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 4.045270472764969*${_u_distance} variable lattice_constant_converted equal 4.045270472764969*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 20.626913078389286*${_u_distance} variable xmax_converted equal 20.626913078389286*1 variable ymin_converted equal -41.25787142725134*${_u_distance} variable ymin_converted equal -41.25787142725134*1 variable ymax_converted equal 41.25787142725134*${_u_distance} variable ymax_converted equal 41.25787142725134*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045270472764969*${_u_distance} variable zmax_converted equal 4.045270472764969*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04527047276497 Lattice spacing in x,y,z = 4.04527 4.04527 4.04527 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 20.6269130783893 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.6269130783893 -41.2578714272513 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.6269130783893 -41.2578714272513 41.2578714272513 ${zmin_converted} ${zmax_converted} units box region whole block 0 20.6269130783893 -41.2578714272513 41.2578714272513 0 ${zmax_converted} units box region whole block 0 20.6269130783893 -41.2578714272513 41.2578714272513 0 4.04527047276497 units box create_box 2 whole Created orthogonal box = (0 -41.2579 0) to (20.6269 41.2579 4.04527) 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 41.2578714272513 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -1 0 orient y 1 5 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 5 -1 0 orient y 1 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.76006 4.76006 4.04527 create_atoms 1 region upper Created 209 atoms create_atoms CPU = 0.000189066 secs group upper type 1 209 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.294558781116753 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -41.2578714272513 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 1 0 orient y -1 5 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 5 1 0 orient y -1 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.76006 4.76006 4.04527 create_atoms 2 region lower Created 209 atoms create_atoms CPU = 4.29153e-05 secs group lower type 2 209 atoms in group lower displace_atoms lower move -2.294558781116753 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_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*4.04527047276497 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02263523638248 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 18 1 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 409 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1385.496 0 -1385.496 -2284.399 180 0 -1388.9489 0 -1388.9489 -6290.9303 Loop time of 0.717932 on 1 procs for 180 steps with 409 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1385.49595689 -1388.94886165 -1388.94886165 Force two-norm initial, final = 7.38593 4.2743e-06 Force max component initial, final = 2.46398 1.43148e-06 Final line search alpha, max atom move = 1 1.43148e-06 Iterations, force evaluations = 180 354 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70344 | 0.70344 | 0.70344 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010384 | 0.010384 | 0.010384 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004104 | | | 0.57 Nlocal: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5345 ave 5345 max 5345 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: 89752 ave 89752 max 89752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89752 Ave neighs/atom = 219.443 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 180 0 -1388.9489 0 -1388.9489 -6290.9303 6885.2326 1180 0 -1389.0408 0 -1389.0408 -1039.4651 6840.0052 Loop time of 4.19951 on 1 procs for 1000 steps with 409 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 = -1388.94886165 -1389.04082934 -1389.04082934 Force two-norm initial, final = 36.1094 0.00246709 Force max component initial, final = 29.3685 0.00145745 Final line search alpha, max atom move = 1 0.00145745 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.978 | 3.978 | 3.978 | 0.0 | 94.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.056076 | 0.056076 | 0.056076 | 0.0 | 1.34 Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1654 | | | 3.94 Nlocal: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5417 ave 5417 max 5417 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: 84930 ave 84930 max 84930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84930 Ave neighs/atom = 207.653 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 4.632 | 4.632 | 4.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1389.0408 0 -1389.0408 -1039.4651 Loop time of 1.19209e-06 on 1 procs for 0 steps with 409 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: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5417 ave 5417 max 5417 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: 87418 ave 87418 max 87418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87418 Ave neighs/atom = 213.736 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) = 4.632 | 4.632 | 4.632 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 -1389.0408 -1389.0408 20.596911 82.515743 4.0245518 -1039.4651 -1039.4651 -0.2365998 -3117.819 -0.33963913 2.4768127 331.81023 Loop time of 1.19209e-06 on 1 procs for 0 steps with 409 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: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5417 ave 5417 max 5417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43709 ave 43709 max 43709 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87418 ave 87418 max 87418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87418 Ave neighs/atom = 213.736 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_022.6199/numatoms.out 409 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1389.04082933866-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1389.04082933866-409*${isolated_atom_energy} variable adjusted_pe_metal equal -1389.04082933866-409*0 print "${adjusted_pe_metal} eV" file output/dump_022.6199/energy.out -1389.04082933866 eV print "${mindist_metal} Angstroms" file output/dump_022.6199/mindistance.out 2.47681268298329 Angstroms write_dump all cfg output/dump_022.6199/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_022.6199/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:04