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

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

#--------------------------------------------
# Create Perfect Lattice Configuration
crystalstructure = diamond-cubic
latticeconst = 5.431 #(A) for Si
latticesize  = [ 4 1 0  1
                -1 4 0  1
                 0 0 1  4 ]
makecrystal
srand48bytime randomposition
writeall = 1 zipfiles = 1 finalcnfile = rand.cn writecn 
} }
#end of proc initmd_prepare_liquid

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

#--------------------------------------------
# Create Perfect Lattice Configuration
crystalstructure = diamond-cubic
latticeconst = 5.431 #(A) for Si
latticesize  = [ 4 1 0  1
                -1 4 0  3
                 0 0 1  4 ]

incnfile = ../si-melt-liquid/liquid-equil-pbc.cn readcn 

makecrystal writeall = 1 zipfiles = 1 finalcnfile = perf.cn writecn
finalcnfile = liquid-solid.cn input = [ 2 0 ] splicecn

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

proc initmd_measure_melting_point { } { MD++ {
setnolog
setoverwrite
dirname = runs/si-liquid-solid

incnfile = liquid-solid-equil.cn readcn writeall = 1 zipfiles = 1
plot_map_pbc = 1
} }

#------------------------------------------------------------
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 = 0.67 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 = [ 1 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 = [ 1 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 = 28.0855 # (g/mol)
DOUBLE_T = 0
saveprop = 1 savepropfreq = 100 openpropfile 
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: measure Tm
# read in status from command line argument
if { $argc == 0 } {
 set status 0
} elseif { $argc > 0 } {
 set status [lindex $argv 0]
}
puts "status = $status"

if { $status == -1 } {
 initmd_prepare_liquid
 readmeam-lammps 
 MD++ makecrystal
 setup_md
 #MD++ T_OBJ = 1400 initvelocity ensemble_type = "NPT" integrator_type = "Gear6" 
 #MD++ totalsteps = 10 savecn = 0 run
 #MD++ finalcnfile = "test.cn" writecn
 MD++ zipfiles = 1
 MD++ closepropfile
 exitmd
}

if { $status == 0 } {  

 initmd_prepare_liquid
 readmeam-lammps
 #openwindow
 relax_fixbox
 MD++ finalcnfile = "rand-relaxed.cn" writecn
 setup_md
 MD++ T_OBJ = 1400 initvelocity ensemble_type = "NPT" integrator_type = "Gear6" 
 MD++ totalsteps = 2000 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-lammps
 #openwindow
 setup_md
 MD++ T_OBJ = 1400 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
 MD++ incnfile = "liquid-solid-equil.cn" readcn writeall = 1
 readmeam-lammps
 #openwindow
 setup_md
 MD++ {
          fixboxvec  = [ 0 1 1
                         1 1 1
                         1 1 0 ]
      }
 MD++ T_OBJ = 1400 initvelocity ensemble_type = "NPH" integrator_type = "VVerlet" 
 MD++ totalsteps = 10000 run
 MD++ finalcnfile = "liquid-solid-equil.cn" writecn
 exitmd

} elseif { $status == 3 } {

 initmd_measure_melting_point
 readmeam-lammps
 #openwindow
 setup_md
 MD++ {
          fixboxvec  = [ 0 1 1
                         1 1 1
                         1 1 0 ]
      }
 MD++ ensemble_type = "NPH" integrator_type = "VVerlet"
 MD++ totalsteps = 10000

 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 

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