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 45.28049079868288*${_u_distance} variable xmax_converted equal 45.28049079868288*1 variable ymin_converted equal -45.28454080890209*${_u_distance} variable ymin_converted equal -45.28454080890209*1 variable ymax_converted equal 45.28454080890209*${_u_distance} variable ymax_converted equal 45.28454080890209*1 variable zmin_converted equal 0.0*${_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 45.2804907986829 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.2804907986829 -45.2845408089021 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.2804907986829 -45.2845408089021 45.2845408089021 ${zmin_converted} ${zmax_converted} units box region whole block 0 45.2804907986829 -45.2845408089021 45.2845408089021 0 ${zmax_converted} units box region whole block 0 45.2804907986829 -45.2845408089021 45.2845408089021 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -45.2845 0) to (45.2805 45.2845 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 45.2845408089021 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -2 0 orient y 2 11 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 11 -2 0 orient y 2 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.70917 4.70917 4.05001 create_atoms 1 region upper Created 502 atoms create_atoms CPU = 0.000252962 secs group upper type 1 502 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.031152949374526 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.2845408089021 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 2 0 orient y -2 11 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 11 2 0 orient y -2 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.70917 4.70917 4.05001 create_atoms 2 region lower Created 502 atoms create_atoms CPU = 0.000118971 secs group lower type 2 502 atoms in group lower displace_atoms lower move -5.031152949374526 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 12 24 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 20 atoms, new total = 984 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 = 12 24 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) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3311.2342 0 -3311.2342 -83.090095 302 0 -3322.1272 0 -3322.1272 -6711.9727 Loop time of 1.43846 on 1 procs for 302 steps with 984 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3311.2342005 -3322.1272271 -3322.1272271 Force two-norm initial, final = 17.5704 6.71516e-06 Force max component initial, final = 4.20092 1.24334e-06 Final line search alpha, max atom move = 1 1.24334e-06 Iterations, force evaluations = 302 597 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4005 | 1.4005 | 1.4005 | 0.0 | 97.36 Neigh | 0.0031998 | 0.0031998 | 0.0031998 | 0.0 | 0.22 Comm | 0.021564 | 0.021564 | 0.021564 | 0.0 | 1.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01318 | | | 0.92 Nlocal: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6666 ave 6666 max 6666 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: 102228 ave 102228 max 102228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102228 Ave neighs/atom = 103.89 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) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 302 0 -3322.1272 0 -3322.1272 -6711.9727 16609.142 1302 0 -3322.3862 0 -3322.3862 -843.94554 16478.504 Loop time of 4.92358 on 1 procs for 1000 steps with 984 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 = -3322.1272271 -3322.3862481 -3322.38624811 Force two-norm initial, final = 92.2229 0.0105572 Force max component initial, final = 66.7101 0.00958901 Final line search alpha, max atom move = 0.0692821 0.000664347 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6123 | 4.6123 | 4.6123 | 0.0 | 93.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.068775 | 0.068775 | 0.068775 | 0.0 | 1.40 Output | 3.2902e-05 | 3.2902e-05 | 3.2902e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2424 | | | 4.92 Nlocal: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656 ave 6656 max 6656 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: 99368 ave 99368 max 99368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99368 Ave neighs/atom = 100.984 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 = 12 24 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) = 5.123 | 5.123 | 5.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3322.3862 0 -3322.3862 -843.94554 Loop time of 1.19209e-06 on 1 procs for 0 steps with 984 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: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6666 ave 6666 max 6666 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: 113168 ave 113168 max 113168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113168 Ave neighs/atom = 115.008 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) = 5.123 | 5.123 | 5.123 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 -3322.3862 -3322.3862 45.080871 90.569082 4.0359475 -843.94554 -843.94554 -0.24831786 -2532.5174 0.92908573 2.5436618 695.94134 Loop time of 9.53674e-07 on 1 procs for 0 steps with 984 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: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6666 ave 6666 max 6666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56584 ave 56584 max 56584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113168 ave 113168 max 113168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113168 Ave neighs/atom = 115.008 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_020.6097/numatoms.out 984 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3322.38624811281-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3322.38624811281-984*${isolated_atom_energy} variable adjusted_pe_metal equal -3322.38624811281-984*0 print "${adjusted_pe_metal} eV" file output/dump_020.6097/energy.out -3322.38624811281 eV print "${mindist_metal} Angstroms" file output/dump_020.6097/mindistance.out 2.54366178858272 Angstroms write_dump all cfg output/dump_020.6097/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_020.6097/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06