# -*-shell-script-*-
# MD++ implementation of Ercolessi-Adams (Al)
# activate Frank-Read source by applying stress
setnolog
setoverwrite
dirname = runs/al-fr
#------------------------------------------------------------
#Read in structure created by al-fr-make.script
#
incnfile = alfr0.cn readcn
#-------------------------------------------------------------
#Enlarge neighbor list size
NNM = 100 # number of neighbors per atom (default: 60)
#-------------------------------------------------------------
#Plot Configuration
atomradius = 1.0 bondradius = 0.3 bondlength = 0
atomcolor = cyan highlightcolor = purple backgroundcolor = gray
bondcolor = red fixatomcolor = yellow
color00 = "orange"  color01 = "red"    color02 = "green"
color03 = "magenta" color04 = "cyan"   color05 = "purple"
color06 = "gray80"  color07 = "white"  color08 = "blue"
#
# Use local energy to plot
#plot_color_windows = [ 2
#                       -3.32  -3.29 6 #color06 = gray80
#                       -3.29   10   8 #color08 = blue
#                      ]
#
# Use CSD to plot
plot_color_axis = 2  #2: use CSD (default 0: use local energy)
#
plot_color_windows = [ 2
                       1  3  8 #color08 = blue
                       3 20  6 #color06 = gray80
                      ]
#
#plot_limits = [ 1 -10 10 -0.05 10 -10 10 ]
plot_atom_info = 1  plotfreq = 10 
rotateangles = [ 0 0 0 1.5 ]
#
win_width = 600 win_height = 600
openwin alloccolors rotate saverot refreshnnlist eval plot
#sleep quit
#-------------------------------------------------------------
#Conjugate-Gradient relaxation
#
conj_ftol = 1e-10 conj_itmax = 1000 conj_fevalmax = 1000
conj_fixbox = 0             #allow box to change shape
conj_fixboxvec = [ 0 0 1    #fix three components of the 
                   1 0 1    # H matrix to prevent rotation
                   0 0 0 ]

stress = [ 0 1 0   #apply stress sigma_xy
           1 0 0
           0 0 0 ]

stressmul = -1200   #multiply factor (in MPa)
relax
eval finalcnfile = alfr-s1200.cn writeall = 1 writecn
#
#Relax at a higher applied stress
conj_fevalmax = 220
stressmul = -1600   #multiply factor (in MPa)
relax
eval finalcnfile = alfr1.cn writeall = 1 writecn
quit
#-------------------------------------------------------------
