# -*-shell-script-*-
# Silicon on Gold
#------------------------------------------------------------
# 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_rand
#------------------------------------------------------------
#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 = "Si2  " ename1 = "Au2  " #leave spaces to be compatible with fortran
rcut = 6.0  kode0 = "library"
readMEAM
NNM = 200 NIC = 200
#
#------------------------------------------------------------
#Read in configuration file
#incnfile = ../si_au/L12-au3si-6x6x6-rlx.cn readcn
#incnfile = ../si_au/L12-au3si-3x3x3-rlx.cn readcn
#incnfile = ../si_au/L12-au3si-3x3x3-rand-rlx.cn readcn
incnfile = ../si_au/L12-au3si-2x2x2-rand-rlx.cn readcn
#--------------------------------------------
# Plot Configuration
#
atomradius = [ 0.67 0.78 ] bondradius = 0.3 bondlength = 0 #2.8285 #for Si
win_width = 600 win_height = 400
atomradius = 0.9 bondradius = 0.3 bondlength = 0 #2.8285 #for Si
atomcolor = orange atomcolor1 = gray80 highlightcolor = purple  bondcolor = red
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 = 3 # energy of atoms
plotfreq = 10  plot_map_pbc = 1
rotateangles = [ 0 0 0 1.2 ]
openwin alloccolors rotate saverot refreshnnlist plot
#sleep quit
#------------------------------------------------------------
# Create free surface
#input = [2 2 1] redefinepbc
#randomposition
#------------------------------------------------------------
#Conjugate-Gradient relaxation
#conj_ftol = 1e-6 conj_itmax = 1000 conj_fevalmax = 1000000
#conj_fixbox = 1 # no strain 
#eval relax 
#eval writeall=1 finalcnfile = relaxed.3.cn writecn
#quit
#sleep quit
#-------------------------------------------------------------
#convert cn files into atomeye cfg files
#finalcnfile = relaxed.cfg writeatomeyecfg 
#
#sleep quit
#-------------------------------------------------------------
#MD setting
#
T_OBJ    = 700  #(in K) (this will settle down to 1000 K)
DOUBLE_T = 1 
# allow thermal expansion 
#input = [ 1 1 0.003 ] shiftbox
#input = [ 2 2 0.003 ] shiftbox
#input = [ 3 3 0.003 ] shiftbox
#
equilsteps = 0 totalsteps = 250000 timestep = 0.0001 # (ps)
integrator_type = 1  # Velocity Verlet
atommass = [ 196.967  28.0855 ] # (g/mol) for Au, Si
#atommass = [ 196.967  196.967 ] # (g/mol) for Au, Au
srand48bytime
initvelocity
#randomposition
#scalevelocity = 1  atomTcpl = 200
usenosehoover = 1  vt2 = 1e28
saveprop = 1 savepropfreq = 100 openpropfile
plotfreq = 100
savecn = 1 savecnfreq = 2500 writeall = 1 openintercnfile run

quit
#-------------------------------------------------------------
#   7 T=   701. E= -.11197155E+03 F= -.11476999E+03 E0= -.11477129E+03  EK= 0.28085E+01 SP= -.10E-01 SK= 0.13E-04
#   8 T=   702. E= -.11197158E+03 F= -.11477243E+03 E0= -.11477376E+03  EK= 0.28122E+01 SP= -.11E-01 SK= 0.10E-04
#   1 T=   696. E= -.11197144E+03 F= -.11475627E+03 E0= -.11475734E+03  EK= 0.27885E+01 SP= -.36E-02 SK= 0.57E-06
   
