# -*-shell-script-*-
# Silicon on Gold
#  create initial configurations
#------------------------------------------------------------
# Test MEAM potential
# Kuo, C.-L., Clancy, P.,  (Kuo04ss-AuSimeam.pdf)
#   MEAM molecular dynamics study of a gold thin film on a silicon substrate,
#   Surface Science, 551, 39-58 (2004).
#
# Chin-Lung Kuo and Paulette Clancy, (Kuo05msmse-AuSiOmeam.pdf)
#  Development of atomistic MEAM potentials for the silicon-oxygen-gold
#  ternary system, Modelling Simul. Mater. Sci. Eng. 13, 1309-1329 (2005).
#------------------------------------------------------------
#setnolog
setoverwrite
dirname = runs/si_au_nw_700K
#------------------------------------------------------------
#Read in MEAM potential
meamfile = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meamf"
meafile  = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meafile_Au_Si"
ntypes = 2  ename0 = "Au2  " ename1 = "Si2  " #leave spaces to be compatible with fortran
#meafile  = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meafile_Mo_Si"
#ntypes = 2  ename0 = "Mo2  " ename1 = "Si1  " #leave spaces to be compatible with fortran
rcut = 8.0  kode0 = "library"
readMEAM
#
#------------------------------------------------------------
# Read initial configuration file
#
incnfile = "../si_au_nw/si_au_nw_relaxed.cn" readcn
NNM = 200 NIC = 200
#------------------------------------------------------------
# Plot Configuration
#
atomradius = [ 0.8 0.5 ] bondradius = 0.3 
win_width = 500 win_height = 500
bondradius = 0.3 bondlength = 0 #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
#------------------------------------------------------------
# Molecular Dynamics Simulation
#
T_OBJ    = 700  #(in K) 
DOUBLE_T = 1 
#
equilsteps = 0 totalsteps = 250000 timestep = 0.0001 # (ps)
integrator_type = 1  # Velocity Verlet
atommass = [ 196.967  28.0855 ] # (g/mol) for Au, Si
srand48bytime  initvelocity
usenosehoover = 1  vt2 = 1e28
saveprop = 1 savepropfreq = 100 openpropfile
plotfreq = 100
savecn = 1 savecnfreq = 2500 writeall = 1 openintercnfile run
#-------------------------------------------------------------
quit

