# -*-shell-script-*-
# melting temperature of Silicon (TCL)
# run by meam-baskes
#------------------------------------------------------------

#*******************************************
# Definition of procedures
#*******************************************
proc initmd_prepare_liquid { } { MD++ {
#setnolog
setoverwrite
dirname = runs/si-au-melt-liquid

#--------------------------------------------
# Create Perfect Lattice Configuration
crystalstructure = diamond-cubic
latticeconst = 5.431 #(A) for Si
latticesize  = [ 1 0 0  5 
                 0 1 0  1
                 0 0 1  5 ]
makecrystal 
fixallatoms input = 1 setfixedatomsspecies freeallatoms
finalcnfile = "perf-si.cn" writeall = 1 writecn

latticesize = [ 1 0 0  5
                0 1 0  4
                0 0 1  5 ]
makecrystal
finalcnfile = "perf-au.cn" writeall = 1 writecn

incnfile = "perf-si.cn" finalcnfile = "perf-si-au.cn" 
input = [ 2 0 ] splicecn writecn

srand48bytime randomposition
writeall = 1 zipfiles = 1 finalcnfile = "rand-si-au.cn" writecn 
} }
#end of proc initmd_prepare_liquid

proc initmd_prepare_liquid_solid { } { MD++ {
#setnolog
setoverwrite
dirname = runs/si-au-liquid-solid

#--------------------------------------------
# Create Perfect Lattice Configuration
crystalstructure = diamond-cubic
latticeconst = 5.431 #(A) for Si
latticesize = [ 1 0 0  3
                0 1 0  2
                0 0 1  3 ]
makecrystal
zipfiles = 0
input = [ 1 1 0.666 ] redefinepbc
input = [ 3 3 0.666 ] redefinepbc
fixallatoms input = 1 setfixedatomsspecies freeallatoms
finalcnfile = "island-si.cn" writeall = 1 writecn

crystalstructure = "face-centered-cubic"
latticesize  = [ 1 0 0  6
                 0 1 0  3
                 0 0 1  6 ]
makecrystal
input = [0 0.09 0] pbcshiftatom
finalcnfile = "substrate-au.cn" writeall = 1 writecn

incnfile = ../si-au-melt-liquid/liquid-equil-pbc.cn readcn
finalcnfile = liquid-equil-pbc.cn zipfiles = 0 writecn
incnfile = substrate-au.cn readcn
incnfile = liquid-equil-pbc.cn finalcnfile = splice.cn
input = [ 2 0 ]  splicecn

incnfile = "island-si.cn" finalcnfile = "splice2.cn"
splicecn
#splicecn only works with unzipped cnfile

zipfiles = 1

input = [ 1 -10 10 -10 -0.45 -10 10 ] fixatoms_by_position
input = [ 2 2 0.5] redefinepbc finalcnfile = "si-au-liquid-solid.cn" writecn
} }
#end of proc initmd_prepare_liquid_solid

proc initmd_measure_melting_point { n } { 
#MD++ setnolog
MD++ setoverwrite
MD++ dirname = runs/si-au-melt-NPH-$n

MD++ incnfile = ../si-au-liquid-solid/liquid-solid-equil.cn readcn 
MD++ writeall = 1 zipfiles = 1
MD++ plot_map_pbc = 1
} 

#------------------------------------------------------------
proc readmeam-baskes { } { MD++ {
#Read in MEAM potential (Baskes format)
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  " 
rcut = 6.0 kode0 = "library" readMEAM
NNM = 300
} }

#------------------------------------------------------------
proc readmeam-lammps { } { MD++ {
#Read in MEAM potential (Baskes format)
meamfile = "/home/caiwei/Codes/lammps-15Dec06/examples/meam/meamf"
nspecies = 1  element0 = "Siz" rcut = 6.0  readMEAM
NNM = 300
} }

#-------------------------------------------------------------
proc openwindow { } { MD++ {
# Plot Configuration
#
atomradius = [ 0.87 0.67 ] bondradius = 0.3 bondlength = 2 #2.8285 #for Si
atomcolor = orange bondcolor = red backgroundcolor = gray70 fixatomcolor = yellow
plotfreq = 100  rotateangles = [ 0 0 0 1.25 ]
openwin  alloccolors rotate saverot eval plot
} }
#end of proc openwindow

#--------------------------------------------
proc exitmd { } { MD++ quit }
#end of proc exitmd

#--------------------------------------------
proc relax_freebox { } { MD++ {
# Conjugate-Gradient relaxation
conj_ftol = 2e-6 conj_itmax = 1000 conj_fevalmax = 10000
conj_fixbox = 0  conj_fixboxvec = [ 0 1 1
                                    1 0 1
                                    1 1 0 ]
relax
} }
#end of proc relax_freebox
#--------------------------------------------
proc relax_fixbox { } { MD++ {
# Conjugate-Gradient relaxation
conj_ftol = 2e-6 conj_itmax = 1000 conj_fevalmax = 10000
conj_fixbox = 1  conj_fixboxvec = [ 0 1 1
                                    1 0 1
                                    1 1 0 ]
relax
} }
#end of proc relax_freebox

#--------------------------------------------
proc setup_md { } { MD++ {     
equilsteps = 0  timestep = 0.0001 # (ps)
atommass = [ 196.96655 28.0855 ] # (g/mol)
DOUBLE_T = 0
saveprop = 1 savepropfreq = 100 openpropfile #run
savecn = 1 savecnfreq = 1000 openintercnfile
plotfreq = 100
vt2 = 2e28  #1e28 2e28 5e28
wallmass = 2e3     # atommass * NP = 14380
boxdamp = 1e-3     # optimal damping for 216 atoms and wallmass 1e-3
saveH # Use current H as reference (H0), needed for specifying stress
fixboxvec  = [ 0 1 1 
               1 0 1
               1 1 0 ]
stress = [ 0 0 0
           0 0 0
           0 0 0 ]
output_fmt = "curstep EPOT KATOM Tinst HELM HELMP TSTRESS_xx TSTRESS_yy TSTRESS_zz H_11 H_22 H_33" 
} }
#end of proc setup_md


#--------------------------------------------
# for diagnosis purposes
proc printfile {fname} { puts [read [open $fname r]] }

proc index3 { ID coord } {
    set ind.x 1; set ind.y 2; set ind.z 3
    expr { $ID * 3 + [set ind.$coord] - 1 }
}

proc MD++_GetVector { name ID coord } {
    MD++_Get $name [index3 $ID $coord]
}

proc MD++_PrintVar { name {unit \?} {fmt %11.4e} } {
    puts "$name\t= [format $fmt [MD++_Get  $name]] (in $unit)"
}

proc MD++_PrintMatrix { name {unit \?} {fmt %11.4e} } {
    puts "$name\t= [format $fmt [MD++_Get $name 0]] [format $fmt [MD++_Get $name 1]] [format $fmt [MD++_Get $name 2]]  (in $unit)"
    puts      "\t  [format $fmt [MD++_Get $name 3]] [format $fmt [MD++_Get $name 4]] [format $fmt [MD++_Get $name 5]]"
    puts      "\t  [format $fmt [MD++_Get $name 6]] [format $fmt [MD++_Get $name 7]] [format $fmt [MD++_Get $name 8]]"
}

proc MD++_PrintArray { name {unit \?} {i0 0} {i1 5} {fmt %11.4e} } {
    for {set ID $i0} {$ID < $i1} {incr ID 1} {
        puts "$name\($ID\)= [format $fmt [MD++_Get  $name $ID]] [expr {$ID==$i0?"(in $unit)":" "}]"
    }
}

proc MD++_PrintVectorArray { name {unit \}?} {i0 0} {i1 0} {fmt %11.4e} } {
    for {set ID $i0} {$ID < $i1} {incr ID 1} {
        puts "$name\($ID\)= ([format $fmt [MD++_GetVector $name $ID x]]\
                           [format $fmt [MD++_GetVector $name $ID y]]\
                           [format $fmt [MD++_GetVector $name $ID z]])\
                           [expr {$ID==$i0?"(in $unit)":" "}]"
    }
}
# end of diagnosis procs

    



#*******************************************
# Main program starts here
#*******************************************
# status 0:prepare liquid, 1: prepare liquid-solid interface, 2,3: measure Tm
# read in status from command line argument
if { $argc == 0 } {
 set status 0
} elseif { $argc > 0 } {
 set status [lindex $argv 0]
}
if { $argc <= 1 } {
 set n 0
} elseif { $argc > 1 } {
 set n [lindex $argv 0]
}
puts "status = $status"
puts "n = $n"


if { $status == 0 } {  

 initmd_prepare_liquid
 readmeam-baskes
 #openwindow
 relax_fixbox
 MD++ finalcnfile = "rand-relaxed.cn" writecn
 setup_md
 MD++ T_OBJ = 700 initvelocity ensemble_type = "NPT" integrator_type = "Gear6" 
 MD++ totalsteps = 10000 run
 MD++ finalcnfile = "liquid-equil.cn" writecn
 MD++ {input = [ 0 0 0 ]} pbcshiftatom finalcnfile = "liquid-equil-pbc.cn" writecn plot
 exitmd

} elseif { $status == 1 } {

 initmd_prepare_liquid_solid
 readmeam-baskes
 #openwindow
 setup_md
 MD++ T_OBJ = 700 initvelocity ensemble_type = "NPT" integrator_type = "Gear6" 
 MD++ totalsteps = 10000 run
 MD++ finalcnfile = "liquid-solid-equil.cn" writecn
 exitmd

} elseif { $status == 2 } {

 initmd_measure_melting_point $n
 readmeam-baskes
 #openwindow
 setup_md
 MD++ { 
          fixboxvec  = [ 0 1 1 
                         1 1 1
                         1 1 0 ]
      }
 MD++ ensemble_type = "NPH" integrator_type = "VVerlet" 
 MD++ totalsteps = 100000 run
 MD++ finalcnfile = "NPH-equil.cn" writecn
 exitmd

} elseif { $status == 3 } {

 initmd_measure_melting_point
 readmeam-baskes
 #openwindow
 setup_md
 MD++ { 
          fixboxvec  = [ 0 1 1 
                         1 1 1
                         1 1 0 ]
      }
 MD++ ensemble_type = "NPH" integrator_type = "VVerlet" 
 MD++ totalsteps = 100000

 set datafile "Tx.dat"
 set fileID [open $datafile w ]

 for {set x 0} {$x<=100} {incr x 1} {

     if { $x > 0 } { MD++ input = 1.01 scaleVel }

     MD++ run

     puts $fileID "$x [MD++_Get Tinst ] [MD++_Get KATOM ] [MD++_Get EPOT ]"

     MD++ finalcnfile = n$x.cn writecn
 }

 close $fileID

 exitmd

} else {

 puts "unknown status = $status"
 exitmd 

} 
#-------------------------------------------
