# -*-shell-script-*-
# Ge Te
#  create initial configurations
#------------------------------------------------------------
setnolog
setoverwrite
dirname = runs/ge_te
#------------------------------------------------------------
#Read in MEAM potential (use Au Si potential as a place holder)
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
#
#------------------------------------------------------------
# Create Perfect Lattice Configuration
#
crystalstructure = NaCl  latticeconst = 3.96026 #(A) L1_2  structure
element0 = "Ge"   element1 = "Te"  
atommass = [ 72.64  127.60 ] # Ge, Te (g/mol)
NNM = 200 NIC = 200
latticesize = [ 1 0 0  1
                0 1 0  1
                0 0 1  1 ]
makecrystal finalcnfile = NaCl-gete-1x1x1.cn writeall = 1 writecn #quit
#--------------------------------------------
# Plot Configuration
#
atomradius = [ 0.5 0.6 ] bondradius = 0.3 
win_width = 500 win_height = 500
bondradius = 0.3 bondlength = 1 #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 = 1000000
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 = relaxed.cn writecn
#quit
plot sleep quit
#-------------------------------------------------------------





























#Appendix
#-------------------------------------------------------------
# meamf file
# elt   lat   z ielement atwt    alpha      b0    b1   b2  b3   alat  esub asub t0  t1   t2    t3  rozero ibar
#'Siz' 'dia'  4.  14     28.086  4.87       4.4   5.5  5.5 5.5  5.431 4.63 1.   1.0 3.13 4.47 -1.80 1.600 0
#'Sis' 'dia'  4.  14     28.086  4.87       4.4   5.5  5.5 5.5  5.431 4.63 1.   1.0 3.13 4.47 -1.80 2.05  0
#
#'Six' 'dia'  4.  14     28.086  4.87       4.4   5.5  5.5 5.5  5.431 4.63 1.   1.0 2.05 4.47 -1.80 1.000 0
#'SiG' 'dia'  4.  14     28.086  4.87       4.1   4.0  1.5 3.5  5.431 4.63 1.   1.0 1.75 4.47 -1.80 1.000 0
#'Si'  'dia'  4.  14     28.086  4.87       4.8   4.8  4.8 4.8  5.431 4.63 1.   1.0 3.30 5.105 -0.80 1.   1
#'Sit' 'dia'  4.  14     28.086  4.87       4.4   5.5  5.5 5.5  5.431 4.63 1.   1.0 2.05 4.47 -0.00 1.000 0
#'Au1' 'fcc'  12. 79     196.967 6.34090112 5.45  2.20 6   2.20 4.07  3.93 1.04 1.0 3.15 1.51  2.60 1.    0
#'Au'  'fcc'  12. 79     196.967 6.34090112 5.449 2.20 6   2.20 4.07  3.93 1.04 1.0 1.58956328 1.50776392 2.60609758 1. 0
#
#'Si2' 'dia'  4.  14     28.086  4.87       4.4   5.5  5.5 5.5  5.4271 4.63 1.   1.0 2.05 4.47 -1.80 2.05 0
#'Au2' 'fcc'  12. 79     196.967 6.34       5.45  1.2  6   1.2  4.0729 3.93 1.04 1.0 2.59 -1.0  4.51 0.87 0
#       y     y   y      y       y          y     y    y   y    c      y    y    y   y    y     y    y                     
#unknown parameters
#alatt - Ri0
#att (only for fitting ? no, can specify in meafile.)
#rep (only for fitting ? no, can specify in meafile.)
#ibar (negative square root calls - specify how rho bar is computed)
#t1 = 2.05 but should be 3.13 is this a typo in Kuo 2004?
# (no, also in Baskes 1999, 3.13 + 3/5*(-1.80) = 2.05 )
# need to add legend = 0.6 to meafile
#
# meafile_Au_Si
#deltas account for the change of esub (Ei0)
# what is legend?
# 8/8/97 added correction to t3 term (legend)
# legendre correction: see Baskes99msea-mosi.pdf
# also see Baskes94msmse-NiSi.pdf
#
# The order Au2-Sis is important
# add repuls(1,2)=1.27 to meafile_Au_Si
#  legend = 0.6 seems to make agreement worse (N/A)
# a and Ecoh not exactly match with reference for L1_2 (should be B1)
#
# ibar - how electron density rhobar is calculated
#
# what is ialloy?
