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 4.024845376610756*${_u_distance} variable lattice_constant_converted equal 4.024845376610756*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 65.51973581288784*${_u_distance} variable xmax_converted equal 65.51973581288784*1 variable ymin_converted equal -65.52376065826445*${_u_distance} variable ymin_converted equal -65.52376065826445*1 variable ymax_converted equal 65.52376065826445*${_u_distance} variable ymax_converted equal 65.52376065826445*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.024845376610756*${_u_distance} variable zmax_converted equal 4.024845376610756*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.02484537661076 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 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 65.5197358128878 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.5197358128878 -65.5237606582645 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.5197358128878 -65.5237606582645 65.5237606582645 ${zmin_converted} ${zmax_converted} units box region whole block 0 65.5197358128878 -65.5237606582645 65.5237606582645 0 ${zmax_converted} units box region whole block 0 65.5197358128878 -65.5237606582645 65.5237606582645 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -65.5238 0) to (65.5197 65.5238 4.02485) 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 65.5237606582645 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68662 5.68662 4.02485 create_atoms 1 region upper Created 1062 atoms create_atoms CPU = 0.000286102 secs group upper type 1 1062 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.325469268244868 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -65.5237606582645 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68662 5.68662 4.02485 create_atoms 2 region lower Created 1062 atoms create_atoms CPU = 0.00018096 secs group lower type 2 1062 atoms in group lower displace_atoms lower move -7.325469268244868 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_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*4.02484537661076 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01242268830538 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 16 32 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2092 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 16 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.657 | 5.657 | 5.657 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5500.1926 0 -5500.1926 -2447.4928 316 0 -5527.0993 0 -5527.0993 -8555.0247 Loop time of 4.33146 on 1 procs for 316 steps with 2092 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5500.19255416 -5527.09933476 -5527.09933476 Force two-norm initial, final = 14.6393 9.1629e-06 Force max component initial, final = 2.49128 2.24784e-06 Final line search alpha, max atom move = 1 2.24784e-06 Iterations, force evaluations = 316 617 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2333 | 4.2333 | 4.2333 | 0.0 | 97.73 Neigh | 0.024176 | 0.024176 | 0.024176 | 0.0 | 0.56 Comm | 0.045213 | 0.045213 | 0.045213 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02874 | | | 0.66 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12688 ave 12688 max 12688 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: 292960 ave 292960 max 292960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292960 Ave neighs/atom = 140.038 Neighbor list builds = 3 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) = 5.658 | 5.658 | 5.658 Mbytes Step Temp E_pair E_mol TotEng Press Volume 316 0 -5527.0993 0 -5527.0993 -8555.0247 34558.123 1316 0 -5527.6982 0 -5527.6982 -2457.7761 34288.196 Loop time of 13.8629 on 1 procs for 1000 steps with 2092 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5527.09933476 -5527.69817575 -5527.69817575 Force two-norm initial, final = 209.253 0.00470979 Force max component initial, final = 160.183 0.00215449 Final line search alpha, max atom move = 0.285674 0.000615482 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.287 | 13.287 | 13.287 | 0.0 | 95.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12747 | 0.12747 | 0.12747 | 0.0 | 0.92 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.448 | | | 3.23 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12723 ave 12723 max 12723 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: 293216 ave 293216 max 293216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293216 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 -0.0307342631051472 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 16 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.796 | 5.796 | 5.796 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5527.6982 0 -5527.6982 -2457.7761 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12743 ave 12743 max 12743 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: 293392 ave 293392 max 293392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293392 Ave neighs/atom = 140.245 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) = 5.796 | 5.796 | 5.796 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 -5527.6982 -5527.6982 65.349413 131.04752 4.0038162 -2457.7761 -2457.7761 0.086846602 -7373.5153 0.10014617 2.5851969 192.01727 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12743 ave 12743 max 12743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146696 ave 146696 max 146696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293392 ave 293392 max 293392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293392 Ave neighs/atom = 140.245 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.0209/numatoms.out 2092 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5527.69817575347-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5527.69817575347-2092*${isolated_atom_energy} variable adjusted_pe_metal equal -5527.69817575347-2092*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_085.0209/energy.out -5463.4020973375 eV print "${mindist_metal} Angstroms" file output/dump_085.0209/mindistance.out 2.58519692226579 Angstroms write_dump all cfg output/dump_085.0209/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_085.0209/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:18