LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
# input for relaxed vacancy formation energy at constant pressure

units           electron
atom_style      atomic

# Atomic volume for MGPT potential
variable        atomic_vol equal 121.863

# Derive effective lattice volume from atomic volume for 249-site cell
variable        lat_vol equal ${atomic_vol}*249/250
variable        lat_vol equal 121.863*249/250

# Derive lattice constant from lattice volume
variable        lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
variable        lattice_constant equal (121.375548*2.0)^(1.0/3.0)

# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice         bcc ${lattice_constant}
lattice         bcc 6.23812011912273
Lattice spacing in x,y,z = 6.2381201 6.2381201 6.2381201
region          box block 0 5 0 5 0 5
create_box      1 box
Created orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
  1 by 2 by 2 MPI processor grid
create_atoms    1 box
Created 250 atoms
  using lattice units in orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
  create_atoms CPU = 0.000 seconds

# Remove central atom from bcc lattice to create vacancy
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
delete_atoms region vacancy
Deleted 1 atoms, new total = 249

# Define potential for use in simulation
pair_style      mgpt

# Set parameters for potential:
#                  parameter files  atomic volume
#pair_coeff      * * parmin potin    ${atomic_vol}
pair_coeff      * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin  ${atomic_vol}
pair_coeff      * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin  121.863
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30

# Set neighbor list parameters
neighbor        0.1 bin
neigh_modify    every 1 delay 0 check yes

# Dump coordinates to file every 50 timesteps
# dump            id all atom 50 dump.vacmin-bcc

# Output thermodynamical data every 10 timesteps
thermo          10

# Set output quantities and output format
thermo_style custom step vol temp pe etotal press

## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e

# minimize total energy
min_style cg
minimize 1.0e-10 1.0e-10 5000 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 13.171237
  ghost atom cutoff = 13.171237
  binsize = 6.5856184, bins = 5 5 5
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair mgpt, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
  (2) pair mgpt, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.855 | 4.855 | 4.855 Mbytes
   Step         Volume          Temp          PotEng         TotEng         Press     
         0   30343.887      0             -73.994511     -73.994511     -1.0504398e+09
        10   30343.887      0             -74.002332     -74.002332     -1.107516e+09 
        20   30343.887      0             -74.00485      -74.00485      -1.1316373e+09
        30   30343.887      0             -74.005762     -74.005762     -1.143304e+09 
        40   30343.887      0             -74.006116     -74.006116     -1.149395e+09 
        50   30343.887      0             -74.006262     -74.006262     -1.1527914e+09
        60   30343.887      0             -74.006323     -74.006323     -1.1547677e+09
        70   30343.887      0             -74.00635      -74.00635      -1.1559529e+09
        80   30343.887      0             -74.006361     -74.006361     -1.1566763e+09
        90   30343.887      0             -74.006366     -74.006366     -1.1571256e+09
       100   30343.887      0             -74.006369     -74.006369     -1.1574093e+09
       110   30343.887      0             -74.00637      -74.00637      -1.1575908e+09
       120   30343.887      0             -74.00637      -74.00637      -1.1577083e+09
       130   30343.887      0             -74.00637      -74.00637      -1.1577849e+09
       139   30343.887      0             -74.006371     -74.006371     -1.1578311e+09
Loop time of 0.972735 on 4 procs for 139 steps with 249 atoms

89.3% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
     -73.9945109564331  -74.0063705487423  -74.0063705556773
  Force two-norm initial, final = 0.036622686 8.090814e-05
  Force max component initial, final = 0.0073094815 8.0524207e-06
  Final line search alpha, max atom move = 1 8.0524207e-06
  Iterations, force evaluations = 139 139

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.9418     | 0.94514    | 0.9488     |   0.3 | 97.16
Neigh   | 0.0083827  | 0.0084423  | 0.0085002  |   0.0 |  0.87
Comm    | 0.011833   | 0.015482   | 0.01882    |   2.0 |  1.59
Output  | 0.0002579  | 0.00029089 | 0.000389   |   0.0 |  0.03
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.003376   |            |       |  0.35

Nlocal:          62.25 ave          68 max          59 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost:         867.75 ave         871 max         862 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs:           1984 ave        2211 max        1853 min
Histogram: 1 1 1 0 0 0 0 0 0 1
FullNghs:         3968 ave        4334 max        3761 min
Histogram: 1 1 0 1 0 0 0 0 0 1

Total # of neighbors = 15872
Ave neighs/atom = 63.742972
Neighbor list builds = 4
Dangerous builds = 0

# Convert energy to rydbergs and pressure to gpa

variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"

print "number of atoms = ${natoms}"
number of atoms = 249
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.863
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.594428679162068
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -1.15783109519336
print "${natoms}   ${atvol}   ${etot}   ${ptotgpa}"
249   121.863   -148.012741111355   -1.15783109519336
print "${atvol}   ${etotry}   ${ptotgpa}"
121.863   -0.594428679162068   -1.15783109519336
Total wall time: 0:00:00
