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 3.987558534741402*${_u_distance} variable lattice_constant_converted equal 3.987558534741402*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 21.473659887678227*${_u_distance} variable xmax_converted equal 21.473659887678227*1 variable ymin_converted equal -42.951307333891194*${_u_distance} variable ymin_converted equal -42.951307333891194*1 variable ymax_converted equal 42.951307333891194*${_u_distance} variable ymax_converted equal 42.951307333891194*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.987558534741402*${_u_distance} variable zmax_converted equal 3.987558534741402*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.9875585347414 Lattice spacing in x,y,z = 3.98756 3.98756 3.98756 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 21.4736598876782 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.4736598876782 -42.9513073338912 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.4736598876782 -42.9513073338912 42.9513073338912 ${zmin_converted} ${zmax_converted} units box region whole block 0 21.4736598876782 -42.9513073338912 42.9513073338912 0 ${zmax_converted} units box region whole block 0 21.4736598876782 -42.9513073338912 42.9513073338912 0 3.9875585347414 units box create_box 2 whole Created orthogonal box = (0 -42.9513 0) to (21.4737 42.9513 3.98756) 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 42.9513073338912 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.1833 5.1833 3.98756 create_atoms 1 region upper Created 234 atoms create_atoms CPU = 0.000154972 secs group upper type 1 234 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.4233241632105265 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.9513073338912 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.1833 5.1833 3.98756 create_atoms 2 region lower Created 234 atoms create_atoms CPU = 5.10216e-05 secs group lower type 2 234 atoms in group lower displace_atoms lower move -2.4233241632105265 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_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*3.9875585347414 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.9937792673707 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 ghost atom cutoff = 8 binsize = 4, bins = 6 22 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 458 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 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1530.0585 0 -1530.0585 5011.3698 270 0 -1543.4843 0 -1543.4843 -5545.892 Loop time of 0.72361 on 1 procs for 270 steps with 458 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1530.05846324 -1543.48429841 -1543.48429841 Force two-norm initial, final = 24.1658 1.16482e-06 Force max component initial, final = 6.62991 2.33824e-07 Final line search alpha, max atom move = 1 2.33824e-07 Iterations, force evaluations = 270 533 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70448 | 0.70448 | 0.70448 | 0.0 | 97.36 Neigh | 0.0012329 | 0.0012329 | 0.0012329 | 0.0 | 0.17 Comm | 0.011933 | 0.011933 | 0.011933 | 0.0 | 1.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00596 | | | 0.82 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4267 ave 4267 max 4267 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: 62820 ave 62820 max 62820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62820 Ave neighs/atom = 137.162 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) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 270 0 -1543.4843 0 -1543.4843 -5545.892 7355.6241 1270 0 -1543.5484 0 -1543.5484 -1017.6977 7318.8718 Loop time of 2.87312 on 1 procs for 1000 steps with 458 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1543.48429841 -1543.54844141 -1543.5484415 Force two-norm initial, final = 32.2333 0.0144901 Force max component initial, final = 25.6362 0.0125186 Final line search alpha, max atom move = 0.336827 0.00421659 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6887 | 2.6887 | 2.6887 | 0.0 | 93.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.043353 | 0.043353 | 0.043353 | 0.0 | 1.51 Output | 3.9101e-05 | 3.9101e-05 | 3.9101e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.141 | | | 4.91 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4282 ave 4282 max 4282 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: 62708 ave 62708 max 62708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62708 Ave neighs/atom = 136.917 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 -1.81000000000002 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 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1543.5484 0 -1543.5484 -1017.6977 Loop time of 1.19209e-06 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4287 ave 4287 max 4287 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: 62796 ave 62796 max 62796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62796 Ave neighs/atom = 137.109 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) = 4.623 | 4.623 | 4.623 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 -1543.5484 -1543.5484 21.365648 85.902615 3.9876928 -1017.6977 -1017.6977 -0.41752117 -3049.9351 -2.740537 2.5139828 344.38885 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4287 ave 4287 max 4287 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31398 ave 31398 max 31398 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62796 ave 62796 max 62796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62796 Ave neighs/atom = 137.109 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_043.6028/numatoms.out 458 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1543.54844150375-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1543.54844150375-458*${isolated_atom_energy} variable adjusted_pe_metal equal -1543.54844150375-458*-1.81000000000002 print "${adjusted_pe_metal} eV" file output/dump_043.6028/energy.out -714.568441503741 eV print "${mindist_metal} Angstroms" file output/dump_043.6028/mindistance.out 2.51398282248367 Angstroms write_dump all cfg output/dump_043.6028/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_043.6028/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03