# different energies in "energy final" and the last line of the log file

Dear lammps users,

I'm trying to calculate vacancy formation energy on an edge dislocation
core in FCC Al under uniaxial tensile and compressive stresses.

To this end I first relax atomic positions for a dislocation without a
vacancy, setting uniaxial stress to +-50 MPa along a Burgers vector.

The log file lists potential energy, stresses, simulation volume size -
one line per ten minimization steps. After minimization is finished
"energy final" is printed as well.

In all the lammps simulations I've made so far the two values: potential
energy at the last line of the corresponding log list and the "energy
final" values coincided, or at most differed by very insignificant
amount less that 0.01 eV. This is not the case in my current dislocation
under pressure modelling.

Here is the table:

Py "last line" Energy "energy final" Energy

-50 MPa -152265.06 -152261.660793
0 MPa -152265.12 -152265.11734
+50 MPa -152265.03 -152268.70936

My first idea looking at this table was: taking into account the facts that
1. for all pressures "last line" Energies are very close,
2 for zero pressure "last line" and "energy final" Energies are very close,
3. for +- 50 MPa "energy final" energies are shifted by about the same
amount but in different directions,
one may suppose that "last line" energy does not include (Pressure) x
(Volume change) term and "energy final" does.

But unfortunately such supposition seems not to be true. I made some
further experiments:
1. The same +- 50 MPa for ideal FCC Al crystal without dislocations with
the same simulation volume size. In this case "last line" and "energy
final" are very close.
2. Deliberately setting somewhat wrong lattice constant thus introducing
extra pressure, "last line" and "energy final" are the same again.

So, can somebody give me a clue, what might this discrepancy between
"last line" and "energy final" mean?

Konstantin

============================= -50 MPa input====================
# Input file for Vacancy Formation Energy

#clear
#units metal
#dimension 3
#boundary p p p
#atom_style atomic

# ------------------------ FORCE FIELDS -----------------------
pair_style eam/alloy
pair_coeff * * ../../Al99.eam.alloy Al
#---------------------------Settings----------------------------
compute csym all centro/atom fcc
compute eng all pe/atom
compute eatoms all reduce sum c_eng
#fix 1 all box/relax x 0.0 y 0.0 z 0.0 vmax 0.001
fix 1 all box/relax x 0.0 y -500.0 z 0.0 vmax 0.001

reset_timestep 0

thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms

dump 1 all custom 1 dump.relax.2.* id type x y z c_csym c_eng fx fy fz
#dump 1 all custom 400 dump.relax.2.* x y z

#min_style sd
#min_style hftn
min_style cg
minimize 1e-25 1e-25 500000 500000

=============================== -50 MPa log ==========================
LAMMPS (14 May 2016)
# Input file for Vacancy Formation Energy

#clear
#units metal
#dimension 3
#boundary p p p
#atom_style atomic

orthogonal box = (0 0 0) to (74.4033 91.641 112.237)
1 by 2 by 2 MPI processor grid
45360 atoms
# ------------------------ FORCE FIELDS -----------------------
pair_style eam/alloy
pair_coeff * * ../../Al99.eam.alloy Al
#---------------------------Settings----------------------------
compute csym all centro/atom fcc
compute eng all pe/atom
compute eatoms all reduce sum c_eng
#fix 1 all box/relax x 0.0 y 0.0 z 0.0 vmax 0.001
fix 1 all box/relax x 0.0 y -500.0 z 0.0 vmax 0.001

reset_timestep 0

thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms

dump 1 all custom 1 dump.relax.2.* id type x y z c_csym c_eng fx fy fz
#dump 1 all custom 400 dump.relax.2.* x y z

#min_style sd
#min_style hftn
min_style cg
minimize 1e-25 1e-25 500000 500000
WARNING: Resetting reneighboring criteria during minimization
(../min.cpp:168)
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.1436 -> bins = 18 23 28
Memory usage per processor = 10.3951 Mbytes
Step PotEng Lx Ly Lz Press Pxx Pyy Pzz eatoms
0 -152200.55 74.403251 91.641039 112.23689
-11855.853 -9455.8598 -17988.508 -8123.1911 -152200.55
10 -152260.06 74.1996 90.724629 112.03954
-419.568 842.70847 -3316.4051 1214.9927 -152260.06
20 -152264.86 74.327298 90.338085 112.27821
-85.131029 85.731173 -426.77391 85.649645 -152264.86
30 -152264.87 74.330271 90.339113 112.28318
-163.50448 5.5088942 -497.31138 1.2890504 -152264.87
40 -152264.88 74.330168 90.338961 112.28332
-163.50159 6.9628234 -498.8159 1.3482988 -152264.88
50 -152264.9 74.330706 90.338522 112.28306
-163.59221 2.0970711 -495.51682 2.6431209 -152264.9
.................

7380 -152265.06 74.335704 90.331457 112.28355
-164.3806 1.0867458 -497.95564 3.7270898 -152265.06
7390 -152265.06 74.335605 90.331148 112.28393
-163.30988 2.8165779 -495.00709 2.2608655 -152265.06
7400 -152265.06 74.335894 90.33112 112.28356
-163.6151 0.1080608 -495.07686 4.1234828 -152265.06
7410 -152265.06 74.33566 90.331197 112.28381
-163.56737 2.1707065 -495.4881 2.6152899 -152265.06
7420 -152265.06 74.33664 90.330737 112.28303
-164.61913 -6.9254688 -493.31943 6.3875139 -152265.06
7430 -152265.06 74.335668 90.331172 112.28381
-163.44074 2.2497751 -495.23289 2.660889 -152265.06
7440 -152265.06 74.335551 90.331632 112.28385
-166.43118 0.98132387 -500.53198 0.25712749 -152265.06
7446 -152265.06 74.335678 90.331182 112.2838
-163.5457 2.1119319 -495.33747 2.5884246 -152265.06
Loop time of 909.591 on 4 procs for 7446 steps with 45360 atoms

Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-152200.54572 -152261.660793 -152261.660793
Force two-norm initial, final = 10258.3 0.062062
Force max component initial, final = 8353.34 0.0380085
Final line search alpha, max atom move = 2.12807e-06 8.08847e-08
Iterations, force evaluations = 7446 14974