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 4.031999975442886*${_u_distance} variable lattice_constant_converted equal 4.031999975442886*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 66.74147527392674*${_u_distance} variable xmax_converted equal 66.74147527392674*1 variable ymin_converted equal -66.74550727390218*${_u_distance} variable ymin_converted equal -66.74550727390218*1 variable ymax_converted equal 66.74550727390218*${_u_distance} variable ymax_converted equal 66.74550727390218*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031999975442886*${_u_distance} variable zmax_converted equal 4.031999975442886*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03199997544289 Lattice spacing in x,y,z = 4.032 4.032 4.032 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 66.7414752739267 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.7414752739267 -66.7455072739022 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.7414752739267 -66.7455072739022 66.7455072739022 ${zmin_converted} ${zmax_converted} units box region whole block 0 66.7414752739267 -66.7455072739022 66.7455072739022 0 ${zmax_converted} units box region whole block 0 66.7414752739267 -66.7455072739022 66.7455072739022 0 4.03199997544289 units box create_box 2 whole Created orthogonal box = (0 -66.7455 0) to (66.7415 66.7455 4.032) 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 66.7455072739022 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -7 0 orient y 7 15 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 15 -7 0 orient y 7 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.3588 5.3588 4.032 create_atoms 1 region upper Created 1098 atoms create_atoms CPU = 0.00027585 secs group upper type 1 1098 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.448825410761081 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -66.7455072739022 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 7 0 orient y -7 15 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 15 7 0 orient y -7 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.3588 5.3588 4.032 create_atoms 2 region lower Created 1098 atoms create_atoms CPU = 0.000185966 secs group lower type 2 1098 atoms in group lower displace_atoms lower move -7.448825410761081 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_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*4.03199997544289 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01599998772144 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 16 31 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2168 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 16 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.951 | 9.951 | 9.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7247.3069 0 -7247.3069 -787.43003 300 0 -7266.5682 0 -7266.5682 -4769.0657 Loop time of 5.19688 on 1 procs for 300 steps with 2168 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7247.30693968 -7266.56824406 -7266.56824406 Force two-norm initial, final = 21.2882 9.40148e-06 Force max component initial, final = 4.37359 1.28705e-06 Final line search alpha, max atom move = 1 1.28705e-06 Iterations, force evaluations = 300 589 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1083 | 5.1083 | 5.1083 | 0.0 | 98.30 Neigh | 0.014844 | 0.014844 | 0.014844 | 0.0 | 0.29 Comm | 0.04612 | 0.04612 | 0.04612 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0276 | | | 0.53 Nlocal: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13423 ave 13423 max 13423 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: 379576 ave 379576 max 379576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379576 Ave neighs/atom = 175.081 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) = 9.951 | 9.951 | 9.951 Mbytes Step Temp E_pair E_mol TotEng Press Volume 300 0 -7266.5682 0 -7266.5682 -4769.0657 35922.649 1300 0 -7266.825 0 -7266.825 -703.39774 35738.631 Loop time of 17.6775 on 1 procs for 1000 steps with 2168 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 = -7266.56824406 -7266.82503892 -7266.82503927 Force two-norm initial, final = 141.971 0.0619978 Force max component initial, final = 101.83 0.0606536 Final line search alpha, max atom move = 0.0249507 0.00151335 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.044 | 17.044 | 17.044 | 0.0 | 96.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1382 | 0.1382 | 0.1382 | 0.0 | 0.78 Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.495 | | | 2.80 Nlocal: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13332 ave 13332 max 13332 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: 379696 ave 379696 max 379696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379696 Ave neighs/atom = 175.137 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 16 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 9.452 | 9.452 | 9.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7266.825 0 -7266.825 -703.39774 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2168 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: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13332 ave 13332 max 13332 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: 379832 ave 379832 max 379832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379832 Ave neighs/atom = 175.199 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) = 9.452 | 9.452 | 9.452 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 -7266.825 -7266.825 66.577172 133.49101 4.021245 -703.39774 -703.39774 -2.7124324 -2107.5754 0.094601043 2.5396884 1252.2142 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2168 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: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13332 ave 13332 max 13332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 189916 ave 189916 max 189916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 379832 ave 379832 max 379832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379832 Ave neighs/atom = 175.199 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_050.0338/numatoms.out 2168 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7266.82503926957-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7266.82503926957-2168*${isolated_atom_energy} variable adjusted_pe_metal equal -7266.82503926957-2168*0 print "${adjusted_pe_metal} eV" file output/dump_050.0338/energy.out -7266.82503926957 eV print "${mindist_metal} Angstroms" file output/dump_050.0338/mindistance.out 2.53968839805371 Angstroms write_dump all cfg output/dump_050.0338/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_050.0338/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:23