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 4.032082714140415*${_u_distance} variable lattice_constant_converted equal 4.032082714140415*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 20.160413570702076*${_u_distance} variable xmax_converted equal 20.160413570702076*1 variable ymin_converted equal -40.32485922411829*${_u_distance} variable ymin_converted equal -40.32485922411829*1 variable ymax_converted equal 40.32485922411829*${_u_distance} variable ymax_converted equal 40.32485922411829*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082714140415*${_u_distance} variable zmax_converted equal 4.032082714140415*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03208271414042 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 20.1604135707021 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.1604135707021 -40.3248592241183 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.1604135707021 -40.3248592241183 40.3248592241183 ${zmin_converted} ${zmax_converted} units box region whole block 0 20.1604135707021 -40.3248592241183 40.3248592241183 0 ${zmax_converted} units box region whole block 0 20.1604135707021 -40.3248592241183 40.3248592241183 0 4.03208271414042 units box create_box 2 whole Created orthogonal box = (0 -40.3249 0) to (20.1604 40.3249 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 40.3248592241183 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 -3 0 orient y 3 4 0 orient z 0 0 1 lattice fcc 4.03208271414042 orient x 4 -3 0 orient y 3 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64492 5.64492 4.03208 create_atoms 1 region upper Created 201 atoms create_atoms CPU = 0.000159025 secs group upper type 1 201 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.25 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -40.3248592241183 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 3 0 orient y -3 4 0 orient z 0 0 1 lattice fcc 4.03208271414042 orient x 4 3 0 orient y -3 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64492 5.64492 4.03208 create_atoms 2 region lower Created 201 atoms create_atoms CPU = 5.29289e-05 secs group lower type 2 201 atoms in group lower displace_atoms lower move -2.25 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_ErcolessiAdams_1994_Al__MO_324507536345_002 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.03208271414042 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604135707021 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 = 6 22 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 10 atoms, new total = 392 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 = 6 22 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1302.4599 0 -1302.4599 1567.9519 207 0 -1312.2931 0 -1312.2931 -10653.153 Loop time of 0.50015 on 1 procs for 207 steps with 392 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1302.45994874 -1312.29307224 -1312.29307224 Force two-norm initial, final = 16.8686 5.63365e-07 Force max component initial, final = 5.27061 2.208e-07 Final line search alpha, max atom move = 1 2.208e-07 Iterations, force evaluations = 207 407 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48853 | 0.48853 | 0.48853 | 0.0 | 97.68 Neigh | 0.00090981 | 0.00090981 | 0.00090981 | 0.0 | 0.18 Comm | 0.0069845 | 0.0069845 | 0.0069845 | 0.0 | 1.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003725 | | | 0.74 Nlocal: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3708 ave 3708 max 3708 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: 42130 ave 42130 max 42130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42130 Ave neighs/atom = 107.474 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press Volume 207 0 -1312.2931 0 -1312.2931 -10653.153 6555.891 1207 0 -1312.4929 0 -1312.4929 -2603.2019 6488.3737 Loop time of 3.01136 on 1 procs for 1000 steps with 392 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 = -1312.29307224 -1312.49290607 -1312.49290607 Force two-norm initial, final = 53.7753 0.000462797 Force max component initial, final = 41.1549 0.00028106 Final line search alpha, max atom move = 1 0.00028106 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8436 | 2.8436 | 2.8436 | 0.0 | 94.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.038753 | 0.038753 | 0.038753 | 0.0 | 1.29 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.129 | | | 4.28 Nlocal: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3718 ave 3718 max 3718 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: 41572 ave 41572 max 41572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41572 Ave neighs/atom = 106.051 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 = 6 22 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) = 4.59 | 4.59 | 4.59 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1312.4929 0 -1312.4929 -2603.2019 Loop time of 9.53674e-07 on 1 procs for 0 steps with 392 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: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3718 ave 3718 max 3718 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: 45428 ave 45428 max 45428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45428 Ave neighs/atom = 115.888 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) = 4.59 | 4.59 | 4.59 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 -1312.4929 -1312.4929 20.039032 80.649718 4.0147292 -2603.2019 -2603.2019 0.068984469 -7809.6223 -0.052337337 2.5327926 247.4002 Loop time of 9.53674e-07 on 1 procs for 0 steps with 392 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: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3718 ave 3718 max 3718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22714 ave 22714 max 22714 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45428 ave 45428 max 45428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45428 Ave neighs/atom = 115.888 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_073.7398/numatoms.out 392 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1312.49290606552-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1312.49290606552-392*${isolated_atom_energy} variable adjusted_pe_metal equal -1312.49290606552-392*0 print "${adjusted_pe_metal} eV" file output/dump_073.7398/energy.out -1312.49290606552 eV print "${mindist_metal} Angstroms" file output/dump_073.7398/mindistance.out 2.53279264783116 Angstroms write_dump all cfg output/dump_073.7398/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_073.7398/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03