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 4.040926471352577*${_u_distance} variable lattice_constant_converted equal 4.040926471352577*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 56.71710578947911*${_u_distance} variable xmax_converted equal 56.71710578947911*1 variable ymin_converted equal -56.72114671595047*${_u_distance} variable ymin_converted equal -56.72114671595047*1 variable ymax_converted equal 56.72114671595047*${_u_distance} variable ymax_converted equal 56.72114671595047*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.040926471352577*${_u_distance} variable zmax_converted equal 4.040926471352577*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04092647135258 Lattice spacing in x,y,z = 4.04093 4.04093 4.04093 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 56.7171057894791 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.7171057894791 -56.7211467159505 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.7171057894791 -56.7211467159505 56.7211467159505 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.7171057894791 -56.7211467159505 56.7211467159505 0 ${zmax_converted} units box region whole block 0 56.7171057894791 -56.7211467159505 56.7211467159505 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -56.7211 0) to (56.7171 56.7211 4.04093) 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 56.7211467159505 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -1 0 orient y 1 14 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 14 -1 0 orient y 1 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.31856 4.31856 4.04093 create_atoms 1 region upper Created 789 atoms create_atoms CPU = 0.000299931 secs group upper type 1 789 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.31605098142819 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.7211467159505 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 1 0 orient y -1 14 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 14 1 0 orient y -1 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.31856 4.31856 4.04093 create_atoms 2 region lower Created 789 atoms create_atoms CPU = 0.000152111 secs group lower type 2 789 atoms in group lower displace_atoms lower move -6.31605098142819 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_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*4.04092647135258 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02046323567629 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 23 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 27 atoms, new total = 1551 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6029.2518 0 -6029.2518 -2083.4016 197 0 -6043.6233 0 -6043.6233 -8491.4172 Loop time of 3.82933 on 1 procs for 197 steps with 1551 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 = -6029.25178492 -6043.62325387 -6043.62325387 Force two-norm initial, final = 9.99714 4.43775e-05 Force max component initial, final = 2.2699 1.02531e-05 Final line search alpha, max atom move = 1 1.02531e-05 Iterations, force evaluations = 197 387 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7805 | 3.7805 | 3.7805 | 0.0 | 98.72 Neigh | 0.0068889 | 0.0068889 | 0.0068889 | 0.0 | 0.18 Comm | 0.028609 | 0.028609 | 0.028609 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01336 | | | 0.35 Nlocal: 1551 ave 1551 max 1551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13218 ave 13218 max 13218 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: 378538 ave 378538 max 378538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 378538 Ave neighs/atom = 244.061 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) = 5.965 | 5.965 | 5.965 Mbytes Step Temp E_pair E_mol TotEng Press Volume 197 0 -6043.6233 0 -6043.6233 -8491.4172 25999.8 1197 0 -6043.9643 0 -6043.9643 -3011.7941 25823.353 Loop time of 21.3514 on 1 procs for 1000 steps with 1551 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 = -6043.62325387 -6043.96428107 -6043.96428107 Force two-norm initial, final = 141.182 0.00902113 Force max component initial, final = 100.386 0.00832874 Final line search alpha, max atom move = 0.433885 0.00361372 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.768 | 20.768 | 20.768 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13956 | 0.13956 | 0.13956 | 0.0 | 0.65 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4439 | | | 2.08 Nlocal: 1551 ave 1551 max 1551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13228 ave 13228 max 13228 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: 378828 ave 378828 max 378828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 378828 Ave neighs/atom = 244.248 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.103 | 6.103 | 6.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6043.9643 0 -6043.9643 -3011.7941 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1551 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: 1551 ave 1551 max 1551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13237 ave 13237 max 13237 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: 380140 ave 380140 max 380140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 380140 Ave neighs/atom = 245.093 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) = 6.103 | 6.103 | 6.103 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 -6043.9643 -6043.9643 56.521603 113.44229 4.0273851 -3011.7941 -3011.7941 0.51496471 -9035.9418 0.044424794 2.6178943 267.11228 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1551 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: 1551 ave 1551 max 1551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13237 ave 13237 max 13237 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 190070 ave 190070 max 190070 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 380140 ave 380140 max 380140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 380140 Ave neighs/atom = 245.093 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_008.1712/numatoms.out 1551 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6043.96428107483-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6043.96428107483-1551*${isolated_atom_energy} variable adjusted_pe_metal equal -6043.96428107483-1551*0 print "${adjusted_pe_metal} eV" file output/dump_008.1712/energy.out -6043.96428107483 eV print "${mindist_metal} Angstroms" file output/dump_008.1712/mindistance.out 2.61789429608115 Angstroms write_dump all cfg output/dump_008.1712/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_008.1712/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:25