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 4.045259781181812*${_u_distance} variable lattice_constant_converted equal 4.045259781181812*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 56.34394891437715*${_u_distance} variable xmax_converted equal 56.34394891437715*1 variable ymin_converted equal -56.34799417415833*${_u_distance} variable ymin_converted equal -56.34799417415833*1 variable ymax_converted equal 56.34799417415833*${_u_distance} variable ymax_converted equal 56.34799417415833*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045259781181812*${_u_distance} variable zmax_converted equal 4.045259781181812*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04525978118181 Lattice spacing in x,y,z = 4.04526 4.04526 4.04526 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 56.3439489143772 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.3439489143772 -56.3479941741583 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.3439489143772 -56.3479941741583 56.3479941741583 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.3439489143772 -56.3479941741583 56.3479941741583 0 ${zmax_converted} units box region whole block 0 56.3439489143772 -56.3479941741583 56.3479941741583 0 4.04525978118181 units box create_box 2 whole Created orthogonal box = (0 -56.348 0) to (56.3439 56.348 4.04526) 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 56.3479941741583 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -5 0 orient y 5 13 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 13 -5 0 orient y 5 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.22779 5.22779 4.04526 create_atoms 1 region upper Created 778 atoms create_atoms CPU = 0.000254154 secs group upper type 1 778 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.267774724732854 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.3479941741583 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 5 0 orient y -5 13 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 13 5 0 orient y -5 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.22779 5.22779 4.04526 create_atoms 2 region lower Created 778 atoms create_atoms CPU = 0.000129938 secs group lower type 2 778 atoms in group lower displace_atoms lower move -6.267774724732854 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_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*4.04525978118181 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0226298905909 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 27 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1530 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.534 | 5.534 | 5.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5187.4157 0 -5187.4157 -1425.7176 378 0 -5200.5235 0 -5200.5235 -5513.633 Loop time of 4.59913 on 1 procs for 378 steps with 1530 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5187.41573484 -5200.52352914 -5200.52352914 Force two-norm initial, final = 17.2577 1.30611e-05 Force max component initial, final = 3.95731 1.58733e-06 Final line search alpha, max atom move = 1 1.58733e-06 Iterations, force evaluations = 378 741 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5271 | 4.5271 | 4.5271 | 0.0 | 98.43 Neigh | 0.004072 | 0.004072 | 0.004072 | 0.0 | 0.09 Comm | 0.042194 | 0.042194 | 0.042194 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0258 | | | 0.56 Nlocal: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9910 ave 9910 max 9910 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: 214932 ave 214932 max 214932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214932 Ave neighs/atom = 140.478 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) = 5.534 | 5.534 | 5.534 Mbytes Step Temp E_pair E_mol TotEng Press Volume 378 0 -5200.5235 0 -5200.5235 -5513.633 25686.336 1378 0 -5200.7903 0 -5200.7903 -829.58101 25533.751 Loop time of 12.172 on 1 procs for 1000 steps with 1530 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 = -5200.52352914 -5200.79034801 -5200.79034801 Force two-norm initial, final = 119.808 0.00664891 Force max component initial, final = 94.5023 0.00309565 Final line search alpha, max atom move = 0.219561 0.000679686 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.693 | 11.693 | 11.693 | 0.0 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10474 | 0.10474 | 0.10474 | 0.0 | 0.86 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3741 | | | 3.07 Nlocal: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900 ave 9900 max 9900 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: 214520 ave 214520 max 214520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214520 Ave neighs/atom = 140.209 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.672 | 5.672 | 5.672 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5200.7903 0 -5200.7903 -829.58101 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1530 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: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9905 ave 9905 max 9905 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: 214964 ave 214964 max 214964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214964 Ave neighs/atom = 140.499 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) = 5.672 | 5.672 | 5.672 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 -5200.7903 -5200.7903 56.247972 112.69599 4.0280911 -829.58101 -829.58101 0.16099032 -2489.0974 0.19341975 2.5669337 991.28805 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1530 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: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9905 ave 9905 max 9905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107482 ave 107482 max 107482 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 214964 ave 214964 max 214964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214964 Ave neighs/atom = 140.499 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_042.0750/numatoms.out 1530 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5200.79034800953-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5200.79034800953-1530*${isolated_atom_energy} variable adjusted_pe_metal equal -5200.79034800953-1530*0 print "${adjusted_pe_metal} eV" file output/dump_042.0750/energy.out -5200.79034800953 eV print "${mindist_metal} Angstroms" file output/dump_042.0750/mindistance.out 2.56693370521045 Angstroms write_dump all cfg output/dump_042.0750/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_042.0750/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:16