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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 9.05607281986945*${_u_distance} variable xmax_converted equal 9.05607281986945*1 variable ymin_converted equal -45.28441409823413*${_u_distance} variable ymin_converted equal -45.28441409823413*1 variable ymax_converted equal 45.28441409823413*${_u_distance} variable ymax_converted equal 45.28441409823413*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 9.05607281986945 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.05607281986945 -45.2844140982341 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.05607281986945 -45.2844140982341 45.2844140982341 ${zmin_converted} ${zmax_converted} units box region whole block 0 9.05607281986945 -45.2844140982341 45.2844140982341 0 ${zmax_converted} units box region whole block 0 9.05607281986945 -45.2844140982341 45.2844140982341 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -45.2844 0) to (9.05607 45.2844 4.05) 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 45.2844140982341 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.43364 5.43364 4.05 create_atoms 1 region upper Created 102 atoms create_atoms CPU = 0.00020504 secs group upper type 1 102 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.0062305898749053 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.2844140982341 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.43364 5.43364 4.05 create_atoms 2 region lower Created 102 atoms create_atoms CPU = 5.50747e-05 secs group lower type 2 102 atoms in group lower displace_atoms lower move -1.0062305898749053 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_721930391003_000-files/b'AlU-library.meam' Al U ./SM_721930391003_000-files/b'AlU.meam' 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 ghost atom cutoff = 7 binsize = 3.5, bins = 3 26 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 8 atoms, new total = 196 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 ghost atom cutoff = 7 binsize = 3.5, bins = 3 26 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.39 | 10.39 | 10.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -650.42205 0 -650.42205 2995.2261 229 0 -655.38904 0 -655.38904 -7053.5387 Loop time of 0.982424 on 1 procs for 229 steps with 196 atoms 100.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -650.422046944 -655.389041807 -655.389041807 Force two-norm initial, final = 13.5773 5.33269e-06 Force max component initial, final = 5.16439 5.92543e-07 Final line search alpha, max atom move = 1 5.92543e-07 Iterations, force evaluations = 229 454 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97221 | 0.97221 | 0.97221 | 0.0 | 98.96 Neigh | 0.00067711 | 0.00067711 | 0.00067711 | 0.0 | 0.07 Comm | 0.0062389 | 0.0062389 | 0.0062389 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003303 | | | 0.34 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2323 ave 2323 max 2323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7698 ave 7698 max 7698 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15396 ave 15396 max 15396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15396 Ave neighs/atom = 78.551 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) = 10.39 | 10.39 | 10.39 Mbytes Step Temp E_pair E_mol TotEng Press Volume 229 0 -655.38904 0 -655.38904 -7053.5387 3321.8006 1229 0 -655.43608 0 -655.43608 -1869.9386 3298.2348 Loop time of 4.5907 on 1 procs for 1000 steps with 196 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -655.389041807 -655.436075484 -655.436075485 Force two-norm initial, final = 17.3493 0.000315794 Force max component initial, final = 13.8569 0.000244727 Final line search alpha, max atom move = 1 0.000244727 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4848 | 4.4848 | 4.4848 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.025726 | 0.025726 | 0.025726 | 0.0 | 0.56 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08012 | | | 1.75 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2323 ave 2323 max 2323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7628 ave 7628 max 7628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15256 ave 15256 max 15256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15256 Ave neighs/atom = 77.8367 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 ghost atom cutoff = 7 binsize = 3.5, bins = 3 26 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 9.271 | 9.271 | 9.271 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -655.43608 0 -655.43608 -1869.9386 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2323 ave 2323 max 2323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7798 ave 7798 max 7798 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15596 ave 15596 max 15596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15596 Ave neighs/atom = 79.5714 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) = 9.271 | 9.271 | 9.271 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 -655.43608 -655.43608 9.0426118 90.568828 4.0272532 -1869.9386 -1869.9386 -0.11870378 -5609.7437 0.046678814 2.5616755 154.09069 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2323 ave 2323 max 2323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7798 ave 7798 max 7798 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15596 ave 15596 max 15596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15596 Ave neighs/atom = 79.5714 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_053.1301/numatoms.out 196 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -655.43607548453-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -655.43607548453-196*${isolated_atom_energy} variable adjusted_pe_metal equal -655.43607548453-196*0 print "${adjusted_pe_metal} eV" file output/dump_053.1301/energy.out -655.43607548453 eV print "${mindist_metal} Angstroms" file output/dump_053.1301/mindistance.out 2.56167551081036 Angstroms write_dump all cfg output/dump_053.1301/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_053.1301/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:05