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 4.045270472764969*${_u_distance} variable lattice_constant_converted equal 4.045270472764969*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 83.00201055567238*${_u_distance} variable xmax_converted equal 83.00201055567238*1 variable ymin_converted equal -83.00605582614514*${_u_distance} variable ymin_converted equal -83.00605582614514*1 variable ymax_converted equal 83.00605582614514*${_u_distance} variable ymax_converted equal 83.00605582614514*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045270472764969*${_u_distance} variable zmax_converted equal 4.045270472764969*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04527047276497 Lattice spacing in x,y,z = 4.04527 4.04527 4.04527 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 83.0020105556724 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0020105556724 -83.0060558261451 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0020105556724 -83.0060558261451 83.0060558261451 ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0020105556724 -83.0060558261451 83.0060558261451 0 ${zmax_converted} units box region whole block 0 83.0020105556724 -83.0060558261451 83.0060558261451 0 4.04527047276497 units box create_box 2 whole Created orthogonal box = (0 -83.0061 0) to (83.002 83.0061 4.04527) 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 83.0060558261451 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71748 5.71748 4.04527 create_atoms 1 region upper Created 1686 atoms create_atoms CPU = 0.000617027 secs group upper type 1 1686 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 9.233228037907434 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -83.0060558261451 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71748 5.71748 4.04527 create_atoms 2 region lower Created 1686 atoms create_atoms CPU = 0.000455856 secs group lower type 2 1686 atoms in group lower displace_atoms lower move -9.233228037907434 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_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*4.04527047276497 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02263523638248 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 18 35 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 38 atoms, new total = 3334 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 18 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.81 | 11.81 | 11.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11327.499 0 -11327.499 -1321.2203 356 0 -11355.179 0 -11355.179 -5298.5367 Loop time of 11.0227 on 1 procs for 356 steps with 3334 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 = -11327.4993993 -11355.1790746 -11355.1790746 Force two-norm initial, final = 18.5653 2.79293e-06 Force max component initial, final = 3.51807 3.32577e-07 Final line search alpha, max atom move = 1 3.32577e-07 Iterations, force evaluations = 356 695 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.859 | 10.859 | 10.859 | 0.0 | 98.52 Neigh | 0.013265 | 0.013265 | 0.013265 | 0.0 | 0.12 Comm | 0.10011 | 0.10011 | 0.10011 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05019 | | | 0.46 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23544 ave 23544 max 23544 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: 703232 ave 703232 max 703232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 703232 Ave neighs/atom = 210.927 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) = 11.81 | 11.81 | 11.81 Mbytes Step Temp E_pair E_mol TotEng Press Volume 356 0 -11355.179 0 -11355.179 -5298.5367 55741.153 1356 0 -11355.512 0 -11355.512 -1798.6516 55493.475 Loop time of 32.7121 on 1 procs for 1000 steps with 3334 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 = -11355.1790746 -11355.5120066 -11355.5120066 Force two-norm initial, final = 195.964 0.00350589 Force max component initial, final = 158.177 0.00267481 Final line search alpha, max atom move = 0.504469 0.00134936 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.683 | 31.683 | 31.683 | 0.0 | 96.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.23624 | 0.23624 | 0.23624 | 0.0 | 0.72 Output | 2.3842e-05 | 2.3842e-05 | 2.3842e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.7928 | | | 2.42 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 22240 ave 22240 max 22240 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: 703380 ave 703380 max 703380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 703380 Ave neighs/atom = 210.972 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 18 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11355.512 0 -11355.512 -1798.6516 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 22546 ave 22546 max 22546 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: 709124 ave 709124 max 709124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 709124 Ave neighs/atom = 212.695 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) = 11.31 | 11.31 | 11.31 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 -11355.512 -11355.512 82.915836 166.01211 4.0314815 -1798.6516 -1798.6516 -0.023431616 -5395.8544 -0.076962239 2.5864036 338.49267 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 22546 ave 22546 max 22546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 354562 ave 354562 max 354562 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 709124 ave 709124 max 709124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 709124 Ave neighs/atom = 212.695 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_086.0501/numatoms.out 3334 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11355.5120065794-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11355.5120065794-3334*${isolated_atom_energy} variable adjusted_pe_metal equal -11355.5120065794-3334*0 print "${adjusted_pe_metal} eV" file output/dump_086.0501/energy.out -11355.5120065794 eV print "${mindist_metal} Angstroms" file output/dump_086.0501/mindistance.out 2.58640356268258 Angstroms write_dump all cfg output/dump_086.0501/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_086.0501/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:44