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 28.639102699089435*${_u_distance} variable xmax_converted equal 28.639102699089435*1 variable ymin_converted equal -57.282255578923994*${_u_distance} variable ymin_converted equal -57.282255578923994*1 variable ymax_converted equal 57.282255578923994*${_u_distance} variable ymax_converted equal 57.282255578923994*1 variable zmin_converted equal 0.0*${_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 28.6391026990894 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.6391026990894 -57.282255578924 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.6391026990894 -57.282255578924 57.282255578924 ${zmin_converted} ${zmax_converted} units box region whole block 0 28.6391026990894 -57.282255578924 57.282255578924 0 ${zmax_converted} units box region whole block 0 28.6391026990894 -57.282255578924 57.282255578924 0 4.05018074512482 units box create_box 2 whole Created orthogonal box = (0 -57.2823 0) to (28.6391 57.2823 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 57.282255578924 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 lattice fcc 4.05018074512482 orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.58226 4.58226 4.05018 create_atoms 1 region upper Created 402 atoms create_atoms CPU = 0.000261068 secs group upper type 1 402 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.181980515339464 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -57.282255578924 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 lattice fcc 4.05018074512482 orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.58226 4.58226 4.05018 create_atoms 2 region lower Created 402 atoms create_atoms CPU = 9.89437e-05 secs group lower type 2 402 atoms in group lower displace_atoms lower move -3.181980515339464 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 7 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 12 atoms, new total = 792 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 = 7 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) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2825.359 0 -2825.359 -308.96491 114 0 -2830.8719 0 -2830.8719 -947.77294 Loop time of 0.73127 on 1 procs for 114 steps with 792 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2825.35896956 -2830.87187885 -2830.87187885 Force two-norm initial, final = 8.63801 0.0188383 Force max component initial, final = 2.55563 0.00363935 Final line search alpha, max atom move = 3.05176e-05 1.11064e-07 Iterations, force evaluations = 114 248 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71035 | 0.71035 | 0.71035 | 0.0 | 97.14 Neigh | 0.0065551 | 0.0065551 | 0.0065551 | 0.0 | 0.90 Comm | 0.0095565 | 0.0095565 | 0.0095565 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004811 | | | 0.66 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6418 ave 6418 max 6418 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: 110972 ave 110972 max 110972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110972 Ave neighs/atom = 140.116 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) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -2830.8719 0 -2830.8719 -947.77294 13288.743 116 0 -2830.8765 0 -2830.8765 -517.98747 13281.178 Loop time of 0.121443 on 1 procs for 2 steps with 792 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2830.87187885 -2830.87646182 -2830.87646182 Force two-norm initial, final = 5.41741 1.65168 Force max component initial, final = 5.05508 1.51367 Final line search alpha, max atom move = 2.80783e-09 4.25011e-09 Iterations, force evaluations = 2 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11546 | 0.11546 | 0.11546 | 0.0 | 95.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001421 | 0.001421 | 0.001421 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004559 | | | 3.75 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6405 ave 6405 max 6405 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: 110940 ave 110940 max 110940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110940 Ave neighs/atom = 140.076 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 = 7 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) = 5.104 | 5.104 | 5.104 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2830.8765 0 -2830.8765 -517.98747 Loop time of 1.90735e-06 on 1 procs for 0 steps with 792 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 | | 1.907e-06 | | |100.00 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6421 ave 6421 max 6421 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: 110944 ave 110944 max 110944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110944 Ave neighs/atom = 140.081 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) = 5.104 | 5.104 | 5.104 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 -2830.8765 -2830.8765 28.627331 114.56451 4.0495393 -517.98747 -517.98747 -79.665485 -1656.8692 182.57233 2.5788848 229.99408 Loop time of 1.90735e-06 on 1 procs for 0 steps with 792 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 | | 1.907e-06 | | |100.00 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6421 ave 6421 max 6421 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55472 ave 55472 max 55472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110944 ave 110944 max 110944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110944 Ave neighs/atom = 140.081 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_016.2602/numatoms.out 792 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2830.87646181766-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2830.87646181766-792*${isolated_atom_energy} variable adjusted_pe_metal equal -2830.87646181766-792*-9.5367431640625e-07 print "${adjusted_pe_metal} eV" file output/dump_016.2602/energy.out -2830.8757065076 eV print "${mindist_metal} Angstroms" file output/dump_016.2602/mindistance.out 2.57888475246984 Angstroms write_dump all cfg output/dump_016.2602/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_016.2602/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00