# -*-shell-script-*-
# Silicon nano wire is constructed
setnolog
setoverwrite
dirname = runs/si-meam
#------------------------------------------------------------
#Read in MEAM potential
meamfile = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meamf"
ntypes = 1  ename0 = "Siz  " #leave spaces to be compatible with fortran
rcut = 6  kode0 = "library"
readMEAM
#------------------------------------------------------------
#Read in configuration file
#incnfile = relaxed.cn readcn
#--------------------------------------------
# Create Perfect Lattice Configuration
#
latticestructure = diamond-cubic
#latticeconst = 5.430949821 #(A) for Si
latticeconst = 5.4271 #(A) for Si (MEAM)
makecnspec = [ 0 0 1  8
               1 -1 0 4 
               1 1 0  4 ]
#makecnspec = [ 1 0 0  4
#               0 1 0  4
#               0 0 1  4 ]
makecrystal

#eval
#--------------------------------------------
input = [2 2 -0.01 ] redefinepbc
#--------------------------------------------
# make a cylinder
#
#mkcylinderspec = [3 2  # zind yind /* 1x/2y/3z */
#                  0 0  # center of circle in reduced coordinate
#                  16 ]   # radius of circle (A) for d=5nm
#makecylinder finalcnfile = cylinder.cn writecn
#eval
#--------------------------------------------
# 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
rotateangles = [ 0 0 0 1.2 ]
#openwin alloccolors rotate saverot refreshnnlist plot
openwin reversergb alloccolors rotate saverot refreshnnlist  plot
#sleep quit
#------------------------------------------------------------
# apply torque
#torquespec = [ 1 0.1 0 ] maketorquehandle
#addtorque plot
#sleep quit
#------------------------------------------------------------
#Conjugate-Gradient relaxation
conj_ftol = 1e-6 conj_itmax = 1000 conj_fevalmax = 1000
#conj_fixbox = 0 # no strain 
conj_fixbox = 1 # with strain
#conj_monitor = 1 conj_summary = 1
eval relax 
eval # evaluate potential energy after relaxation
writeall=1 
finalcnfile = relaxed.cn writecn
quit
sleep quit
#-------------------------------------------------------------
#convert cn files into atomeye cfg files
#finalcnfile = relaxed.cfg writeatomeyecfg 
#
#sleep quit
#-------------------------------------------------------------
#MD setting
T_OBJ = 300 #(in K) # Desired Temperature
atommass = 28.0855 # (g/mol) for Si 
#atommass = 72.59 # (g/mol) for Ge 
# molar mass is from http://www.noblemind.com
timestep = 0.0005 # (ps)
DOUBLE_T = 1 # to get T_OBJ as initial condition
#DOUBLE_T = 0 # something strange for sw potential
# otherwise, temperature will become around half of T_OBJ
#initvelocity # Initialize velocity of particles according to T_OBJ 

#for equilibration
#-------------------------------------------------------------
