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[lammps-users] CG Energy Minimization returning NaN for specific potentials


From: Ian Chesser <ichesser@...1789...>
Date: Fri, 10 Nov 2017 13:57:42 -0500

Hello, 

I am calculating the twinning fault energy of a number of EAM potentials for FCC metals (from this site https://sites.google.com/site/eampotentials/). 
I have a simple script that automatically generates perfect, oriented FCC crystals by stacking up two half crystals (defined by regions), and minimizes the energy of the structure via cg. Dump files before minimization show that a perfect crystal is generated in each case (boundary conditions are p p f). However, during minimization, nan values are returned for certain potentials. I attach a "good" and "bad" case below. Note that the potential calls are correct and used in other scripts. My question is, what could be causing the nan values during minimization? 

I have read that "bad" structures lead to NaN values, but dumping them beforehand shows that the structures are as intended. Could it be numerical instability of the dimensions input to the region command that are causing these nan values? I am using variables as the box dimensions input to the region command. I have found in other scripts for the potentials that are giving NaN below that explicitly entering numbers into the region command rather than variables defined as those numbers does not produce this issue. Any insight into why nan values are being produced is welcome. See log file attached as well. 

Thank you for the help,
--
Ian Chesser / ichesser@...1789... / 713-516-2491

PNG image

shell mkdir out_Al_GTFE
shell rm params_Al_GTFE.txt
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1283)
# --------------------- Define Variables ------------------
# Defining variables here is important to run loops correctly
variable latparam1 equal 4.05
variable nshiftsx equal 2
variable nshiftsy equal 2
variable nx equal 20
variable ny equal 20
variable nz equal 20
variable cnt equal 0 #total count
variable x_displace equal -1/${nshiftsx}*(${latparam1}*sqrt(6)/2)
variable x_displace equal -1/2*(${latparam1}*sqrt(6)/2)
variable x_displace equal -1/2*(4.05*sqrt(6)/2)
variable y_displace equal -1/${nshiftsy}*(${latparam1}*sqrt(2)/2)
variable y_displace equal -1/2*(${latparam1}*sqrt(2)/2)
variable y_displace equal -1/2*(4.05*sqrt(2)/2)
variable xdim equal ${latparam1}*sqrt(6)/2*${nx} # spacing in <112> direction
variable xdim equal 4.05*sqrt(6)/2*${nx} 
variable xdim equal 4.05*sqrt(6)/2*20 
variable ydim equal ${latparam1}*sqrt(2)/2*${ny} # spacing in <110> direction
variable ydim equal 4.05*sqrt(2)/2*${ny} 
variable ydim equal 4.05*sqrt(2)/2*20 
variable zdim equal ${latparam1}*sqrt(3)*${nz}/2
variable zdim equal 4.05*sqrt(3)*${nz}/2
variable zdim equal 4.05*sqrt(3)*20/2
variable zdim2 equal ${latparam1}*sqrt(3)*${nz}
variable zdim2 equal 4.05*sqrt(3)*${nz}
variable zdim2 equal 4.05*sqrt(3)*20
print "zdim: ${zdim}"
zdim: 70.1480577065395
print "zdim2: ${zdim2}"
zdim2: 140.296115413079
variable zplus equal (${zdim}+${latparam1}*sqrt(3)/3)-1 #for shifting on top of SF
variable zplus equal (70.1480577065395+${latparam1}*sqrt(3)/3)-1 
variable zplus equal (70.1480577065395+4.05*sqrt(3)/3)-1 
variable xsf equal ${latparam1}*sqrt(6)/6*${nx}
variable xsf equal 4.05*sqrt(6)/6*${nx}
variable xsf equal 4.05*sqrt(6)/6*20
label loopi
variable i loop 0 ${nshiftsx}
variable i loop 0 2
label loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*0 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*0 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 0+1
print "count: ${cnt}"
count: 1
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.385857 on 1 procs for 1 steps with 48000 atoms

97.5% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.37543    | 0.37543    | 0.37543    |   0.0 | 97.30
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0015078  | 0.0015078  | 0.0015078  |   0.0 |  0.39
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00053787 | 0.00053787 | 0.00053787 |   0.0 |  0.14
Other   |            | 0.008383   |            |       |  2.17

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.122106 on 1 procs for 1 steps with 48000 atoms

Performance: 0.708 ns/day, 33.918 hours/ns, 8.190 timesteps/s
98.4% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12102    | 0.12102    | 0.12102    |   0.0 | 99.11
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00046921 | 0.00046921 | 0.00046921 |   0.0 |  0.38
Output  | 0.00029588 | 0.00029588 | 0.00029588 |   0.0 |  0.24
Modify  | 0.00018597 | 0.00018597 | 0.00018597 |   0.0 |  0.15
Other   |            | 0.0001311  |            |       |  0.11

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -0 ${ys} 0.0 units box
displace_atoms upper_plus move -0 -0 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160659.32   -160659.32 
       3   -160661.68   -160661.68 
Loop time of 0.395092 on 1 procs for 1 steps with 48000 atoms

98.4% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160659.315522     -160659.315522     -160661.677346
  Force two-norm initial, final = 4.3937 3.7093
  Force max component initial, final = 0.0974279 0.0742982
  Final line search alpha, max atom move = 1 0.0742982
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.38994    | 0.38994    | 0.38994    |   0.0 | 98.70
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00097823 | 0.00097823 | 0.00097823 |   0.0 |  0.25
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00074577 | 0.00074577 | 0.00074577 |   0.0 |  0.19
Other   |            | 0.003424   |            |       |  0.87

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.1 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160661.68   -160661.68 
       4   -160661.68   -160661.68 
Loop time of 0.222687 on 1 procs for 1 steps with 48000 atoms

Performance: 0.388 ns/day, 61.858 hours/ns, 4.491 timesteps/s
96.2% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12109    | 0.12109    | 0.12109    |   0.0 | 54.38
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00037503 | 0.00037503 | 0.00037503 |   0.0 |  0.17
Output  | 0.1006     | 0.1006     | 0.1006     |   0.0 | 45.17
Modify  | 0.00051022 | 0.00051022 | 0.00051022 |   0.0 |  0.23
Other   |            | 0.0001161  |            |       |  0.05

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.1 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.1 out_Al_GTFE/dump.Al_GTFE.1
next j
jump SELF loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*0 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*1 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 1+1
print "count: ${cnt}"
count: 2
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.388372 on 1 procs for 1 steps with 48000 atoms

98.8% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.38189    | 0.38189    | 0.38189    |   0.0 | 98.33
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00094867 | 0.00094867 | 0.00094867 |   0.0 |  0.24
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00055838 | 0.00055838 | 0.00055838 |   0.0 |  0.14
Other   |            | 0.004971   |            |       |  1.28

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.124924 on 1 procs for 1 steps with 48000 atoms

Performance: 0.692 ns/day, 34.701 hours/ns, 8.005 timesteps/s
98.2% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12372    | 0.12372    | 0.12372    |   0.0 | 99.04
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00050282 | 0.00050282 | 0.00050282 |   0.0 |  0.40
Output  | 0.00035501 | 0.00035501 | 0.00035501 |   0.0 |  0.28
Modify  | 0.00019789 | 0.00019789 | 0.00019789 |   0.0 |  0.16
Other   |            | 0.0001435  |            |       |  0.11

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -0 ${ys} 0.0 units box
displace_atoms upper_plus move -0 -1.43189123190276 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160513.25   -160513.25 
       3   -160576.15   -160576.15 
Loop time of 0.397336 on 1 procs for 1 steps with 48000 atoms

98.2% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160513.248863     -160513.248863      -160576.15223
  Force two-norm initial, final = 36.3661 11.7808
  Force max component initial, final = 0.918997 0.307643
  Final line search alpha, max atom move = 0.108814 0.0334759
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.39191    | 0.39191    | 0.39191    |   0.0 | 98.63
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.001159   | 0.001159   | 0.001159   |   0.0 |  0.29
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00061011 | 0.00061011 | 0.00061011 |   0.0 |  0.15
Other   |            | 0.00366    |            |       |  0.92

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3032e+06 ave 3.3032e+06 max 3.3032e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3303200
Ave neighs/atom = 68.8167
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.2 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160576.15   -160576.15 
       4   -160576.15   -160576.15 
Loop time of 0.229748 on 1 procs for 1 steps with 48000 atoms

Performance: 0.376 ns/day, 63.819 hours/ns, 4.353 timesteps/s
96.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.1285     | 0.1285     | 0.1285     |   0.0 | 55.93
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.000453   | 0.000453   | 0.000453   |   0.0 |  0.20
Output  | 0.1001     | 0.1001     | 0.1001     |   0.0 | 43.57
Modify  | 0.00057387 | 0.00057387 | 0.00057387 |   0.0 |  0.25
Other   |            | 0.000123   |            |       |  0.05

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3e+06 ave 3.3e+06 max 3.3e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3300000
Ave neighs/atom = 68.75
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.2 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.2 out_Al_GTFE/dump.Al_GTFE.2
next j
jump SELF loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*0 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*2 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 2+1
print "count: ${cnt}"
count: 3
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.37765 on 1 procs for 1 steps with 48000 atoms

98.8% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.37225    | 0.37225    | 0.37225    |   0.0 | 98.57
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00086021 | 0.00086021 | 0.00086021 |   0.0 |  0.23
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00058484 | 0.00058484 | 0.00058484 |   0.0 |  0.15
Other   |            | 0.003958   |            |       |  1.05

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.122889 on 1 procs for 1 steps with 48000 atoms

Performance: 0.703 ns/day, 34.136 hours/ns, 8.137 timesteps/s
98.5% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12168    | 0.12168    | 0.12168    |   0.0 | 99.02
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0005281  | 0.0005281  | 0.0005281  |   0.0 |  0.43
Output  | 0.00035095 | 0.00035095 | 0.00035095 |   0.0 |  0.29
Modify  | 0.00019884 | 0.00019884 | 0.00019884 |   0.0 |  0.16
Other   |            | 0.0001299  |            |       |  0.11

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -0 ${ys} 0.0 units box
displace_atoms upper_plus move -0 -2.86378246380552 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160659.32   -160659.32 
       3   -160661.68   -160661.68 
Loop time of 0.399815 on 1 procs for 1 steps with 48000 atoms

98.9% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160659.315522     -160659.315522     -160661.677346
  Force two-norm initial, final = 4.3937 3.7093
  Force max component initial, final = 0.0974279 0.0742982
  Final line search alpha, max atom move = 1 0.0742982
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.39332    | 0.39332    | 0.39332    |   0.0 | 98.38
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0011997  | 0.0011997  | 0.0011997  |   0.0 |  0.30
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00071359 | 0.00071359 | 0.00071359 |   0.0 |  0.18
Other   |            | 0.004578   |            |       |  1.14

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.3 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160661.68   -160661.68 
       4   -160661.68   -160661.68 
Loop time of 0.243697 on 1 procs for 1 steps with 48000 atoms

Performance: 0.355 ns/day, 67.694 hours/ns, 4.103 timesteps/s
95.3% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.13192    | 0.13192    | 0.13192    |   0.0 | 54.13
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00042582 | 0.00042582 | 0.00042582 |   0.0 |  0.17
Output  | 0.11067    | 0.11067    | 0.11067    |   0.0 | 45.41
Modify  | 0.00054908 | 0.00054908 | 0.00054908 |   0.0 |  0.23
Other   |            | 0.0001287  |            |       |  0.05

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.3 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.3 out_Al_GTFE/dump.Al_GTFE.3
next j
jump SELF loopj
variable j delete
next i
jump SELF loopi
variable i loop 0 ${nshiftsx}
variable i loop 0 2
label loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*1 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*0 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 3+1
print "count: ${cnt}"
count: 4
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.383884 on 1 procs for 1 steps with 48000 atoms

98.6% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.37753    | 0.37753    | 0.37753    |   0.0 | 98.35
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00089097 | 0.00089097 | 0.00089097 |   0.0 |  0.23
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00057697 | 0.00057697 | 0.00057697 |   0.0 |  0.15
Other   |            | 0.004881   |            |       |  1.27

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.124942 on 1 procs for 1 steps with 48000 atoms

Performance: 0.692 ns/day, 34.706 hours/ns, 8.004 timesteps/s
98.3% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12396    | 0.12396    | 0.12396    |   0.0 | 99.21
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00040603 | 0.00040603 | 0.00040603 |   0.0 |  0.32
Output  | 0.00029111 | 0.00029111 | 0.00029111 |   0.0 |  0.23
Modify  | 0.00017595 | 0.00017595 | 0.00017595 |   0.0 |  0.14
Other   |            | 0.000113   |            |       |  0.09

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -2.48010836456797 ${ys} 0.0 units box
displace_atoms upper_plus move -2.48010836456797 -0 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160513.25   -160513.25 
       3   -160576.15   -160576.15 
Loop time of 0.380688 on 1 procs for 1 steps with 48000 atoms

99.2% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160513.248863     -160513.248863      -160576.15223
  Force two-norm initial, final = 36.3661 11.7808
  Force max component initial, final = 0.918997 0.307643
  Final line search alpha, max atom move = 0.108814 0.0334759
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.37559    | 0.37559    | 0.37559    |   0.0 | 98.66
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0009129  | 0.0009129  | 0.0009129  |   0.0 |  0.24
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00055981 | 0.00055981 | 0.00055981 |   0.0 |  0.15
Other   |            | 0.003626   |            |       |  0.95

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3032e+06 ave 3.3032e+06 max 3.3032e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3303200
Ave neighs/atom = 68.8167
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.4 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160576.15   -160576.15 
       4   -160576.15   -160576.15 
Loop time of 0.215654 on 1 procs for 1 steps with 48000 atoms

Performance: 0.401 ns/day, 59.904 hours/ns, 4.637 timesteps/s
96.5% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12291    | 0.12291    | 0.12291    |   0.0 | 57.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00042486 | 0.00042486 | 0.00042486 |   0.0 |  0.20
Output  | 0.091676   | 0.091676   | 0.091676   |   0.0 | 42.51
Modify  | 0.00052691 | 0.00052691 | 0.00052691 |   0.0 |  0.24
Other   |            | 0.0001132  |            |       |  0.05

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3e+06 ave 3.3e+06 max 3.3e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3300000
Ave neighs/atom = 68.75
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.4 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.4 out_Al_GTFE/dump.Al_GTFE.4
next j
jump SELF loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*1 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*1 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 4+1
print "count: ${cnt}"
count: 5
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.381591 on 1 procs for 1 steps with 48000 atoms

96.8% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.37394    | 0.37394    | 0.37394    |   0.0 | 97.99
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0014842  | 0.0014842  | 0.0014842  |   0.0 |  0.39
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00057697 | 0.00057697 | 0.00057697 |   0.0 |  0.15
Other   |            | 0.005592   |            |       |  1.47

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.124301 on 1 procs for 1 steps with 48000 atoms

Performance: 0.695 ns/day, 34.528 hours/ns, 8.045 timesteps/s
97.6% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12314    | 0.12314    | 0.12314    |   0.0 | 99.06
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00052595 | 0.00052595 | 0.00052595 |   0.0 |  0.42
Output  | 0.00031495 | 0.00031495 | 0.00031495 |   0.0 |  0.25
Modify  | 0.00018406 | 0.00018406 | 0.00018406 |   0.0 |  0.15
Other   |            | 0.0001402  |            |       |  0.11

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -2.48010836456797 ${ys} 0.0 units box
displace_atoms upper_plus move -2.48010836456797 -1.43189123190276 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160659.32   -160659.32 
       3   -160661.68   -160661.68 
Loop time of 0.48719 on 1 procs for 1 steps with 48000 atoms

94.7% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160659.315522     -160659.315522     -160661.677346
  Force two-norm initial, final = 4.3937 3.7093
  Force max component initial, final = 0.0974279 0.0742982
  Final line search alpha, max atom move = 1 0.0742982
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.48074    | 0.48074    | 0.48074    |   0.0 | 98.68
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0012298  | 0.0012298  | 0.0012298  |   0.0 |  0.25
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00072074 | 0.00072074 | 0.00072074 |   0.0 |  0.15
Other   |            | 0.004496   |            |       |  0.92

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.5 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160661.68   -160661.68 
       4   -160661.68   -160661.68 
Loop time of 0.284444 on 1 procs for 1 steps with 48000 atoms

Performance: 0.304 ns/day, 79.012 hours/ns, 3.516 timesteps/s
86.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.14071    | 0.14071    | 0.14071    |   0.0 | 49.47
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00050712 | 0.00050712 | 0.00050712 |   0.0 |  0.18
Output  | 0.14141    | 0.14141    | 0.14141    |   0.0 | 49.72
Modify  | 0.001652   | 0.001652   | 0.001652   |   0.0 |  0.58
Other   |            | 0.0001612  |            |       |  0.06

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.5 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.5 out_Al_GTFE/dump.Al_GTFE.5
next j
jump SELF loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*1 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*2 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 5+1
print "count: ${cnt}"
count: 6
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.4281 on 1 procs for 1 steps with 48000 atoms

91.6% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.42073    | 0.42073    | 0.42073    |   0.0 | 98.28
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0014141  | 0.0014141  | 0.0014141  |   0.0 |  0.33
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00071406 | 0.00071406 | 0.00071406 |   0.0 |  0.17
Other   |            | 0.005238   |            |       |  1.22

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.137829 on 1 procs for 1 steps with 48000 atoms

Performance: 0.627 ns/day, 38.286 hours/ns, 7.255 timesteps/s
92.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.13677    | 0.13677    | 0.13677    |   0.0 | 99.23
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00044227 | 0.00044227 | 0.00044227 |   0.0 |  0.32
Output  | 0.00031614 | 0.00031614 | 0.00031614 |   0.0 |  0.23
Modify  | 0.00018787 | 0.00018787 | 0.00018787 |   0.0 |  0.14
Other   |            | 0.0001109  |            |       |  0.08

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -2.48010836456797 ${ys} 0.0 units box
displace_atoms upper_plus move -2.48010836456797 -2.86378246380552 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160513.25   -160513.25 
       3   -160576.15   -160576.15 
Loop time of 0.425412 on 1 procs for 1 steps with 48000 atoms

95.4% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160513.248863     -160513.248863      -160576.15223
  Force two-norm initial, final = 36.3661 11.7808
  Force max component initial, final = 0.918997 0.307643
  Final line search alpha, max atom move = 0.108814 0.0334759
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.41928    | 0.41928    | 0.41928    |   0.0 | 98.56
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0013039  | 0.0013039  | 0.0013039  |   0.0 |  0.31
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00086808 | 0.00086808 | 0.00086808 |   0.0 |  0.20
Other   |            | 0.003961   |            |       |  0.93

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3032e+06 ave 3.3032e+06 max 3.3032e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3303200
Ave neighs/atom = 68.8167
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.6 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160576.15   -160576.15 
       4   -160576.15   -160576.15 
Loop time of 0.253463 on 1 procs for 1 steps with 48000 atoms

Performance: 0.341 ns/day, 70.406 hours/ns, 3.945 timesteps/s
94.1% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.13716    | 0.13716    | 0.13716    |   0.0 | 54.11
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00051618 | 0.00051618 | 0.00051618 |   0.0 |  0.20
Output  | 0.1151     | 0.1151     | 0.1151     |   0.0 | 45.41
Modify  | 0.00056601 | 0.00056601 | 0.00056601 |   0.0 |  0.22
Other   |            | 0.0001199  |            |       |  0.05

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3e+06 ave 3.3e+06 max 3.3e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3300000
Ave neighs/atom = 68.75
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.6 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.6 out_Al_GTFE/dump.Al_GTFE.6
next j
jump SELF loopj
variable j delete
next i
jump SELF loopi
variable i loop 0 ${nshiftsx}
variable i loop 0 2
label loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*2 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*0 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 6+1
print "count: ${cnt}"
count: 7
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.414622 on 1 procs for 1 steps with 48000 atoms

94.5% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.40737    | 0.40737    | 0.40737    |   0.0 | 98.25
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0015228  | 0.0015228  | 0.0015228  |   0.0 |  0.37
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00061297 | 0.00061297 | 0.00061297 |   0.0 |  0.15
Other   |            | 0.00512    |            |       |  1.23

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.123076 on 1 procs for 1 steps with 48000 atoms

Performance: 0.702 ns/day, 34.188 hours/ns, 8.125 timesteps/s
97.2% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.12199    | 0.12199    | 0.12199    |   0.0 | 99.12
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00049019 | 0.00049019 | 0.00049019 |   0.0 |  0.40
Output  | 0.00028801 | 0.00028801 | 0.00028801 |   0.0 |  0.23
Modify  | 0.000175   | 0.000175   | 0.000175   |   0.0 |  0.14
Other   |            | 0.0001318  |            |       |  0.11

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -4.96021672913594 ${ys} 0.0 units box
displace_atoms upper_plus move -4.96021672913594 -0 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160659.32   -160659.32 
       3   -160661.68   -160661.68 
Loop time of 0.504332 on 1 procs for 1 steps with 48000 atoms

93.7% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160659.315522     -160659.315522     -160661.677346
  Force two-norm initial, final = 4.3937 3.7093
  Force max component initial, final = 0.0974279 0.0742982
  Final line search alpha, max atom move = 1 0.0742982
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.49836    | 0.49836    | 0.49836    |   0.0 | 98.82
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0012262  | 0.0012262  | 0.0012262  |   0.0 |  0.24
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00082612 | 0.00082612 | 0.00082612 |   0.0 |  0.16
Other   |            | 0.003924   |            |       |  0.78

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.7 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160661.68   -160661.68 
       4   -160661.68   -160661.68 
Loop time of 0.230832 on 1 procs for 1 steps with 48000 atoms

Performance: 0.374 ns/day, 64.120 hours/ns, 4.332 timesteps/s
93.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.1266     | 0.1266     | 0.1266     |   0.0 | 54.85
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00051785 | 0.00051785 | 0.00051785 |   0.0 |  0.22
Output  | 0.10298    | 0.10298    | 0.10298    |   0.0 | 44.61
Modify  | 0.00057411 | 0.00057411 | 0.00057411 |   0.0 |  0.25
Other   |            | 0.0001559  |            |       |  0.07

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.7 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.7 out_Al_GTFE/dump.Al_GTFE.7
next j
jump SELF loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*2 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*1 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 7+1
print "count: ${cnt}"
count: 8
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.372569 on 1 procs for 1 steps with 48000 atoms

97.6% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.36528    | 0.36528    | 0.36528    |   0.0 | 98.04
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0010569  | 0.0010569  | 0.0010569  |   0.0 |  0.28
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00057006 | 0.00057006 | 0.00057006 |   0.0 |  0.15
Other   |            | 0.005667   |            |       |  1.52

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.133341 on 1 procs for 1 steps with 48000 atoms

Performance: 0.648 ns/day, 37.039 hours/ns, 7.500 timesteps/s
95.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.13198    | 0.13198    | 0.13198    |   0.0 | 98.98
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00052691 | 0.00052691 | 0.00052691 |   0.0 |  0.40
Output  | 0.00043797 | 0.00043797 | 0.00043797 |   0.0 |  0.33
Modify  | 0.00026488 | 0.00026488 | 0.00026488 |   0.0 |  0.20
Other   |            | 0.0001311  |            |       |  0.10

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
variable E equal "c_eatoms"
variable Eo equal $E
variable Eo equal -160659.315522634
# ------------------- Displace top block with specified (xs,ys) coordinates -------------------
#displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B)
displace_atoms upper_plus move ${xs} ${ys} 0.0 units box
displace_atoms upper_plus move -4.96021672913594 ${ys} 0.0 units box
displace_atoms upper_plus move -4.96021672913594 -1.43189123190276 0.0 units box
#only relax forces in z direction during energy minimization
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 23.2978 Mbytes
Step PotEng c_eatoms 
       2   -160513.25   -160513.25 
       3   -160576.15   -160576.15 
Loop time of 0.40282 on 1 procs for 1 steps with 48000 atoms

96.7% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160513.248863     -160513.248863      -160576.15223
  Force two-norm initial, final = 36.3661 11.7808
  Force max component initial, final = 0.918997 0.307643
  Final line search alpha, max atom move = 0.108814 0.0334759
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.39714    | 0.39714    | 0.39714    |   0.0 | 98.59
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0011621  | 0.0011621  | 0.0011621  |   0.0 |  0.29
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.00063705 | 0.00063705 | 0.00063705 |   0.0 |  0.16
Other   |            | 0.003886   |            |       |  0.96

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3032e+06 ave 3.3032e+06 max 3.3032e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3303200
Ave neighs/atom = 68.8167
Neighbor list builds = 0
Dangerous builds = 0
variable Ef equal "c_eatoms"
variable Cf equal 1.60217657e-16
variable A equal (${xdim}*${ydim})*1e-20
variable A equal (99.2043345827187*${ydim})*1e-20
variable A equal (99.2043345827187*57.2756492761104)*1e-20
variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A})
variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17)
#variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done
#variable A is the area of the Stacking fault plane in m^2
#variable Cf is the conversion factor of electro volts to millijoules
#variable SFE is the stacking-fault energy of the system in mJ/m^2
dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
dump 2 all custom 1 dump.Al_GTFE.8 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom
shell cd ..
fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " "
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 27.7187 Mbytes
Step PotEng c_eatoms 
       3   -160576.15   -160576.15 
       4   -160576.15   -160576.15 
Loop time of 0.241203 on 1 procs for 1 steps with 48000 atoms

Performance: 0.358 ns/day, 67.001 hours/ns, 4.146 timesteps/s
95.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.13873    | 0.13873    | 0.13873    |   0.0 | 57.52
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.000422   | 0.000422   | 0.000422   |   0.0 |  0.17
Output  | 0.10135    | 0.10135    | 0.10135    |   0.0 | 42.02
Modify  | 0.00058007 | 0.00058007 | 0.00058007 |   0.0 |  0.24
Other   |            | 0.0001187  |            |       |  0.05

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23909 ave 23909 max 23909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.3e+06 ave 3.3e+06 max 3.3e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3300000
Ave neighs/atom = 68.75
Neighbor list builds = 0
Dangerous builds = 0
undump 2
shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.8 out_Al_GTFE/dump.Al_GTFE.${cnt}
shell mv dump.Al_GTFE.8 out_Al_GTFE/dump.Al_GTFE.8
next j
jump SELF loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.48010836456797*${i} 
variable xs equal -2.48010836456797*2 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.43189123190276*${j} 
variable ys equal -1.43189123190276*2 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 8+1
print "count: ${cnt}"
count: 9
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box
region		1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box
region 		2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box
region 		3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box
region		whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms	1 region 1
Created 24000 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.61362 5.72756 7.01481
create_atoms    1 region 2
Created 24000 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Al.eam Al
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
24000 atoms in group bot
group top region 2
24000 atoms in group top
group upper_plus region 3
23200 atoms in group upper_plus
shell cd out_Al_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 100
thermo_style custom step pe c_eatoms
#create stacking fault to start
displace_atoms top move ${xsf} 0.0 0.0 units box
displace_atoms top move 33.0681115275729 0.0 0.0 units box
fix 1 all setforce 0 0 NULL
min_style cg
minimize 1e-10 1e-10 1 1 #10000 10000
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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 22.6728 Mbytes
Step PotEng c_eatoms 
       0    -160651.8    -160651.8 
       1   -160659.32   -160659.32 
Loop time of 0.450189 on 1 procs for 1 steps with 48000 atoms

87.8% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max force evaluations
  Energy initial, next-to-last, final = 
        -160651.800226     -160651.800226     -160659.315522
  Force two-norm initial, final = 6.85786 4.3937
  Force max component initial, final = 0.154943 0.0974279
  Final line search alpha, max atom move = 0.645399 0.0628799
  Iterations, force evaluations = 1 2

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.43958    | 0.43958    | 0.43958    |   0.0 | 97.64
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.002389   | 0.002389   | 0.002389   |   0.0 |  0.53
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.0010788  | 0.0010788  | 0.0010788  |   0.0 |  0.24
Other   |            | 0.007137   |            |       |  1.59

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym
undump 1
run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25 -> bins = 24 14 33
Memory usage per processor = 17.6728 Mbytes
Step PotEng c_eatoms 
       1   -160659.32   -160659.32 
       2   -160659.32   -160659.32 
Loop time of 0.140208 on 1 procs for 1 steps with 48000 atoms

Performance: 0.616 ns/day, 38.947 hours/ns, 7.132 timesteps/s
98.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.1391     | 0.1391     | 0.1391     |   0.0 | 99.21
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0004499  | 0.0004499  | 0.0004499  |   0.0 |  0.32
Output  | 0.00033402 | 0.00033402 | 0.00033402 |   0.0 |  0.24
Modify  | 0.000211   | 0.000211   | 0.000211   |   0.0 |  0.15
Other   |            | 0.0001099  |            |       |  0.08

Nlocal:    48000 ave 48000 max 48000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23900 ave 23900 max 23900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3296800
Ave neighs/atom = 68.6833
Neighbor list builds = 0
Dangerous builds = 0
shell mkdir out_Ag_GTFE
WARNING: Shell command 'mkdir' failed with error 'File exists' (../input.cpp:1262)
shell rm params_Ag_GTFE.txt
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1283)
# --------------------- Define Variables ------------------
# Defining variables here is important to run loops correctly
variable latparam1 equal 4.09
variable nshiftsx equal 2
variable nshiftsy equal 2
variable nx equal 20
variable ny equal 20
variable nz equal 20
variable cnt equal 0 #total count
variable x_displace equal -1/${nshiftsx}*(${latparam1}*sqrt(6)/2)
variable x_displace equal -1/2*(${latparam1}*sqrt(6)/2)
variable x_displace equal -1/2*(4.09*sqrt(6)/2)
variable y_displace equal -1/${nshiftsy}*(${latparam1}*sqrt(2)/2)
variable y_displace equal -1/2*(${latparam1}*sqrt(2)/2)
variable y_displace equal -1/2*(4.09*sqrt(2)/2)
variable xdim equal ${latparam1}*sqrt(6)/2*${nx} # spacing in <112> direction
variable xdim equal 4.09*sqrt(6)/2*${nx} 
variable xdim equal 4.09*sqrt(6)/2*20 
variable ydim equal ${latparam1}*sqrt(2)/2*${ny} # spacing in <110> direction
variable ydim equal 4.09*sqrt(2)/2*${ny} 
variable ydim equal 4.09*sqrt(2)/2*20 
variable zdim equal ${latparam1}*sqrt(3)*${nz}/2
variable zdim equal 4.09*sqrt(3)*${nz}/2
variable zdim equal 4.09*sqrt(3)*20/2
variable zdim2 equal ${latparam1}*sqrt(3)*${nz}
variable zdim2 equal 4.09*sqrt(3)*${nz}
variable zdim2 equal 4.09*sqrt(3)*20
print "zdim: ${zdim}"
zdim: 70.8408780295671
print "zdim2: ${zdim2}"
zdim2: 141.681756059134
variable zplus equal (${zdim}+${latparam1}*sqrt(3)/3) #for shifting on top of SF
variable zplus equal (70.8408780295671+${latparam1}*sqrt(3)/3) 
variable zplus equal (70.8408780295671+4.09*sqrt(3)/3) 
variable xsf equal ${latparam1}*sqrt(6)/6*${nx}
variable xsf equal 4.09*sqrt(6)/6*${nx}
variable xsf equal 4.09*sqrt(6)/6*20
label loopi
variable i loop 0 ${nshiftsx}
variable i loop 0 2
label loopj
variable j loop 0 ${nshiftsy}
variable j loop 0 2
variable xs equal ${x_displace}*${i} # shift applied in x direction
variable xs equal -2.5046032619958*${i} 
variable xs equal -2.5046032619958*0 
variable ys equal ${y_displace}*${j} # shift applied in z direction
variable ys equal -1.44603336752649*${j} 
variable ys equal -1.44603336752649*0 
# Increment counter
variable cnt equal ${cnt}+1
variable cnt equal 0+1
print "count: ${cnt}"
count: 1
#-------------------- Initialize Simulation ----------------
clear
units		metal
dimension	3
boundary	p p s #fixed surface along z
atom_style	atomic
# --------------------- Initial structure definition---------------------
# block oriented s.t. <112> || x, <110> || y, <111> || z
lattice		fcc ${latparam1}
lattice		fcc 4.09
Lattice spacing in x,y,z = 4.09 4.09 4.09
region		1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 100.184130479832 -.001 ${ydim} -.001 ${zdim} units box
region		1 block -.001 100.184130479832 -.001 57.8413347010596 -.001 ${zdim} units box
region		1 block -.001 100.184130479832 -.001 57.8413347010596 -.001 70.8408780295671 units box
region 		2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 100.184130479832 -.001 ${ydim} ${zdim} ${zdim2} units box
region 		2 block -.001 100.184130479832 -.001 57.8413347010596 ${zdim} ${zdim2} units box
region 		2 block -.001 100.184130479832 -.001 57.8413347010596 70.8408780295671 ${zdim2} units box
region 		2 block -.001 100.184130479832 -.001 57.8413347010596 70.8408780295671 141.681756059134 units box
region 		3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 100.184130479832 -.001 ${ydim} ${zplus} ${zdim2} units box
region 		3 block -.001 100.184130479832 -.001 57.8413347010596 ${zplus} ${zdim2} units box
region 		3 block -.001 100.184130479832 -.001 57.8413347010596 73.2022406305527 ${zdim2} units box
region 		3 block -.001 100.184130479832 -.001 57.8413347010596 73.2022406305527 141.681756059134 units box
region		whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 100.184130479832 0 ${ydim} 0 ${zdim2} units box
region		whole block 0 100.184130479832 0 57.8413347010596 0 ${zdim2} units box
region		whole block 0 100.184130479832 0 57.8413347010596 0 141.681756059134 units box
create_box 	1 whole
Created orthogonal box = (0 0 0) to (100.184 57.8413 141.682)
  1 by 1 by 1 MPI processor grid
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.09 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.67894 5.78413 7.08409
create_atoms	1 region 1
Created 24800 atoms
lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
lattice fcc 4.09 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1
Lattice spacing in x,y,z = 6.67894 5.78413 7.08409
create_atoms    1 region 2
Created 23540 atoms
# --------------------- Associate structure with interatomic potential ---------------------
pair_style eam/alloy
pair_coeff * * Ag.eam Ag
# --------------------- Define groups, computes, minimize initial structure ---------------------
group bot region 1
25140 atoms in group bot
group top region 2
23880 atoms in group top
group upper_plus region 3
22400 atoms in group upper_plus
shell cd out_Ag_GTFE
compute peratom all pe/atom
compute eatoms all reduce sum c_peratom
compute csym all centro/atom fcc
compute disp all displace/atom
# compute dxtot bottom reduce sum c_disp[1]
thermo 1
thermo_style custom step pe c_eatoms

dump first all custom 1 dump.Ag_unmin id type xs ys zs

run 1
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8
  ghost atom cutoff = 8
  binsize = 4 -> bins = 26 15 36
Memory usage per processor = 22.1489 Mbytes
Step PotEng c_eatoms 
       0          nan          nan 
       1          nan          nan 
Loop time of 0.147091 on 1 procs for 1 steps with 48340 atoms

Performance: 0.587 ns/day, 40.859 hours/ns, 6.799 timesteps/s
96.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.092363   | 0.092363   | 0.092363   |   0.0 | 62.79
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00088096 | 0.00088096 | 0.00088096 |   0.0 |  0.60
Output  | 0.05372    | 0.05372    | 0.05372    |   0.0 | 36.52
Modify  | 2.861e-06  | 2.861e-06  | 2.861e-06  |   0.0 |  0.00
Other   |            | 0.000124   |            |       |  0.08

Nlocal:    48340 ave 48340 max 48340 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23070 ave 23070 max 23070 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.19718e+06 ave 3.19718e+06 max 3.19718e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3197179
Ave neighs/atom = 66.1394
Neighbor list builds = 0
Dangerous builds = 0

PNG image