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 4.050199627876282*${_u_distance} variable lattice_constant_converted equal 4.050199627876282*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 40.70400250086675*${_u_distance} variable xmax_converted equal 40.70400250086675*1 variable ymin_converted equal -40.708052700494626*${_u_distance} variable ymin_converted equal -40.708052700494626*1 variable ymax_converted equal 40.708052700494626*${_u_distance} variable ymax_converted equal 40.708052700494626*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050199627876282*${_u_distance} variable zmax_converted equal 4.050199627876282*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05019962787628 Lattice spacing in x,y,z = 4.0502 4.0502 4.0502 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 40.7040025008667 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 40.7040025008667 -40.7080527004946 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 40.7040025008667 -40.7080527004946 40.7080527004946 ${zmin_converted} ${zmax_converted} units box region whole block 0 40.7040025008667 -40.7080527004946 40.7080527004946 0 ${zmax_converted} units box region whole block 0 40.7040025008667 -40.7080527004946 40.7080527004946 0 4.05019962787628 units box create_box 2 whole Created orthogonal box = (0 -40.7081 0) to (40.704 40.7081 4.0502) 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 40.7080527004946 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -1 0 orient y 1 10 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 10 -1 0 orient y 1 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.43311 4.43311 4.0502 create_atoms 1 region upper Created 406 atoms create_atoms CPU = 0.000228882 secs group upper type 1 406 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.522444029504401 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -40.7080527004946 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 1 0 orient y -1 10 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 10 1 0 orient y -1 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.43311 4.43311 4.0502 create_atoms 2 region lower Created 406 atoms create_atoms CPU = 0.000102997 secs group lower type 2 406 atoms in group lower displace_atoms lower move -4.522444029504401 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Al__MO_060567868558_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*4.05019962787628 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02509981393814 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 = 10 20 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 16 atoms, new total = 796 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 = 10 20 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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2835.2608 0 -2835.2608 -677.49329 106 0 -2844.1076 0 -2844.1076 -2288.0396 Loop time of 0.591709 on 1 procs for 106 steps with 796 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2835.26078228 -2844.10755461 -2844.10755461 Force two-norm initial, final = 10.3248 0.00601554 Force max component initial, final = 3.21286 0.000877052 Final line search alpha, max atom move = 0.000244141 2.14124e-07 Iterations, force evaluations = 106 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57533 | 0.57533 | 0.57533 | 0.0 | 97.23 Neigh | 0.0045609 | 0.0045609 | 0.0045609 | 0.0 | 0.77 Comm | 0.0074592 | 0.0074592 | 0.0074592 | 0.0 | 1.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004359 | | | 0.74 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5975 ave 5975 max 5975 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: 111504 ave 111504 max 111504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111504 Ave neighs/atom = 140.08 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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -2844.1076 0 -2844.1076 -2288.0396 13422.205 112 0 -2844.1198 0 -2844.1198 -1067.0087 13400.105 Loop time of 0.109392 on 1 procs for 6 steps with 796 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2844.10755461 -2844.1198293 -2844.1198293 Force two-norm initial, final = 15.9516 0.253307 Force max component initial, final = 12.0682 0.23178 Final line search alpha, max atom move = 1.59679e-07 3.70104e-08 Iterations, force evaluations = 6 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10429 | 0.10429 | 0.10429 | 0.0 | 95.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012312 | 0.0012312 | 0.0012312 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003868 | | | 3.54 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6005 ave 6005 max 6005 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: 111568 ave 111568 max 111568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111568 Ave neighs/atom = 140.161 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 10 20 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2844.1198 0 -2844.1198 -1067.0087 Loop time of 9.53674e-07 on 1 procs for 0 steps with 796 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: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6005 ave 6005 max 6005 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: 111604 ave 111604 max 111604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111604 Ave neighs/atom = 140.206 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) = 5.089 | 5.089 | 5.089 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 -2844.1198 -2844.1198 40.663276 81.416105 4.0475807 -1067.0087 -1067.0087 -11.998088 -3216.7227 27.694706 2.6063909 246.53643 Loop time of 1.19209e-06 on 1 procs for 0 steps with 796 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: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6005 ave 6005 max 6005 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55802 ave 55802 max 55802 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111604 ave 111604 max 111604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111604 Ave neighs/atom = 140.206 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_011.4212/numatoms.out 796 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2844.11982929819-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2844.11982929819-796*${isolated_atom_energy} variable adjusted_pe_metal equal -2844.11982929819-796*0 print "${adjusted_pe_metal} eV" file output/dump_011.4212/energy.out -2844.11982929819 eV print "${mindist_metal} Angstroms" file output/dump_011.4212/mindistance.out 2.60639085542334 Angstroms write_dump all cfg output/dump_011.4212/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_011.4212/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00