# -*-shell-script-*-
#TCL script file created from scripts/work/si_ge/si-T-expans.script
# Silicon bulk, thermal expansion by Parrinello-Rahman MD

#*******************************************
# Definition of procedures
#*******************************************
proc initmd { n } { 
#MD++ setnolog
MD++ setoverwrite
MD++ dirname = "runs/si-expans-$n"
}
#end of proc initmd

#------------------------------------------------------------
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 readmeam_newpot { } { MD++ {
#Read in MEAM potential (Baskes format)
meamfile = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meamf"
# new MEAM potential
meafile  = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meafile_Sin"
ntypes = 1  ename0 = "Sin  " #leave spaces to be compatible with fortran
rcut = 6  kode0 = "library"
readMEAM
NNM = 300
} }
#end of proc readmeam

#------------------------------------------------------------
proc readmeam { } { MD++ {
#Read in MEAM potential (Baskes format)
meamfile = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meamf"
# original MEAM potential
ntypes = 1  ename0 = "Siz  " #leave spaces to be compatible with fortran
rcut = 6  kode0 = "library"
readMEAM
NNM = 300
} }
#end of proc readmeam


proc create_crystal { } { MD++ {
#--------------------------------------------
# Create Perfect Lattice Configuration
#
latticestructure = diamond-cubic
latticeconst = 5.430949821 #(A) for Si
latticesize  = [ 1 0 0  4
                 0 1 0  4
                 0 0 1  4 ]
makecrystal finalcnfile = perf.cn writecn
} }
#end of proc create_crystal

#--------------------------------------------
proc setup_md { } { MD++ {     
equilsteps = 0  timestep = 0.0001 # (ps)
atommass = 28.0855 # (g/mol)
DOUBLE_T = 0  equilsteps = 0
saveprop = 1 savepropfreq = 100 openpropfile #run
savecn = 1 savecnfreq = 10000 openintercnfile
plotfreq = 20
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"
writeall = 1
} }
#end of proc setup_md

#-------------------------------------------------------------
proc openwindow { } { MD++ {
# Plot Configuration
#
atomradius = 0.67 bondradius = 0.3 bondlength = 2.8285 #for Si
atomcolor = orange bondcolor = red backgroundcolor = gray70
plotfreq = 10  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 = 1e-6 conj_itmax = 1000 conj_fevalmax = 1000
conj_fixbox = 0  relax
} }
#end of proc relax_freebox

#--------------------------------------------
# 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
#*******************************************
if { $argc == 0 } {
 set status 0
} elseif { $argc > 0 } {
 set status [lindex $argv 0]
}
puts "status = $status"



initmd $status
create_crystal
setup_md

#openwindow

MD++ randseed = 12345 srand48
#MD++  srand48bytime 

MD++ totalsteps = 500000

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

for {set x 100} {$x<=1700} {incr x 100} {

    MD++ T_OBJ = $x initvelocity  ensemble_type = "NPT" integrator_type = "Gear6"
    
    MD++ run

    set H11 [ MD++_Get H 0 ]
    set H22 [ MD++_Get H 4 ]
    set H33 [ MD++_Get H 8 ]
    set Vol [ expr $H11 * $H22 * $H33 ]
    
    puts $fileID "$x  $H11 $H22 $H33 $Vol"
}

close $fileID

exitmd

