# -*-shell-script-*-
# SiGe in Rhombohedral (RH) structure
#setnolog
setoverwrite
dirname = runs/sige-meam
#------------------------------------------------------------
#Read in MEAM potential
meamfile = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meamf"
meafile  = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meafile_Si_Ge"
ntypes = 2  ename0 = "Siz  " ename1 = "Ge   " #leave spaces to be compatible with fortran
rcut = 6.0  kode0 = "library"
readMEAM
#
#------------------------------------------------------------
# Create Perfect Lattice Configuration
#
latticestructure = rhombohedral-Si-Ge
#latticeconst = 3.8403 #(A) for Si    5.4309 / sqrt(2)
latticeconst = 3.9161 #(A) for SiGe  5.5379 / sqrt(2)
#latticeconst = 4.0004 #(A) for Ge    5.5675 / sqrt(2)

makecnspec = [ 1 0 0  4
               0 1 0  3
               0 0 1  2 ]
nspecies = 2 
makecrystal
#finalcnfile = perf0.cn writeall = 0 writecn quit
#
#Conjugate-Gradient relaxation
conj_ftol = 1e-6 conj_fevalmax = 1000 conj_fixbox = 1

latticeconst = 3.908 makecrystal relax eval
latticeconst = 3.909 makecrystal relax eval
latticeconst = 3.910 makecrystal relax eval
latticeconst = 3.911 makecrystal relax eval
latticeconst = 3.912 makecrystal relax eval
latticeconst = 3.913 makecrystal relax eval
latticeconst = 3.914 makecrystal relax eval
latticeconst = 3.915 makecrystal relax eval
latticeconst = 3.916 makecrystal relax eval
latticeconst = 3.917 makecrystal relax eval
latticeconst = 3.918 makecrystal relax eval
latticeconst = 3.919 makecrystal relax eval
latticeconst = 3.920 makecrystal relax eval
latticeconst = 3.921 makecrystal relax eval
latticeconst = 3.922 makecrystal relax eval
quit
#
# set all atoms to Si
#input = [ 1 -10 10 -10 10 -10 10 ] fixatoms_by_position input = 0 setfixedatomsspecies freeallatoms
# set all atoms to Ge
#input = [ 1 -10 10 -10 10 -10 10 ] fixatoms_by_position input = 1 setfixedatomsspecies freeallatoms
#
#eval quit
#--------------------------------------------
# Plot Configuration
#
atomradius = [ 0.5 0.8 ] bondradius = 0.3 
win_width = 500 win_height = 500
bondradius = 0.3 bondlength = 2.5 #2.8285 #for Si
atomcolor = orange atomcolor1 = gray90 highlightcolor = purple  bondcolor = green
fixatomcolor = yellow backgroundcolor = gray70
color00 = "orange"  color01 = "purple" color02 = "green"
color03 = "magenta" color04 = "cyan"   color05 = "purple"
color06 = "gray80"  color07 = "white"
#plot_color_windows = [ 2
#                          -10 -3.8 0  #color00 = orange
#                          -3.8 10  1  #color01 = purple
#                     ]
plot_atom_info = 2 #2: real coordinates, 3: energy of atoms
plotfreq = 10
rotateangles = [ 0 0 0 1.2 ]
openwin alloccolors rotate saverot refreshnnlist plot
#eval sleep quit
#------------------------------------------------------------
#Conjugate-Gradient relaxation
conj_ftol = 1e-6 conj_itmax = 1000 conj_fevalmax = 1000
conj_fixbox = 1
conj_fixboxvec = [ 0 1 1   # only allow box length to change
                   1 0 1   # box remain rectangular
                   1 1 0 ]  
eval relax eval
sleep
quit
