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 4.049999177455902*${_u_distance} variable lattice_constant_converted equal 4.049999177455902*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 67.40542006736545*${_u_distance} variable xmax_converted equal 67.40542006736545*1 variable ymin_converted equal -67.40947006654291*${_u_distance} variable ymin_converted equal -67.40947006654291*1 variable ymax_converted equal 67.40947006654291*${_u_distance} variable ymax_converted equal 67.40947006654291*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049999177455902*${_u_distance} variable zmax_converted equal 4.049999177455902*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0499991774559 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 67.4054200673655 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.4054200673655 -67.4094700665429 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.4054200673655 -67.4094700665429 67.4094700665429 ${zmin_converted} ${zmax_converted} units box region whole block 0 67.4054200673655 -67.4094700665429 67.4094700665429 0 ${zmax_converted} units box region whole block 0 67.4054200673655 -67.4094700665429 67.4094700665429 0 4.0499991774559 units box create_box 2 whole Created orthogonal box = (0 -67.4095 0) to (67.4054 67.4095 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 67.4094700665429 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59684 5.59684 4.05 create_atoms 1 region upper Created 1109 atoms create_atoms CPU = 0.000423193 secs group upper type 1 1109 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.489492639691956 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -67.4094700665429 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 lattice fcc 4.0499991774559 orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59684 5.59684 4.05 create_atoms 2 region lower Created 1109 atoms create_atoms CPU = 0.000322104 secs group lower type 2 1109 atoms in group lower displace_atoms lower move -7.489492639691956 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_656517352485_000-files/b'library.meam' Al Si Mg Cu Fe ./SM_656517352485_000-files/b'AlSiMgCuFe.meam' Al Al Reading potential file ./SM_656517352485_000-files/b'library.meam' with DATE: 2012-06-29 Reading potential file ./SM_656517352485_000-files/b'AlSiMgCuFe.meam' with DATE: 2012-06-29 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*4.0499991774559 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499958872795 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 = 20 39 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 26 atoms, new total = 2192 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 = 20 39 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) = 14.74 | 14.74 | 14.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7303.5736 0 -7303.5736 -209.54099 251 0 -7329.3077 0 -7329.3077 -5623.3933 Loop time of 18.0895 on 1 procs for 251 steps with 2192 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7303.57362037 -7329.30766333 -7329.30766333 Force two-norm initial, final = 18.6107 1.39409e-05 Force max component initial, final = 3.83529 2.84875e-06 Final line search alpha, max atom move = 1 2.84875e-06 Iterations, force evaluations = 251 494 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.029 | 18.029 | 18.029 | 0.0 | 99.66 Neigh | 0.006289 | 0.006289 | 0.006289 | 0.0 | 0.03 Comm | 0.031848 | 0.031848 | 0.031848 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02261 | | | 0.12 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10835 ave 10835 max 10835 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86207 ave 86207 max 86207 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172414 ave 172414 max 172414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172414 Ave neighs/atom = 78.656 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) = 14.77 | 14.77 | 14.77 Mbytes Step Temp E_pair E_mol TotEng Press Volume 251 0 -7329.3077 0 -7329.3077 -5623.3933 36804.478 1251 0 -7329.6252 0 -7329.6252 -1317.9821 36595.617 Loop time of 73.0389 on 1 procs for 1000 steps with 2192 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 = -7329.30766333 -7329.62518806 -7329.62518808 Force two-norm initial, final = 156.612 0.0198324 Force max component initial, final = 114.844 0.0194285 Final line search alpha, max atom move = 0.233369 0.00453402 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 72.517 | 72.517 | 72.517 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10944 | 0.10944 | 0.10944 | 0.0 | 0.15 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4129 | | | 0.57 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9992 ave 9992 max 9992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86193 ave 86193 max 86193 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172386 ave 172386 max 172386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172386 Ave neighs/atom = 78.6432 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 = 20 39 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) = 13.68 | 13.68 | 13.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7329.6252 0 -7329.6252 -1317.9821 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2192 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: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10230 ave 10230 max 10230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88285 ave 88285 max 88285 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 176570 ave 176570 max 176570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176570 Ave neighs/atom = 80.552 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) = 13.68 | 13.68 | 13.68 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 -7329.6252 -7329.6252 67.244092 134.81894 4.0366773 -1317.9821 -1317.9821 0.84855564 -3954.8306 0.035834318 2.437007 976.67566 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2192 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: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10230 ave 10230 max 10230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88285 ave 88285 max 88285 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 176570 ave 176570 max 176570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176570 Ave neighs/atom = 80.552 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_065.4705/numatoms.out 2192 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7329.62518807611-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7329.62518807611-2192*${isolated_atom_energy} variable adjusted_pe_metal equal -7329.62518807611-2192*0 print "${adjusted_pe_metal} eV" file output/dump_065.4705/energy.out -7329.62518807611 eV print "${mindist_metal} Angstroms" file output/dump_065.4705/mindistance.out 2.43700700922976 Angstroms write_dump all cfg output/dump_065.4705/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_065.4705/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:31