# -*-shell-script-*-
# MD code of Stillinger-Weber Si
# (constrained minimization to find saddle points)
# (kink migration on 30 partial dislocations)
#setnolog
setoverwrite
dirname = runs/sipartial
#------------------------------------------------------------
#Read in structure
#
incnfile = ~/Codes/MD++/structures/CSD-book/chap3/sect3.5/partial30dkp-6x6x4relax.cn readcn setconfig1 #A
incnfile = ~/Codes/MD++/structures/CSD-book/chap3/sect3.5/partial30rkp-6x6x4relax.cn readcn setconfig2 #B
incnfile = ~/Codes/MD++/structures/CSD-book/chap3/sect3.5/partial30dkp-6x6x4relax.cn readcn #A
#incnfile = ~/Codes/MD++/structures/CSD-book/chap3/sect3.5/partial30rkp-6x6x4relax.cn readcn #B
#incnfile = relaxed.cn readcn
#------------------------------------------------------------
#Create Perfect Lattice Configuration
#
#latticestructure = diamond-cubic
#latticeconst = 5.4309529817532409 #(A) for Si
#makecnspec = [ 1  1 -2 2   #(x)
#               1  1  1 1   #(y)
#               1 -1  0 2  ] #(z)
#makecn finalcnfile = perf.cn writecn quit
#-------------------------------------------------------------
#Move kink (LK)
#moveatomspec = [ 1  0.7 0.2 0.0 1437 ] moveatom   
#moveatomspec = [ 1 -0.7 0.0 0.0 1453 ] moveatom
#-------------------------------------------------------------
#
#Plot Configuration
#
atomradius = 0.67 bondradius = 0.2 bondlength = 2.8285 #for Si
atomcolor = orange highlightcolor = purple  bondcolor = red
backgroundcolor = gray fixatomcolor = yellow
#energycolorbar = [ 1 -4.70 -4.50 ]  highlightcolor = red
highlightenergy = [ 1 -4.44 ]
#highlightenergy = [ 1 -4.52 ]
#hideatomenergy = [ 1 -4.55 -4 ]
plot_select = 1 plot_highlight = [ 0 0 1 2 3 4 5 6 7 8 9 ]
#plot_restrict = 1 plot_zmin = -0.08 plot_zmax = 0.08
plot_restrict = 1 plot_zmin = -0.05 plot_zmax = 0.05
plotfreq = 1000
rotateangles = [ 0 0 0 1.6 ]
win_width = 600 win_height = 600
openwin reversergb alloccolors rotate saverot refreshnnlist eval plot
#openwin alloccolors rotate saverot refreshnnlist eval plot
#sleep quit
#-------------------------------------------------------------
#Conjugate-Gradient relaxation
#
conj_ftol = 1e-7 conj_itmax = 1000 conj_fevalmax = 3000
conj_fixbox = 1 #conj_monitor = 1 conj_summary = 1
#relax finalcnfile = relaxed.cn writecn
#sleep quit
#-------------------------------------------------------------
#constrained Conjugate-Gradient relaxation
#
conj_ftol = 1e-7 conj_itmax = 1000 conj_fevalmax = 3000 conj_fixbox = 1
constrainatoms = [ 8 1453 1437 1439 2604 1455 1431 2594 1436 ]
#constrainS = 0.05 constrainedrelax finalcnfile = relaxed.cn writecn
#sleep
#quit
#-------------------------------------------------------------
#Calling Fortran code for conjugate-gradient or quasi-newton relaxation
#
#fortranpath = ~/Codes/MD++/src/F90SW potfile = Si.pot fortranexe = RelaxSW
fortranpath = ~/Codes/MD++/src/F90SW potfile = Si.pot fortranexe = RelaxSW_QN
#
conj_fixbox = 1  #stress is meaningful only if allow box to relax
#stress = [ 0 100 0
#           100 0 0
#           0 0 0 ] #(stress in MPa)
#conj_fevalmax = 3000  fortranrelax eval plot
#sleep quit
#-------------------------------------------------------------
constrainS = 0.02 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.04 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.06 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.08 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.10 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.12 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.14 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.16 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.18 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.20 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.22 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.24 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.26 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.28 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.30 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.32 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.34 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.36 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.38 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.40 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.42 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.44 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.46 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.48 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.50 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.52 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.54 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.56 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.58 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.60 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.62 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.64 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.66 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.68 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.70 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.72 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.74 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.76 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.78 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.80 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.82 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.84 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.86 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.88 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.90 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.92 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.94 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.96 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 0.98 constrainedrelax finalcnfile = relaxed.cn writecn
constrainS = 1.00 constrainedrelax finalcnfile = relaxed.cn writecn

quit
