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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 57.98715936886292*${_u_distance} variable xmax_converted equal 57.98715936886292*1 variable ymin_converted equal -57.9912093677498*${_u_distance} variable ymin_converted equal -57.9912093677498*1 variable ymax_converted equal 57.9912093677498*${_u_distance} variable ymax_converted equal 57.9912093677498*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 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 57.9871593688629 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.9871593688629 -57.9912093677498 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.9871593688629 -57.9912093677498 57.9912093677498 ${zmin_converted} ${zmax_converted} units box region whole block 0 57.9871593688629 -57.9912093677498 57.9912093677498 0 ${zmax_converted} units box region whole block 0 57.9871593688629 -57.9912093677498 57.9912093677498 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -57.9912 0) to (57.9872 57.9912 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 57.9912093677498 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -3 0 orient y 3 14 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 14 -3 0 orient y 3 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.80869 4.80869 4.05 create_atoms 1 region upper Created 822 atoms create_atoms CPU = 0.000316858 secs group upper type 1 822 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.44301947847436 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -57.9912093677498 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 3 0 orient y -3 14 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 14 3 0 orient y -3 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.80869 4.80869 4.05 create_atoms 2 region lower Created 822 atoms create_atoms CPU = 0.000204086 secs group lower type 2 822 atoms in group lower displace_atoms lower move -6.44301947847436 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_721930391003_000-files/b'AlU-library.meam' Al U ./SM_721930391003_000-files/b'AlU.meam' 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 ghost atom cutoff = 7 binsize = 3.5, bins = 17 34 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 24 atoms, new total = 1620 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 ghost atom cutoff = 7 binsize = 3.5, bins = 17 34 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 13.62 | 13.62 | 13.62 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5389.5568 0 -5389.5568 3947.5809 310 0 -5422.608 0 -5422.608 -3334.9197 Loop time of 10.4275 on 1 procs for 310 steps with 1620 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 = -5389.55684888 -5422.60796378 -5422.60796378 Force two-norm initial, final = 43.1895 1.97314e-05 Force max component initial, final = 10.2017 3.51326e-06 Final line search alpha, max atom move = 1 3.51326e-06 Iterations, force evaluations = 310 615 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.371 | 10.371 | 10.371 | 0.0 | 99.46 Neigh | 0.003581 | 0.003581 | 0.003581 | 0.0 | 0.03 Comm | 0.030778 | 0.030778 | 0.030778 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02195 | | | 0.21 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488 ave 8488 max 8488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63644 ave 63644 max 63644 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127288 ave 127288 max 127288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127288 Ave neighs/atom = 78.5728 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) = 13.64 | 13.64 | 13.64 Mbytes Step Temp E_pair E_mol TotEng Press Volume 310 0 -5422.608 0 -5422.608 -3334.9197 27238.231 1310 0 -5422.6912 0 -5422.6912 -866.63439 27148.217 Loop time of 33.861 on 1 procs for 1000 steps with 1620 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 = -5422.60796378 -5422.69121423 -5422.69121424 Force two-norm initial, final = 67.1439 0.0194026 Force max component initial, final = 53.2616 0.0147799 Final line search alpha, max atom move = 0.101403 0.00149873 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.424 | 33.424 | 33.424 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.091953 | 0.091953 | 0.091953 | 0.0 | 0.27 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3446 | | | 1.02 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8429 ave 8429 max 8429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63648 ave 63648 max 63648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127296 ave 127296 max 127296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127296 Ave neighs/atom = 78.5778 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 ghost atom cutoff = 7 binsize = 3.5, bins = 17 34 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5422.6912 0 -5422.6912 -866.63439 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1620 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: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8459 ave 8459 max 8459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64020 ave 64020 max 64020 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128040 ave 128040 max 128040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128040 Ave neighs/atom = 79.037 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) = 12.52 | 12.52 | 12.52 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 -5422.6912 -5422.6912 57.939432 115.98242 4.0399401 -866.63439 -866.63439 -0.87153147 -2598.859 -0.17262997 2.5033546 850.41051 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1620 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: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8459 ave 8459 max 8459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64020 ave 64020 max 64020 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128040 ave 128040 max 128040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128040 Ave neighs/atom = 79.037 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_024.1895/numatoms.out 1620 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5422.69121424494-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5422.69121424494-1620*${isolated_atom_energy} variable adjusted_pe_metal equal -5422.69121424494-1620*0 print "${adjusted_pe_metal} eV" file output/dump_024.1895/energy.out -5422.69121424494 eV print "${mindist_metal} Angstroms" file output/dump_024.1895/mindistance.out 2.50335458021485 Angstroms write_dump all cfg output/dump_024.1895/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_024.1895/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:44