# -*-shell-script-*-
# illustrate dislocation using simple cubic lattice
#------------------------------------------------------------
setnolog
setoverwrite
dirname = runs/CSD-book/tmp0
shmsize = 20971520 shmallocate #20MB
#--------------------------------------------
#Read in potential file
#
potfile = ~/Codes/MD++/potentials/ta_pot readpot
#------------------------------------------------------------
#Read in structure
#
#incnfile = ~/Codes/MD++/structures/disl-sc.cn
#readcn
#------------------------------------------------------------
#Create Perfect Lattice Configuration
#
#latticestructure = body-centered-cubic latticeconst = 3.3058 #(A) for Ta
latticestructure = simple-cubic latticeconst = 3.3058 #(A) for Ta
makecnspec = [  1   0   0   18
                0   1   0   18
                0   0   1   3 ]
makecn finalcnfile = perf.cn writecn
#-------------------------------------------------------------
#Cut away boundary atoms
#input = [ 1  0.35 10   -10 10 -10 10 ] fixatoms_by_position
input = [ 1  0.30 10   -10 10 -10 10 ] fixatoms_by_position
input = [ 1  -10 -0.30 -10 10 -10 10 ] fixatoms_by_position
input = [ 1  -10 10 0.35 10   -10 10 ] fixatoms_by_position
input = [ 1  -10 10 -10 -0.35 -10 10 ] fixatoms_by_position
removefixedatoms
#-------------------------------------------------------------
#Create Dislocation
#by inserting atom
#mkdipole = [
#             3 2 #z(dislocation line), y(dipole direction)
#            -0.0625 0 0 #(burgers vector relative to box)
#            -0.01 0.01 0.5
#             0.305 #\nu
#             0 0 0 0 0  #number of images
#             0 0 0 0 ]
#makedipole finalcnfile = makedp.cn writecn

#by removing atom
#mkdipole = [
#             3 2 #z(dislocation line), y(dipole direction)
#             0.0625 0 0 #(burgers vector relative to box)
#             0.03125 -0.5 0.03125
#             0.01 -0.5 0.03125
#             0.305 #\nu
#             0 0 0 0 0  #number of images
#             0 0 0 0 ]
#makedipole finalcnfile = makedp.cn writecn

#by cut and shift
#mkdipole = [
#             3 1 #z(dislocation line), y(dipole direction)
#            -0.0625 0 0 #(burgers vector relative to box)
#             0.03125 -0.5 0.01
#             0.01 -0.5 0.03125
#             0.305 #\nu
#             0 0 0 0 0  #number of images
#             0 0 0 0 ]
#makedipole finalcnfile = makedp.cn writecn

#by cut and shift
mkdipole = [
             3 1 #z(dislocation line), y(dipole direction)
             0 0 0.333333 #(burgers vector relative to box)
             0.03125 -0.5 -0.03125
             0.01 -0.5 0.03125
             0.305 #\nu
             0 0 0 0 0  #number of images
             0 0 0 0 ]
makedipole finalcnfile = makedp.cn writecn
#------------------------------------------------------------
#
#Plot Configuration
#
atomradius = 0.8 bondradius = 0.1 bondlength = 3.85 #4.0
#atomradius = 1.3 bondradius = 0.7 bondlength = 3.85 #4.0
atomcolor = orange highlightcolor = purple  bondcolor = gray60 
fixatomcolor = gray80 #red #yellow
win_width = 400 win_height = 400 backgroundcolor = gray70
#highlightenergy = [ 1 -8.05 ]
#hideatomenergy = [ 1 -8.09 -6 ]
#plot_restrict = 1
#plot_zmin = 0 plot_zmax = 0.3
plot_select = 1
plotfreq = 10 
rotateangles = [ 0 0 0 1.4 ]
win_width = 500 win_height = 500
openwin alloccolors rotate saverot refreshnnlist eval plot
#openwin reversergb alloccolors rotate saverot refreshnnlist eval plot
sleep quit
#-------------------------------------------------------------
