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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 4.050010219216347*${_u_distance} variable xmax_converted equal 4.050010219216347*1 variable ymin_converted equal -40.504152202382684*${_u_distance} variable ymin_converted equal -40.504152202382684*1 variable ymax_converted equal 40.504152202382684*${_u_distance} variable ymax_converted equal 40.504152202382684*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 4.05001021921635 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 4.05001021921635 -40.5041522023827 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 4.05001021921635 -40.5041522023827 40.5041522023827 ${zmin_converted} ${zmax_converted} units box region whole block 0 4.05001021921635 -40.5041522023827 40.5041522023827 0 ${zmax_converted} units box region whole block 0 4.05001021921635 -40.5041522023827 40.5041522023827 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -40.5042 0) to (4.05001 40.5042 4.05001) 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 40.5041522023827 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 create_atoms 1 region upper Created 42 atoms create_atoms CPU = 0.00012207 secs group upper type 1 42 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 0.45 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -40.5041522023827 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 create_atoms 2 region lower Created 42 atoms create_atoms CPU = 1.3113e-05 secs group lower type 2 42 atoms in group lower displace_atoms lower move -0.45 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 2 22 2 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 80 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.388 | 4.388 | 4.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -267.0212 0 -267.0212 14115.315 113 0 -271.20015 0 -271.20015 -76.832028 Loop time of 0.0341151 on 1 procs for 113 steps with 80 atoms 87.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -267.021195371 -271.200150711 -271.200150711 Force two-norm initial, final = 11.7806 1.33611e-06 Force max component initial, final = 3.91288 2.98749e-07 Final line search alpha, max atom move = 1 2.98749e-07 Iterations, force evaluations = 113 222 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031523 | 0.031523 | 0.031523 | 0.0 | 92.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020156 | 0.0020156 | 0.0020156 | 0.0 | 5.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005763 | | | 1.69 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2035 ave 2035 max 2035 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: 10488 ave 10488 max 10488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10488 Ave neighs/atom = 131.1 Neighbor list builds = 0 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) = 4.388 | 4.388 | 4.388 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -271.20015 0 -271.20015 -76.832028 1328.7454 192 0 -271.20015 0 -271.20015 -12.455055 1328.6343 Loop time of 0.027158 on 1 procs for 79 steps with 80 atoms 110.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -271.200150711 -271.200153075 -271.200153075 Force two-norm initial, final = 0.079866 5.80308e-09 Force max component initial, final = 0.0564738 3.42753e-09 Final line search alpha, max atom move = 1 3.42753e-09 Iterations, force evaluations = 79 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022726 | 0.022726 | 0.022726 | 0.0 | 83.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012681 | 0.0012681 | 0.0012681 | 0.0 | 4.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003164 | | | 11.65 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1823 ave 1823 max 1823 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: 10720 ave 10720 max 10720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10720 Ave neighs/atom = 134 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -271.20015 0 -271.20015 -12.455055 Loop time of 1.19209e-06 on 1 procs for 0 steps with 80 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: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1823 ave 1823 max 1823 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: 10720 ave 10720 max 10720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10720 Ave neighs/atom = 134 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) = 4.524 | 4.524 | 4.524 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 -271.20015 -271.20015 4.0498408 81.008304 4.0498408 -12.455055 -12.455055 3.1774852e-06 -37.365173 4.133026e-06 2.8636699 2.8222998e-17 Loop time of 9.53674e-07 on 1 procs for 0 steps with 80 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: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1823 ave 1823 max 1823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5360 ave 5360 max 5360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10720 ave 10720 max 10720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10720 Ave neighs/atom = 134 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_000.0000/numatoms.out 80 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -271.200153074711-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -271.200153074711-80*${isolated_atom_energy} variable adjusted_pe_metal equal -271.200153074711-80*0 print "${adjusted_pe_metal} eV" file output/dump_000.0000/energy.out -271.200153074711 eV print "${mindist_metal} Angstroms" file output/dump_000.0000/mindistance.out 2.86366990089942 Angstroms write_dump all cfg output/dump_000.0000/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_000.0000/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00