# -*-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_view/
#dirname = runs/si_au_nw_0500K/
dirname = runs/si-melt/
#------------------------------------------------------------
#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 = "Sis  " 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_T1800_alpha03_surf/inter0010.cn readcn
#incnfile = ../si_au_T1800_alpha03/inter0010.cn readcn
#incnfile = ../si_au_T0900_alpha03_surf/inter0067.cn readcn
#incnfile = ../si_au_T0900_alpha03/inter0045.cn readcn
#incnfile = ../si_au_rand_T0500/inter0009.cn readcn
#incnfile = ../si_au_nwsub/si_au_nw_relaxed.cn readcn
#incnfile = inter0004.cn readcn
#--------------------------------------------
input = [1 4] convertCNtoCFG
quit
#--------------------------------------------
# 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 ]
# for visualization
input = [ 1 -10 10 -10 10 -10 -0.11 ] fixatoms_by_position
#
openwin alloccolors rotate saverot refreshnnlist plot
#
#atomeyepath = "/home/caiwei/Codes/MD++/Tools/AtomEye"
#atomeyeexe = "A.i686" atomeye
#sleep quit
#------------------------------------------------------------
incnfile="inter0001.cn" readcn finalcnfile = "inter0001.cfg" writeatomeyecfg
incnfile="inter0002.cn" readcn finalcnfile = "inter0002.cfg" writeatomeyecfg
incnfile="inter0003.cn" readcn finalcnfile = "inter0003.cfg" writeatomeyecfg
incnfile="inter0004.cn" readcn finalcnfile = "inter0004.cfg" writeatomeyecfg
incnfile="inter0005.cn" readcn finalcnfile = "inter0005.cfg" writeatomeyecfg
incnfile="inter0006.cn" readcn finalcnfile = "inter0006.cfg" writeatomeyecfg
incnfile="inter0007.cn" readcn finalcnfile = "inter0007.cfg" writeatomeyecfg
incnfile="inter0008.cn" readcn finalcnfile = "inter0008.cfg" writeatomeyecfg
incnfile="inter0009.cn" readcn finalcnfile = "inter0009.cfg" writeatomeyecfg
incnfile="inter0010.cn" readcn finalcnfile = "inter0010.cfg" writeatomeyecfg
incnfile="inter0011.cn" readcn finalcnfile = "inter0011.cfg" writeatomeyecfg
incnfile="inter0012.cn" readcn finalcnfile = "inter0012.cfg" writeatomeyecfg
incnfile="inter0013.cn" readcn finalcnfile = "inter0013.cfg" writeatomeyecfg
incnfile="inter0014.cn" readcn finalcnfile = "inter0014.cfg" writeatomeyecfg
incnfile="inter0015.cn" readcn finalcnfile = "inter0015.cfg" writeatomeyecfg
incnfile="inter0016.cn" readcn finalcnfile = "inter0016.cfg" writeatomeyecfg
incnfile="inter0017.cn" readcn finalcnfile = "inter0017.cfg" writeatomeyecfg
incnfile="inter0018.cn" readcn finalcnfile = "inter0018.cfg" writeatomeyecfg
incnfile="inter0019.cn" readcn finalcnfile = "inter0019.cfg" writeatomeyecfg
incnfile="inter0020.cn" readcn finalcnfile = "inter0020.cfg" writeatomeyecfg
incnfile="inter0021.cn" readcn finalcnfile = "inter0021.cfg" writeatomeyecfg
incnfile="inter0022.cn" readcn finalcnfile = "inter0022.cfg" writeatomeyecfg
incnfile="inter0023.cn" readcn finalcnfile = "inter0023.cfg" writeatomeyecfg
incnfile="inter0024.cn" readcn finalcnfile = "inter0024.cfg" writeatomeyecfg
incnfile="inter0025.cn" readcn finalcnfile = "inter0025.cfg" writeatomeyecfg
incnfile="inter0026.cn" readcn finalcnfile = "inter0026.cfg" writeatomeyecfg
incnfile="inter0027.cn" readcn finalcnfile = "inter0027.cfg" writeatomeyecfg
incnfile="inter0028.cn" readcn finalcnfile = "inter0028.cfg" writeatomeyecfg
incnfile="inter0029.cn" readcn finalcnfile = "inter0029.cfg" writeatomeyecfg
incnfile="inter0030.cn" readcn finalcnfile = "inter0030.cfg" writeatomeyecfg
incnfile="inter0031.cn" readcn finalcnfile = "inter0031.cfg" writeatomeyecfg
incnfile="inter0032.cn" readcn finalcnfile = "inter0032.cfg" writeatomeyecfg
incnfile="inter0033.cn" readcn finalcnfile = "inter0033.cfg" writeatomeyecfg
incnfile="inter0034.cn" readcn finalcnfile = "inter0034.cfg" writeatomeyecfg
incnfile="inter0035.cn" readcn finalcnfile = "inter0035.cfg" writeatomeyecfg
incnfile="inter0036.cn" readcn finalcnfile = "inter0036.cfg" writeatomeyecfg
incnfile="inter0037.cn" readcn finalcnfile = "inter0037.cfg" writeatomeyecfg
incnfile="inter0038.cn" readcn finalcnfile = "inter0038.cfg" writeatomeyecfg
incnfile="inter0039.cn" readcn finalcnfile = "inter0039.cfg" writeatomeyecfg
incnfile="inter0040.cn" readcn finalcnfile = "inter0040.cfg" writeatomeyecfg
incnfile="inter0041.cn" readcn finalcnfile = "inter0041.cfg" writeatomeyecfg
incnfile="inter0042.cn" readcn finalcnfile = "inter0042.cfg" writeatomeyecfg
incnfile="inter0043.cn" readcn finalcnfile = "inter0043.cfg" writeatomeyecfg
incnfile="inter0044.cn" readcn finalcnfile = "inter0044.cfg" writeatomeyecfg
incnfile="inter0045.cn" readcn finalcnfile = "inter0045.cfg" writeatomeyecfg
incnfile="inter0046.cn" readcn finalcnfile = "inter0046.cfg" writeatomeyecfg
incnfile="inter0047.cn" readcn finalcnfile = "inter0047.cfg" writeatomeyecfg
incnfile="inter0048.cn" readcn finalcnfile = "inter0048.cfg" writeatomeyecfg
incnfile="inter0049.cn" readcn finalcnfile = "inter0049.cfg" writeatomeyecfg
incnfile="inter0050.cn" readcn finalcnfile = "inter0050.cfg" writeatomeyecfg
incnfile="inter0051.cn" readcn finalcnfile = "inter0051.cfg" writeatomeyecfg
incnfile="inter0052.cn" readcn finalcnfile = "inter0052.cfg" writeatomeyecfg
incnfile="inter0053.cn" readcn finalcnfile = "inter0053.cfg" writeatomeyecfg
incnfile="inter0054.cn" readcn finalcnfile = "inter0054.cfg" writeatomeyecfg
incnfile="inter0055.cn" readcn finalcnfile = "inter0055.cfg" writeatomeyecfg
incnfile="inter0056.cn" readcn finalcnfile = "inter0056.cfg" writeatomeyecfg
incnfile="inter0057.cn" readcn finalcnfile = "inter0057.cfg" writeatomeyecfg
incnfile="inter0058.cn" readcn finalcnfile = "inter0058.cfg" writeatomeyecfg
incnfile="inter0059.cn" readcn finalcnfile = "inter0059.cfg" writeatomeyecfg
incnfile="inter0060.cn" readcn finalcnfile = "inter0060.cfg" writeatomeyecfg
incnfile="inter0061.cn" readcn finalcnfile = "inter0061.cfg" writeatomeyecfg
incnfile="inter0062.cn" readcn finalcnfile = "inter0062.cfg" writeatomeyecfg
incnfile="inter0063.cn" readcn finalcnfile = "inter0063.cfg" writeatomeyecfg
incnfile="inter0064.cn" readcn finalcnfile = "inter0064.cfg" writeatomeyecfg
incnfile="inter0065.cn" readcn finalcnfile = "inter0065.cfg" writeatomeyecfg
incnfile="inter0066.cn" readcn finalcnfile = "inter0066.cfg" writeatomeyecfg
incnfile="inter0067.cn" readcn finalcnfile = "inter0067.cfg" writeatomeyecfg
incnfile="inter0068.cn" readcn finalcnfile = "inter0068.cfg" writeatomeyecfg
incnfile="inter0069.cn" readcn finalcnfile = "inter0069.cfg" writeatomeyecfg
incnfile="inter0070.cn" readcn finalcnfile = "inter0070.cfg" writeatomeyecfg
incnfile="inter0071.cn" readcn finalcnfile = "inter0071.cfg" writeatomeyecfg
incnfile="inter0072.cn" readcn finalcnfile = "inter0072.cfg" writeatomeyecfg
incnfile="inter0073.cn" readcn finalcnfile = "inter0073.cfg" writeatomeyecfg
incnfile="inter0074.cn" readcn finalcnfile = "inter0074.cfg" writeatomeyecfg
incnfile="inter0075.cn" readcn finalcnfile = "inter0075.cfg" writeatomeyecfg
incnfile="inter0076.cn" readcn finalcnfile = "inter0076.cfg" writeatomeyecfg
incnfile="inter0077.cn" readcn finalcnfile = "inter0077.cfg" writeatomeyecfg
incnfile="inter0078.cn" readcn finalcnfile = "inter0078.cfg" writeatomeyecfg
incnfile="inter0079.cn" readcn finalcnfile = "inter0079.cfg" writeatomeyecfg
incnfile="inter0080.cn" readcn finalcnfile = "inter0080.cfg" writeatomeyecfg
incnfile="inter0081.cn" readcn finalcnfile = "inter0081.cfg" writeatomeyecfg
incnfile="inter0082.cn" readcn finalcnfile = "inter0082.cfg" writeatomeyecfg
incnfile="inter0083.cn" readcn finalcnfile = "inter0083.cfg" writeatomeyecfg
incnfile="inter0084.cn" readcn finalcnfile = "inter0084.cfg" writeatomeyecfg
incnfile="inter0085.cn" readcn finalcnfile = "inter0085.cfg" writeatomeyecfg
incnfile="inter0086.cn" readcn finalcnfile = "inter0086.cfg" writeatomeyecfg
incnfile="inter0087.cn" readcn finalcnfile = "inter0087.cfg" writeatomeyecfg
incnfile="inter0088.cn" readcn finalcnfile = "inter0088.cfg" writeatomeyecfg
incnfile="inter0089.cn" readcn finalcnfile = "inter0089.cfg" writeatomeyecfg
incnfile="inter0090.cn" readcn finalcnfile = "inter0090.cfg" writeatomeyecfg
incnfile="inter0091.cn" readcn finalcnfile = "inter0091.cfg" writeatomeyecfg
incnfile="inter0092.cn" readcn finalcnfile = "inter0092.cfg" writeatomeyecfg
incnfile="inter0093.cn" readcn finalcnfile = "inter0093.cfg" writeatomeyecfg
incnfile="inter0094.cn" readcn finalcnfile = "inter0094.cfg" writeatomeyecfg
incnfile="inter0095.cn" readcn finalcnfile = "inter0095.cfg" writeatomeyecfg
incnfile="inter0096.cn" readcn finalcnfile = "inter0096.cfg" writeatomeyecfg
incnfile="inter0097.cn" readcn finalcnfile = "inter0097.cfg" writeatomeyecfg
incnfile="inter0098.cn" readcn finalcnfile = "inter0098.cfg" writeatomeyecfg
incnfile="inter0099.cn" readcn finalcnfile = "inter0099.cfg" writeatomeyecfg
quit
#------------------------------------------------------------
#Conjugate-Gradient relaxation
conj_ftol = 1e-6 conj_itmax = 1000 conj_fevalmax = 5000
conj_fixbox = 0
conj_fixboxvec = [ 0 1 1   #box remain rectangular
                   1 0 1
                   1 1 0 ]
eval relax 
eval # evaluate potential energy after relaxation
writeall=1 
finalcnfile = si_au_nw_relaxed.cn writecn
plot sleep quit

quit
#-------------------------------------------------------------
