# -*-shell-script-*-
# Silicon nano wire is constructed
#setnolog
setoverwrite
#dirname = runs/sinw_5D_long_seq_SWMOD
dirname = runs/sinw_5D_long_seq_MEAM
#dirname = runs/sinw_5D_disl_seq_SW
#dirname = runs/sinw_5D_tersoff_36pstrain
#dirname = runs/genw_15D_tersoff_p3strain
#dirname = runs/genw_20D_tersoff_8pstrain
#dirname = runs/genanowire
#dirname = runs/genw_sw_5D_p1strain
#shmsize = 31457280 shmallocate #10MB
#------------------------------------------------------------
#Read in MEAM potential
meamfile = "/home/kwkang/Codes/MD++/Fortran/MEAM-Baskes/meamf"
ntypes = 1  ename0 = "Si  " #leave spaces to be compatible with fortran
rcut = 4  cmin0 = 0.8 kode0 = "library"
readMEAM
#------------------------------------------------------------
#Read in configuration file
#incnfile = "~/Codes/MD++/structures/genanowire/gewire_D5_L5.cn" readcn
#incnfile = "~/Codes/MD++/runs/genanowire2/relaxed.cn" readcn
#incnfile = "~/Codes/MD++/runs/sinw_5D_tersoff_nostrain/relaxed.cn" readcn
incnfile = relaxed.cn readcn
#incnfile = ./SW/relaxed.cn readcn
#incnfile = ~/Codes/MD++.kw/runs/sinw_5D_long_seq_SW/Totalstep2ps/300K_15pstrain_NVT.cn readcn
#incnfile = 300K_nostrain_NVT.cn readcn
#incnfile = sinw_5D_39pstrain2.cn readcn
#incnfile = relax-1000steps.cn readcn
#atommass = 72.59  timestep = 0.00005 eval
#writeall = 1 finalcnfile = 300K4.cn writecn
#quit
#------------------------------------------------------------

#--------------------------------------------
# Create Perfect Lattice Configuration
#
crystalstructure = diamond-cubic
#latticeconst = 5.430949821 #(A) for Si
latticeconst = 5.4309529817532409 #(A) for Si
#latticeconst = 5.65362106225 #(A) for Ge
# Si(1-x)Ge(x) 5.431+0.20x+0.027x^2 (at 300K)
latticesize = [ 0 0 1 10   # box size 54nm X 54nm 
               1 -1 0 7 
               1 1 0 65 ] # length ~ 500nm
#makecnspec = [ 0 0 1 10   # box size 54nm X 54nm X 54nm
#               1 -1 0 7 
#               1 1 0 7 ] 
#makecrystal #finalcnfile = perf.cn writecn #eval
#--------------------------------------------
# make a cylinder
#
input = [	3 2  # zind yind /* 1x/2y/3z */
	  		0.01 0  # center of circle in reduced coordinate
            25   # radius of circle (A)
			0 ]  # 0 remove all atoms outside a cylinder, 1 fix them
#makecylinder #finalcnfile = 5Dcylinder.cn writecn #eval
#--------------------------------------------
# redefine pbc
#input = [1 1 2] changeH_keepS 
#input = [2 2 2] changeH_keepS 
#finalcnfile = 5Dcylinder.cn writecn #eval
#shiftspec = [3 3 0.01] shiftbox
#--------------------------------------------
#(a) Create a single dislocation line without removing atoms
#(1)
mkdislspec = [ 1           #1: activated, 0: not activated
               5.430949821 #a: lattice constant in Angstrom
               -0.5 0.3536 0.3536 #bx, by, bz in unit of a
               0   1   0   #lx, ly, lz : line direction vector
               1   0   1.4142   #nx, ny, nz : normal vector of cut plane
               0.01  0.01 0.001 #x0, y0, z0 : a point of dislocation in A
               #0.324       #nu : Poisson's ratio for Ge
               0.305       #nu : Poisson's ratio for Si 
               1           #0: commit, 1: store
           ]
#makedislocation #finalcnfile = makedisl.cn writecn #create dislocation line
#(2)
mkdislspec = [ 1           #1: activated, 0: not activated
               5.430949821 #a: lattice constant in Angstrom
               0.5 -0.3536 -0.3536 #bx, by, bz in unit of a
               0   1   0   #lx, ly, lz : line direction vector
               1   0   1.4142   #nx, ny, nz : normal vector of cut plane
             141.43  0.01 -99.999 #x0, y0, z0 : a point of dislocation in A
               #0.324       #nu : Poisson's ratio for Ge
               0.305       #nu : Poisson's ratio for Si 
               0           #0: commit, 1: store
           ]
#makedislocation #finalcnfile = makedisl.cn writecn #create dislocation line
#(3)
mkdislspec = [ 1           #1: activated, 0: not activated
               5.430949821 #a: lattice constant in Angstrom
              -0.5 0.3536 0.3536 #bx, by, bz in unit of a
               0   1   0   #lx, ly, lz : line direction vector
               1   0   1.4142   #nx, ny, nz : normal vector of cut plane
               0.01  0.01 239.861 #x0, y0, z0 : a point of dislocation in A
               #0.324       #nu : Poisson's ratio for Ge
               0.305       #nu : Poisson's ratio for Si 
               1           #0: commit, 1: store
           ]
#makedislocation #finalcnfile = makedisl.cn writecn #create dislocation line
#(4)
mkdislspec = [ 1           #1: activated, 0: not activated
               5.430949821 #a: lattice constant in Angstrom
               0.5 -0.3536 -0.3536 #bx, by, bz in unit of a
               0   1   0   #lx, ly, lz : line direction vector
               1   0   1.4142   #nx, ny, nz : normal vector of cut plane
             141.43  0.01 139.861 #x0, y0, z0 : a point of dislocation in A
               #0.324       #nu : Poisson's ratio for Ge
               0.305       #nu : Poisson's ratio for Si 
               1           #0: commit, 1: store
           ]
#makedislocation #finalcnfile = makedisl.cn writecn #create dislocation line
#(5)
mkdislspec = [ 1           #1: activated, 0: not activated
               5.430949821 #a: lattice constant in Angstrom
               -0.5 0.3536 0.3536 #bx, by, bz in unit of a
               0   1   0   #lx, ly, lz : line direction vector
               1   0   1.4142   #nx, ny, nz : normal vector of cut plane
               0.01  0.01 -239.859 #x0, y0, z0 : a point of dislocation in A
               #0.324       #nu : Poisson's ratio for Ge
               0.305       #nu : Poisson's ratio for Si 
               1           #0: commit, 1: store
           ]
#makedislocation #finalcnfile = makedisl.cn writecn #create dislocation line
#(6)
mkdislspec = [ 1           #1: activated, 0: not activated
               5.430949821 #a: lattice constant in Angstrom
               0.5 -0.3536 -0.3536 #bx, by, bz in unit of a
               0   1   0   #lx, ly, lz : line direction vector
               1   0   1.4142   #nx, ny, nz : normal vector of cut plane
             141.43  0.01 -339.859 #x0, y0, z0 : a point of dislocation in A
               #0.324       #nu : Poisson's ratio for Ge
               0.305       #nu : Poisson's ratio for Si 
               0           #0: commit, 1: store
           ]
#makedislocation #finalcnfile = makedisl.cn writecn #create dislocation line
#finalcnfile = makedisl.cn writecn #create dislocation line
#------------------------------------------------------------
#colors for Central symmetry view
color00 = "red" color01 = "blue" color02 = "green"
color03 = "magenta" color04 = "cyan" color05 = "purple"
color06 = "gray80" color07 = "white" color08 = "orange"
#--------------------------------------------
# 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 highlightcolor = purple  bondcolor = red
fixatomcolor = yellow backgroundcolor = gray70
#atomcolor = lightgrey highlightcolor = purple  bondcolor = darkgrey
#highlightenergy = [ 1 -2 ]
#highlightenergy = [ 1 -3.80 ]
#hideatomenergy = [ 1 -3.80 -3 ]
#hideatomenergy = [ 1 -3.60 -3 ]
#hideatomenergy = [ 1 -4.50 -3 ]
#plot_atom_info = 1 # reduced coordinates of atoms
#plot_atom_info = 2 # real coordinates of atoms
plot_atom_info = 3 # energy of atoms
#plot_highlight = [ 0 0 1 2 3 4 5 6 7 8 9 ]
plotfreq = 10
rotateangles = [ 0 0 0 1.9 ]
#openwin alloccolors rotate saverot plot
#openwin alloccolors rotate saverot eval plot
#sleep quit
#-------------------------------------------------------------
#(central symmetry)
#coloraxis = 3 # In case of coloraxis = 2, color_ind = _TOPOL
#NCS = 4 calcenteroffset
#energyhistspec = [ 0.1 8 50 ] GnuPlotEnergyHistogram sleep quit
#color_window = [ 2
#                 0.05 0.7 8   #color00 = red
#                 0.7  10  6   #color06 = gray80
#                ]
#color_window = [ 4
#                 0.2  2 2   #color02 = green
#                 2    4 1   #color01 = blue
#                 4   10 0   #color00 = red
#                 10   20  6 # color06 = gray80
#                ]
#plot sleep quit
#-------------------------------------------------------------
#Conjugate-Gradient relaxation
conj_ftol = 1e-4 conj_itmax = 1000 conj_fevalmax = 1000 #14000
conj_fixbox = 0
#conj_fixboxvec = [ 0 1 0
#                   0 0 0
#                   1 1 0 ]
conj_fixboxvec = [ 0 1 1
                   1 0 1
                   1 1 0 ]
#conj_fixbox = 1 #conj_monitor = 1 conj_summary = 1
eval
relax finalcnfile = relaxed.cn writecn
eval ## evaluate vacancy formation energy after relaxation
#sleep quit
quit
#------------------------------------------------------------
# apply strain
#readcn shiftspec = [ 3 3 -0.02 ] shiftbox relax eval 
#finalcnfile = genw_5D_disl_c2p.cn writecn
#readcn shiftspec = [ 3 3 -0.01 ] shiftbox relax eval 
#finalcnfile = genw_5D_disl_c1p.cn writecn
#readcn shiftspec = [ 3 3 0.01 ] shiftbox relax eval 
#finalcnfile = genw_5D_disl_1p.cn writecn
#readcn shiftspec = [ 3 3 0.02 ] shiftbox relax eval 
#finalcnfile = genw_5D_disl_2p.cn writecn
#quit
#------------------------------------------------------------
# apply stress
#stress = [0 0 0      # external applied stress
#          0 0 0        # zz component => z-directional force
#          0 0 10000]   # in MPa
#conj_fixboxvec = [ 0 0 1   # for applying yz component stress
#                   1 0 1
#                   0 0 0 ]
#conj_fixboxvec = [ 0 1 1
#                   0 0 1
#                   0 0 0 ]
#-------------------------------------------------------------
#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 = 0.00005 # for high strain 
timestep = 0.0001 # (ps) for Si
#timestep = 0.0002 # (ps) for Ge
#DOUBLE_T = 1 # to get T_OBJ as initial condition
#DOUBLE_T = 1 # 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
#-------------------------------------------------------------
#potavgfreq = 100 # How frequently calculate time avg. potential
#equilsteps = 0  totalsteps = 200000 # 
#equilsteps = 0  totalsteps = 20000 # for 2ps at each 1% strain
equilsteps = 0  totalsteps = 2000 # for initialization 
#plotfreq = 100
# showavgpot = 1 # no such variable in source code
#saveprop = 0
saveprop = 1 savepropfreq = 100
#outpropfile = 300K_16p_NVT.out
#openpropfile
# output properties are just like:
# current step, Kinetic E., Potential E., pressure, stress xy,
# stress yz, stress zx, total stress, HELM, HELMP,
# temperature, zeta, dE/dlambda
savecn = 1 savecnfreq = 1000
intercnfile = intercn300K_16p_ts20ps.cn
openintercnfile
#run
#writeall=1 finalcnfile = 300K_0p_NVE.cn writecn
#closepropfile
#eval 
#sleep 
#quit

#-------------------------------------------------------------
# automate
#incnfile = "~/Codes/MD++/structures/genanowire/gewire_D5_L5.cn" 
#readcn shiftspec = [ 3 3 0.01 ] shiftbox  relax eval
##finalcnfile = sinw_5D_disl_1pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.02 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_2pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.03 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_3pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.04 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_4pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.05 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_5pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.06 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_6pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.07 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_7pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.08 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_8pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.09 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_9pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.10 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_10pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.11 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_11pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.12 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_12pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.13 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_13pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.14 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_14pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.15 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_15pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.16 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_16pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.17 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_17pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.18 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_18pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.19 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_19pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.20 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_20pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.21 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_21pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.22 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_22pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.23 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_23pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.24 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_24pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.25 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_25pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.26 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_26pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.27 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_27pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.28 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_28pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.29 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_29pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.30 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_30pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.31 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_31pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.32 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_32pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.33 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_33pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.34 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_34pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.35 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_35pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.36 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_36pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.37 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_37pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.38 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_38pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.39 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_39pstrain.cn writecn
#readcn shiftspec = [ 3 3 0.40 ] shiftbox  relax eval
#finalcnfile = sinw_5D_disl_40pstrain.cn writecn
#quit
#-------------------------------------------------------------
# automate MD simulation
writeall=1
#incnfile = "~/Codes/MD++/runs/genw_5D_disl/genw_5D_1pstrain.cn" readcn
#initvelocity
#outpropfile = 300K_nostrain_NVE.out openpropfile run 
#finalcnfile = 300K_nostrain_NVE.cn writecn closepropfile 
usenosehoover=1 vt2=1e28 #1e14
#totalsteps = 20000
totalsteps = 200000
#outpropfile = 300K_nostrain_NVT.out openpropfile run
#finalcnfile = 300K_nostrain_NVT.cn writecn closepropfile 
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_nostrain_NVT_vt2_1e28.cn" readcn
#input = [ 3 3 0.01 ] changeH_keepR
#outpropfile = 300K_1pstrain_NVT.out openpropfile run 
#finalcnfile = 300K_1pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_1pstrain_NVT.cn" readcn
#input = [ 3 3 0.0099009901 ] changeH_keepR
#outpropfile = 300K_2pstrain_NVT.out openpropfile run
#finalcnfile = 300K_2pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_2pstrain_NVT.cn" readcn
#input = [ 3 3 0.0098039216 ] changeH_keepR
#outpropfile = 300K_3pstrain_NVT.out openpropfile run
#finalcnfile = 300K_3pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_3pstrain_NVT.cn" readcn
#input = [ 3 3 0.0097087378 ] changeH_keepR
#outpropfile = 300K_4pstrain_NVT.out openpropfile run
#finalcnfile = 300K_4pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_4pstrain_NVT.cn" readcn
#input = [ 3 3 0.0096153847] changeH_keepR
#outpropfile = 300K_5pstrain_NVT.out openpropfile run
#finalcnfile = 300K_5pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_5pstrain_NVT.cn" readcn
#input = [ 3 3 0.0095238095 ] changeH_keepR
#outpropfile = 300K_6pstrain_NVT.out openpropfile run
#finalcnfile = 300K_6pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_6pstrain_NVT.cn" readcn
#input = [ 3 3 0.0094339622 ] changeH_keepR
#outpropfile = 300K_7pstrain_NVT.out openpropfile run
#finalcnfile = 300K_7pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_7pstrain_NVT.cn" readcn
#input = [ 3 3 0.0093457944 ] changeH_keepR
#outpropfile = 300K_8pstrain_NVT.out openpropfile run
#finalcnfile = 300K_8pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_8pstrain_NVT.cn" readcn
#input = [ 3 3 0.0092592593] changeH_keepR #initvelocity
#intercnfile = intercn300K_9p openintercnfile
#outpropfile = 300K_9pstrain_NVT.out openpropfile run
#finalcnfile = 300K_9pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_9pstrain_NVT.cn" readcn
#input = [ 3 3 0.0091743119] changeH_keepR #initvelocity
#outpropfile = 300K_10pstrain_NVT.out openpropfile run
#finalcnfile = 300K_10pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_10pstrain_NVT.cn" readcn
#input = [ 3 3 0.0090909091 ] changeH_keepR #initvelocity
#outpropfile = 300K_11pstrain_NVT.out openpropfile run
#finalcnfile = 300K_11pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_11pstrain_NVT.cn" readcn
#input = [ 3 3 0.0090090090 ] changeH_keepR #initvelocity
#outpropfile = 300K_12pstrain_NVT.out openpropfile run
#finalcnfile = 300K_12pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_12pstrain_NVT.cn" readcn
#input = [ 3 3 0.0089285714 ] changeH_keepR #initvelocity
#outpropfile = 300K_13pstrain_NVT.out openpropfile run
#finalcnfile = 300K_13pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_13pstrain_NVT.cn" readcn
#input = [ 3 3 0.0088495576 ] changeH_keepR #initvelocity
#outpropfile = 300K_14pstrain_NVT.out openpropfile run
#finalcnfile = 300K_14pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_14pstrain_NVT.cn" readcn
#input = [ 3 3 0.0087719298 ] changeH_keepR #initvelocity
#outpropfile = 300K_15pstrain_NVT.out openpropfile run
#finalcnfile = 300K_15pstrain_NVT.cn writecn closepropfile
#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_15pstrain_NVT.cn" readcn
	input = [ 3 3 0.0086956522 ] changeH_keepR #initvelocity
	outpropfile = 300K_16pstrain_NVT_ts20ps.out openpropfile run
	finalcnfile = 300K_16pstrain_NVT_ts20ps.cn writecn closepropfile
quit
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_16pstrain_NVT.cn" readcn
	input = [ 3 3 0.0086206896 ] changeH_keepR #initvelocity
	outpropfile = 300K_17pstrain_NVT.out openpropfile run
	finalcnfile = 300K_17pstrain_NVT.cn writecn closepropfile
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_17pstrain_NVT.cn" readcn
	input = [ 3 3 0.0085470086] changeH_keepR #initvelocity
	outpropfile = 300K_18pstrain_NVT.out openpropfile run
	finalcnfile = 300K_18pstrain_NVT.cn writecn closepropfile
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_18pstrain_NVT.cn" readcn
	input = [ 3 3 0.0084745762] changeH_keepR #initvelocity
	outpropfile = 300K_19pstrain_NVT.out openpropfile run
	finalcnfile = 300K_19pstrain_NVT.cn writecn closepropfile
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_19pstrain_NVT.cn" readcn
	input = [ 3 3 0.0084033614] changeH_keepR #initvelocity
	outpropfile = 300K_20pstrain_NVT.out openpropfile run
	finalcnfile = 300K_20pstrain_NVT.cn writecn closepropfile
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_20pstrain_NVT.cn" readcn
	input = [ 3 3 0.0083333333] changeH_keepR #initvelocity
	outpropfile = 300K_21pstrain_NVT.out openpropfile run
	finalcnfile = 300K_21pstrain_NVT.cn writecn closepropfile
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_21pstrain_NVT.cn" readcn
	input = [ 3 3 0.0082644628] changeH_keepR #initvelocity
	outpropfile = 300K_22pstrain_NVT.out openpropfile run
	finalcnfile = 300K_22pstrain_NVT.cn writecn closepropfile
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_22pstrain_NVT.cn" readcn
	input = [ 3 3 0.0081967213] changeH_keepR #initvelocity
	outpropfile = 300K_23pstrain_NVT.out openpropfile run
	finalcnfile = 300K_23pstrain_NVT.cn writecn closepropfile 
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_23pstrain_NVT.cn" readcn
	input = [ 3 3 0.0081300813] changeH_keepR #initvelocity
	outpropfile = 300K_24pstrain_NVT.out openpropfile run
	finalcnfile = 300K_24pstrain_NVT.cn writecn closepropfile 
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_24pstrain_NVT.cn" readcn
	input = [ 3 3 0.0080645162] changeH_keepR #initvelocity
	outpropfile = 300K_25pstrain_NVT.out openpropfile run
	finalcnfile = 300K_25pstrain_NVT.cn writecn closepropfile 
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_25pstrain_NVT.cn" readcn
	input = [ 3 3 0.0080000000] changeH_keepR #initvelocity
	outpropfile = 300K_26pstrain_NVT.out openpropfile run
	finalcnfile = 300K_26pstrain_NVT.cn writecn closepropfile 
	#incnfile = "~/Codes/MD++/runs/genw_5D_disl_seq/300K_26pstrain_NVT.cn" readcn
	input = [ 3 3 0.0079365079] changeH_keepR #initvelocity
	outpropfile = 300K_27pstrain_NVT.out openpropfile run
	finalcnfile = 300K_27pstrain_NVT.cn writecn closepropfile 
	#intercnfile = intercn300K_26to27 openintercnfile run
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_27pstrain_NVT.cn" readcn
	input = [ 3 3 0.0078740157] changeH_keepR #initvelocity
	outpropfile = 300K_28pstrain_NVT.out openpropfile run
	finalcnfile = 300K_28pstrain_NVT.cn writecn closepropfile 
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_28pstrain_NVT.cn" readcn
	input = [ 3 3 0.0078125000] changeH_keepR #initvelocity
	outpropfile = 300K_29pstrain_NVT.out openpropfile run
	finalcnfile = 300K_29pstrain_NVT.cn writecn closepropfile 
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_29pstrain_NVT.cn" readcn
	input = [ 3 3 0.0077519380] changeH_keepR #initvelocity
	outpropfile = 300K_30pstrain_NVT.out openpropfile run
	finalcnfile = 300K_30pstrain_NVT.cn writecn closepropfile 
quit
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_30pstrain_NVT.cn" readcn
	input = [ 3 3  0.0076923077] changeH_keepR #initvelocity
	outpropfile = 300K_31pstrain_NVT.out openpropfile run
	finalcnfile = 300K_31pstrain_NVT.cn writecn closepropfile 
	#incnfile = "~/Codes/MD++/runs/genw_5D_long_seq/300K_31pstrain_NVT.cn" readcn
	input = [ 3 3 0.0076335878] changeH_keepR
	outpropfile = 300K_32pstrain_NVT.out openpropfile run
	finalcnfile = 300K_32pstrain_NVT.cn writecn closepropfile 
	#incnfile = 32pstrain.cn readcn
	input = [ 3 3 0.0075757576] changeH_keepR
	outpropfile = 300K_33pstrain_NVT.out openpropfile run
	finalcnfile = 300K_33pstrain_NVT.cn writecn closepropfile 
	#incnfile = 32pstrain.cn readcn
	input = [ 3 3 0.0075187970] changeH_keepR
	outpropfile = 300K_34pstrain_NVT.out openpropfile run
	finalcnfile = 300K_34pstrain_NVT.cn writecn closepropfile 
	#incnfile = 34pstrain.cn readcn
	#input = [ 3 3 0.0074626866] changeH_keepR  relax eval
	quit

	#-------------------------------------------------------------
	#finalcnfile = sinw_5D_disl_1pstrain.cn writecn closepropfile
	# automate
	#incnfile = "~/Codes/MD++/structures/genanowire/gewire_5D_L5.cn"  #readcn
	#incnfile = "~/Codes/MD++/structures/genanowire/gewire_5D_L5_e27.cn"  #readcn
	#conj_fevalmax = 10000
	#setHspec = [ 2 2 4.79725654965128072e+01 ] setH input = [ 3 3 0.27 ] changeH_keepR  relax eval
	#setHspec = [ 2 2 4.79725654965128072e+01 ] setH input = [ 3 3 0.28 ] changeH_keepR  relax eval
#setHspec = [ 2 2 4.79725654965128072e+01 ] setH input = [ 3 3 0.29 ] changeH_keepR  relax eval
