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 4.050180745124819*${_u_distance} variable lattice_constant_converted equal 4.050180745124819*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 56.846995711571495*${_u_distance} variable xmax_converted equal 56.846995711571495*1 variable ymin_converted equal -56.85104589231662*${_u_distance} variable ymin_converted equal -56.85104589231662*1 variable ymax_converted equal 56.85104589231662*${_u_distance} variable ymax_converted equal 56.85104589231662*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050180745124819*${_u_distance} variable zmax_converted equal 4.050180745124819*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05018074512482 Lattice spacing in x,y,z = 4.05018 4.05018 4.05018 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 56.8469957115715 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.8469957115715 -56.8510458923166 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.8469957115715 -56.8510458923166 56.8510458923166 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.8469957115715 -56.8510458923166 56.8510458923166 0 ${zmax_converted} units box region whole block 0 56.8469957115715 -56.8510458923166 56.8510458923166 0 4.05018074512482 units box create_box 2 whole Created orthogonal box = (0 -56.851 0) to (56.847 56.851 4.05018) 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 56.8510458923166 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -1 0 orient y 1 14 0 orient z 0 0 1 lattice fcc 4.05018074512482 orient x 14 -1 0 orient y 1 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.32845 4.32845 4.05018 create_atoms 1 region upper Created 790 atoms create_atoms CPU = 0.000224113 secs group upper type 1 790 atoms in group upper mass 1 26.981538*${_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 -56.8510458923166 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 1 0 orient y -1 14 0 orient z 0 0 1 lattice fcc 4.05018074512482 orient x 14 1 0 orient y -1 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.32845 4.32845 4.05018 create_atoms 2 region lower Created 790 atoms create_atoms CPU = 0.000110865 secs group lower type 2 790 atoms in group lower displace_atoms lower move -6.31605098142819 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_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*4.05018074512482 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02509037256241 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 14 28 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 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1552 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 14 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5537.2417 0 -5537.2417 -2833.1491 85 0 -5549.0497 0 -5549.0497 -5390.2555 Loop time of 0.93714 on 1 procs for 85 steps with 1552 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5537.24171396 -5549.04972406 -5549.04972406 Force two-norm initial, final = 6.76044 0.0126821 Force max component initial, final = 1.18105 0.00101771 Final line search alpha, max atom move = 6.10352e-05 6.2116e-08 Iterations, force evaluations = 85 188 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91616 | 0.91616 | 0.91616 | 0.0 | 97.76 Neigh | 0.004035 | 0.004035 | 0.004035 | 0.0 | 0.43 Comm | 0.010859 | 0.010859 | 0.010859 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006083 | | | 0.65 Nlocal: 1552 ave 1552 max 1552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10013 ave 10013 max 10013 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: 217336 ave 217336 max 217336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217336 Ave neighs/atom = 140.036 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) = 5.538 | 5.538 | 5.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -5549.0497 0 -5549.0497 -5390.2555 26178.839 90 0 -5549.2248 0 -5549.2248 -1713.5705 26050.762 Loop time of 0.195008 on 1 procs for 5 steps with 1552 atoms 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5549.04972406 -5549.22476267 -5549.22476267 Force two-norm initial, final = 94.5176 0.166936 Force max component initial, final = 67.6395 0.122454 Final line search alpha, max atom move = 3.57551e-07 4.37837e-08 Iterations, force evaluations = 5 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18675 | 0.18675 | 0.18675 | 0.0 | 95.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019665 | 0.0019665 | 0.0019665 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006289 | | | 3.23 Nlocal: 1552 ave 1552 max 1552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10028 ave 10028 max 10028 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: 217292 ave 217292 max 217292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217292 Ave neighs/atom = 140.008 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 -9.5367431640625e-07 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 14 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 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) = 5.676 | 5.676 | 5.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5549.2248 0 -5549.2248 -1713.5705 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1552 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 | | 1.192e-06 | | |100.00 Nlocal: 1552 ave 1552 max 1552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10041 ave 10041 max 10041 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: 217544 ave 217544 max 217544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217544 Ave neighs/atom = 140.17 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) = 5.676 | 5.676 | 5.676 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 -5549.2248 -5549.2248 56.703894 113.70209 4.0405371 -1713.5705 -1713.5705 5.9197101 -5154.1444 7.513266 2.6369002 244.93836 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1552 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: 1552 ave 1552 max 1552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10041 ave 10041 max 10041 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108772 ave 108772 max 108772 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 217544 ave 217544 max 217544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217544 Ave neighs/atom = 140.17 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_008.1712/numatoms.out 1552 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5549.22476267182-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5549.22476267182-1552*${isolated_atom_energy} variable adjusted_pe_metal equal -5549.22476267182-1552*-9.5367431640625e-07 print "${adjusted_pe_metal} eV" file output/dump_008.1712/energy.out -5549.22328256928 eV print "${mindist_metal} Angstroms" file output/dump_008.1712/mindistance.out 2.63690017019106 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: 0:00:01