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 4.031036108732224*${_u_distance} variable lattice_constant_converted equal 4.031036108732224*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 56.000943360012116*${_u_distance} variable xmax_converted equal 56.000943360012116*1 variable ymin_converted equal -56.00497439612085*${_u_distance} variable ymin_converted equal -56.00497439612085*1 variable ymax_converted equal 56.00497439612085*${_u_distance} variable ymax_converted equal 56.00497439612085*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031036108732224*${_u_distance} variable zmax_converted equal 4.031036108732224*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03103610873222 Lattice spacing in x,y,z = 4.03104 4.03104 4.03104 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 56.0009433600121 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.0009433600121 -56.0049743961209 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.0009433600121 -56.0049743961209 56.0049743961209 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.0009433600121 -56.0049743961209 56.0049743961209 0 ${zmax_converted} units box region whole block 0 56.0009433600121 -56.0049743961209 56.0049743961209 0 4.03103610873222 units box create_box 2 whole Created orthogonal box = (0 -56.005 0) to (56.0009 56.005 4.03104) 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 56.0049743961209 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.51305 5.51305 4.03104 create_atoms 1 region upper Created 774 atoms create_atoms CPU = 0.000262022 secs group upper type 1 774 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.251599795252412 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.0049743961209 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.51305 5.51305 4.03104 create_atoms 2 region lower Created 774 atoms create_atoms CPU = 0.000136852 secs group lower type 2 774 atoms in group lower displace_atoms lower move -6.251599795252412 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_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*4.03103610873222 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01551805436611 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 15 30 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1524 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 15 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.49 | 5.49 | 5.49 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5081.4286 0 -5081.4286 1026.6001 214 0 -5105.7386 0 -5105.7386 -5641.6361 Loop time of 1.59472 on 1 procs for 214 steps with 1524 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5081.42862656 -5105.7385561 -5105.7385561 Force two-norm initial, final = 27.4113 8.17403e-06 Force max component initial, final = 6.44671 1.88436e-06 Final line search alpha, max atom move = 1 1.88436e-06 Iterations, force evaluations = 214 422 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.56 | 1.56 | 1.56 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021176 | 0.021176 | 0.021176 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01353 | | | 0.85 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9436 ave 9436 max 9436 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: 200000 ave 200000 max 200000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200000 Ave neighs/atom = 131.234 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) = 5.49 | 5.49 | 5.49 Mbytes Step Temp E_pair E_mol TotEng Press Volume 214 0 -5105.7386 0 -5105.7386 -5641.6361 25285.33 1214 0 -5106.0392 0 -5106.0392 -867.23592 25119.515 Loop time of 8.15602 on 1 procs for 1000 steps with 1524 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5105.7385561 -5106.03920584 -5106.03920587 Force two-norm initial, final = 123.045 0.0161853 Force max component initial, final = 98.8046 0.011419 Final line search alpha, max atom move = 0.0566495 0.000646883 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7083 | 7.7083 | 7.7083 | 0.0 | 94.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.096658 | 0.096658 | 0.096658 | 0.0 | 1.19 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.351 | | | 4.30 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9476 ave 9476 max 9476 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: 199724 ave 199724 max 199724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199724 Ave neighs/atom = 131.052 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 15 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 5.628 | 5.628 | 5.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5106.0392 0 -5106.0392 -867.23592 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1524 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 | | 1.907e-06 | | |100.00 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9486 ave 9486 max 9486 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: 199952 ave 199952 max 199952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199952 Ave neighs/atom = 131.202 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) = 5.628 | 5.628 | 5.628 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 -5106.0392 -5106.0392 55.736721 112.00995 4.0235855 -867.23592 -867.23592 0.72489451 -2602.8227 0.39007029 2.5699542 1008.3647 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1524 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: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9486 ave 9486 max 9486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99976 ave 99976 max 99976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199952 ave 199952 max 199952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199952 Ave neighs/atom = 131.202 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_060.5129/numatoms.out 1524 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5106.0392058679-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5106.0392058679-1524*${isolated_atom_energy} variable adjusted_pe_metal equal -5106.0392058679-1524*0 print "${adjusted_pe_metal} eV" file output/dump_060.5129/energy.out -5106.0392058679 eV print "${mindist_metal} Angstroms" file output/dump_060.5129/mindistance.out 2.56995418914612 Angstroms write_dump all cfg output/dump_060.5129/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_060.5129/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09