0 -80.0386 0) to (80.0345 80.0386 4.03208) 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 80.0385752225513 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 lattice fcc 4.03208203315735 orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68773 5.68773 4.03208 create_atoms 1 region upper Created 1578 atoms create_atoms CPU = 0.000503063 secs group upper type 1 1578 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.932244958575643 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -80.0385752225513 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 lattice fcc 4.03208203315735 orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68773 5.68773 4.03208 create_atoms 2 region lower Created 1578 atoms create_atoms CPU = 0.000388861 secs group lower type 2 1578 atoms in group lower displace_atoms lower move -8.932244958575643 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_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*4.03208203315735 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604101657867 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 22 43 2 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 3120 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 22 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.51 | 10.51 | 10.51 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10437.692 0 -10437.692 -375.09554 438 0 -10464.337 0 -10464.337 -5518.9628 Loop time of 6.01381 on 1 procs for 438 steps with 3120 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 = -10437.6918837 -10464.3372004 -10464.3372004 Force two-norm initial, final = 23.7484 1.17404e-05 Force max component initial, final = 5.83597 1.99357e-06 Final line search alpha, max atom move = 1 1.99357e-06 Iterations, force evaluations = 438 866 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.872 | 5.872 | 5.872 | 0.0 | 97.64 Neigh | 0.010385 | 0.010385 | 0.010385 | 0.0 | 0.17 Comm | 0.079558 | 0.079558 | 0.079558 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05184 | | | 0.86 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17160 ave 17160 max 17160 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: 356640 ave 356640 max 356640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 356640 Ave neighs/atom = 114.308 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) = 10.51 | 10.51 | 10.51 Mbytes Step Temp E_pair E_mol TotEng Press Volume 438 0 -10464.337 0 -10464.337 -5518.9628 51657.832 1438 0 -10464.677 0 -10464.677 -1694.3139 51409.208 Loop time of 14.4446 on 1 procs for 1000 steps with 3120 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 = -10464.3372004 -10464.6774076 -10464.6774076 Force two-norm initial, final = 199.228 0.0218554 Force max component initial, final = 144.267 0.0202591 Final line search alpha, max atom move = 0.0285356 0.000578105 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.645 | 13.645 | 13.645 | 0.0 | 94.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.17158 | 0.17158 | 0.17158 | 0.0 | 1.19 Output | 2.2888e-05 | 2.2888e-05 | 2.2888e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.628 | | | 4.35 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17160 ave 17160 max 17160 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: 347888 ave 347888 max 347888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 347888 Ave neighs/atom = 111.503 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 22 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 9.645 | 9.645 | 9.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10464.677 0 -10464.677 -1694.3139 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3120 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: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17160 ave 17160 max 17160 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: 366072 ave 366072 max 366072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366072 Ave neighs/atom = 117.331 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) = 9.645 | 9.645 | 9.645 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 -10464.677 -10464.677 79.846204 160.07715 4.022141 -1694.3139 -1694.3139 0.014391088 -5082.3262 -0.62982215 2.5043572 861.43824 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3120 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: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17160 ave 17160 max 17160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183036 ave 183036 max 183036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 366072 ave 366072 max 366072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366072 Ave neighs/atom = 117.331 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.8288/numatoms.out 3120 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10464.6774076473-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10464.6774076473-3120*${isolated_atom_energy} variable adjusted_pe_metal equal -10464.6774076473-3120*0 print "${adjusted_pe_metal} eV" file output/dump_081.8288/energy.out -10464.6774076473 eV print "${mindist_metal} Angstroms" file output/dump_081.8288/mindistance.out 2.50435723022315 Angstroms write_dump all cfg output/dump_081.8288/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_081.8288/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:20