LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.039798453450203*${_u_distance} variable lattice_constant_converted equal 4.039798453450203*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 62.71453692904202*${_u_distance} variable xmax_converted equal 62.71453692904202*1 variable ymin_converted equal -62.71857672749547*${_u_distance} variable ymin_converted equal -62.71857672749547*1 variable ymax_converted equal 62.71857672749547*${_u_distance} variable ymax_converted equal 62.71857672749547*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.039798453450203*${_u_distance} variable zmax_converted equal 4.039798453450203*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0397984534502 Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 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 62.714536929042 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.714536929042 -62.7185767274955 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.714536929042 -62.7185767274955 62.7185767274955 ${zmin_converted} ${zmax_converted} units box region whole block 0 62.714536929042 -62.7185767274955 62.7185767274955 0 ${zmax_converted} units box region whole block 0 62.714536929042 -62.7185767274955 62.7185767274955 0 4.0397984534502 units box create_box 2 whole Created orthogonal box = (0 -62.7186 0) to (62.7145 62.7186 4.0398) 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 62.7185767274955 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9443 4.9443 4.0398 create_atoms 1 region upper Created 965 atoms create_atoms CPU = 0.00029707 secs group upper type 1 965 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.985878613317011 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -62.7185767274955 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9443 4.9443 4.0398 create_atoms 2 region lower Created 965 atoms create_atoms CPU = 0.000156879 secs group lower type 2 965 atoms in group lower displace_atoms lower move -6.985878613317011 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Al__MO_279544746097_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.0397984534502 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0198992267251 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1904 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 11 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.9 | 11.9 | 11.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5421.7517 0 -5421.7517 203.52025 314 0 -5464.877 0 -5464.877 -6093.0156 Loop time of 8.72175 on 1 procs for 314 steps with 1904 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 = -5421.75169364 -5464.87698629 -5464.87698629 Force two-norm initial, final = 24.69 2.87439e-06 Force max component initial, final = 4.42515 4.90508e-07 Final line search alpha, max atom move = 1 4.90508e-07 Iterations, force evaluations = 314 615 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.6212 | 8.6212 | 8.6212 | 0.0 | 98.85 Neigh | 0.024822 | 0.024822 | 0.024822 | 0.0 | 0.28 Comm | 0.054763 | 0.054763 | 0.054763 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02101 | | | 0.24 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19866 ave 19866 max 19866 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: 751562 ave 751562 max 751562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 751562 Ave neighs/atom = 394.728 Neighbor list builds = 2 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) = 11.9 | 11.9 | 11.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 314 0 -5464.877 0 -5464.877 -6093.0156 31780.016 1314 0 -5465.3211 0 -5465.3211 -993.88966 31561.057 Loop time of 28.8201 on 1 procs for 1000 steps with 1904 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 = -5464.87698629 -5465.32103507 -5465.32107222 Force two-norm initial, final = 159.047 0.593493 Force max component initial, final = 127.907 0.567776 Final line search alpha, max atom move = 0.025269 0.0143471 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.165 | 28.165 | 28.165 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.17229 | 0.17229 | 0.17229 | 0.0 | 0.60 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4833 | | | 1.68 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19880 ave 19880 max 19880 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: 746340 ave 746340 max 746340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 746340 Ave neighs/atom = 391.985 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 11.04 | 11.04 | 11.04 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5465.3211 0 -5465.3211 -993.88966 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1904 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: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19894 ave 19894 max 19894 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: 767456 ave 767456 max 767456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 767456 Ave neighs/atom = 403.076 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:52) Per MPI rank memory allocation (min/avg/max) = 11.04 | 11.04 | 11.04 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 -5465.3211 -5465.3211 62.291872 125.43715 4.0391871 -993.88966 -993.88966 -7.8288511 -3002.6586 28.818437 2.5629473 988.4851 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1904 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: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19894 ave 19894 max 19894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 383728 ave 383728 max 383728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 767456 ave 767456 max 767456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 767456 Ave neighs/atom = 403.076 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_029.8628/numatoms.out 1904 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5465.32107221565-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5465.32107221565-1904*${isolated_atom_energy} variable adjusted_pe_metal equal -5465.32107221565-1904*0 print "${adjusted_pe_metal} eV" file output/dump_029.8628/energy.out -5465.32107221565 eV print "${mindist_metal} Angstroms" file output/dump_029.8628/mindistance.out 2.56294732857785 Angstroms write_dump all cfg output/dump_029.8628/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_029.8628/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:37