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 54.48731487614331*${_u_distance}
variable xmax_converted equal 54.48731487614331*1
variable ymin_converted equal -54.491364886362526*${_u_distance}
variable ymin_converted equal -54.491364886362526*1
variable ymax_converted equal 54.491364886362526*${_u_distance}
variable ymax_converted equal 54.491364886362526*1
variable zmin_converted equal 0.0*${_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 54.4873148761433 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 54.4873148761433 -54.4913648863625 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 54.4873148761433 -54.4913648863625 54.4913648863625 ${zmin_converted} ${zmax_converted} units box
region             whole block 0 54.4873148761433 -54.4913648863625 54.4913648863625 0 ${zmax_converted} units box
region             whole block 0 54.4873148761433 -54.4913648863625 54.4913648863625 0 4.05001021921635 units box
create_box         2 whole
Created orthogonal box = (0 -54.4914 0) to (54.4873 54.4914 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 54.4913648863625 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 10 -9 0 orient y 9 10 0 orient z 0 0 1
lattice            fcc 4.05001021921635 orient x 10 -9 0 orient y 9 10 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.71966 5.71966 4.05001
create_atoms       1 region upper
Created 726 atoms
  create_atoms CPU = 0.000250101 secs
group              upper type 1
726 atoms in group upper
mass               1 26.981538*${_u_mass}
mass               1 26.981538*1
displace_atoms     upper move 6.054130821183169 0 0.3333333333333333 units lattice
region             lower block INF INF ${ymin_converted}  0.0 INF INF units box
region             lower block INF INF -54.4913648863625  0.0 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 10 9 0 orient y -9 10 0 orient z 0 0 1
lattice            fcc 4.05001021921635 orient x 10 9 0 orient y -9 10 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.71966 5.71966 4.05001
create_atoms       2 region lower
Created 726 atoms
  create_atoms CPU = 0.000129938 secs
group              lower type 2
726 atoms in group lower
displace_atoms     lower move -6.054130821183169 0 -0.3333333333333333 units lattice
mass               2 26.981538*${_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 = 15 29 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 28 atoms, new total = 1424
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 = 15 29 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) = 5.086 | 5.086 | 5.086 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -4796.1361            0   -4796.1361    -751.8758 
     323            0   -4818.8131            0   -4818.8131   -11176.663 
Loop time of 2.02635 on 1 procs for 323 steps with 1424 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 = 
        -4796.13607435     -4818.81314619     -4818.81314619
  Force two-norm initial, final = 16.6276 1.64693e-06
  Force max component initial, final = 3.59224 1.84074e-07
  Final line search alpha, max atom move = 1 1.84074e-07
  Iterations, force evaluations = 323 613

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.9595     | 1.9595     | 1.9595     |   0.0 | 96.70
Neigh   | 0.019235   | 0.019235   | 0.019235   |   0.0 |  0.95
Comm    | 0.029377   | 0.029377   | 0.029377   |   0.0 |  1.45
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.0182     |            |       |  0.90

Nlocal:    1424 ave 1424 max 1424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8946 ave 8946 max 8946 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:  146504 ave 146504 max 146504 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 146504
Ave neighs/atom = 102.882
Neighbor list builds = 5
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) = 5.086 | 5.086 | 5.086 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
     323            0   -4818.8131            0   -4818.8131   -11176.663    24049.675 
    1323            0   -4819.5844            0   -4819.5844   -3314.7771    23799.141 
Loop time of 6.92213 on 1 procs for 1000 steps with 1424 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 = 
        -4818.81314619     -4819.58440793     -4819.58440858
  Force two-norm initial, final = 175.767 0.0765979
  Force max component initial, final = 144.178 0.0590227
  Final line search alpha, max atom move = 0.0226982 0.00133971
  Iterations, force evaluations = 1000 1990

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.5117     | 6.5117     | 6.5117     |   0.0 | 94.07
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.089762   | 0.089762   | 0.089762   |   0.0 |  1.30
Output  | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.3207     |            |       |  4.63

Nlocal:    1424 ave 1424 max 1424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8926 ave 8926 max 8926 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:  144832 ave 144832 max 144832 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 144832
Ave neighs/atom = 101.708
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 = 15 29 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) = 5.224 | 5.224 | 5.224 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -4819.5844            0   -4819.5844   -3314.7771 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 1424 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:    1424 ave 1424 max 1424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8926 ave 8926 max 8926 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:  160048 ave 160048 max 160048 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 160048
Ave neighs/atom = 112.393
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) = 5.224 | 5.224 | 5.224 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   -4819.5844   -4819.5844    54.526505    108.98273    4.0049393   -3314.7771   -3314.7771   -1.2976979   -9939.1042   -3.9292346    2.6167249    179.72275 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 1424 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:    1424 ave 1424 max 1424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8926 ave 8926 max 8926 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    80024 ave 80024 max 80024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  160048 ave 160048 max 160048 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 160048
Ave neighs/atom = 112.393
Neighbor list builds = 0
Dangerous builds = 0
variable           num_atoms equal "count(all)"
print              "${num_atoms}" file output/dump_083.9744/numatoms.out
1424
variable  adjusted_pe_metal  equal ${pe_metal}-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -4819.58440857788-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -4819.58440857788-1424*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -4819.58440857788-1424*0
print              "${adjusted_pe_metal} eV" file output/dump_083.9744/energy.out
-4819.58440857788 eV
print              "${mindist_metal} Angstroms" file output/dump_083.9744/mindistance.out
2.61672493721117 Angstroms
write_dump         all cfg output/dump_083.9744/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_083.9744/success.out
This indicates that LAMMPS ran successfully
Total wall time: 0:00:09