# -*-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 { } { MD++ {
setnolog
setoverwrite
dirname = runs/si-md-test
#------------------------------------------------------------
# Read in MEAM potential
#meamfile = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meamf"
# original MEAM potential
#ntypes = 1  ename0 = "Siz  " #leave spaces to be compatible with fortran
# 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
#NIC = 200 NNM = 200
#--------------------------------------------
# Create Perfect Lattice Configuration
#
latticestructure = diamond-cubic
latticeconst = 5.430949821 #(A) for Si
latticesize  = [ 1 0 0  8
                 0 1 0  8
                 0 0 1  8 ]
} }
#end of proc initmd

#-------------------------------------------------------------
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
#*******************************************
initmd

MD++  {

latticeconst = 5.431 makecrystal    

saveH # Use current H as reference (H0)

usenosehoover = 1  vt2 = 2e28  

fixbox = 0 # Parrinello-Rahman, but box remain rectangular
fixboxvec = [ 0 1 1
              1 0 1
              1 1 0 ]

atommass = 28.0855 # (g/mol)
wallmass = 2e3     # atommass * NP = 14380
boxdamp = 1e-3     # optimal damping for 216 atoms and wallmass 1e-3

srand48bytime  DOUBLE_T = 0  timestep = 0.0001 # (ps)

totalsteps = 10    equilsteps = 0  
integrator_type = 0 #0: Gear6, 1: Velocity Verlet
saveprop = 1 savepropfreq = 1 openpropfile
savecn = 1 savecnfreq = 10000 openintercnfile writeall = 1 
plotfreq = 20
output_fmt = "curstep EPOT Tinst TSTRESS_xy TSTRESS(1)"
}

MD++ eval

MD++ T_OBJ = 1000 initvelocity

puts [MD++_Get VSR(10)]
puts [MD++_Get VSR 10]

MD++ run

puts [MD++_Get VSR(10)]
puts [MD++_Get VSR 10]

puts [MD++_Get EPOT_IND(10)]
puts [MD++_Get EPOT_IND(11)]

puts [MD++_Get EPOT_IND 10]
puts [MD++_Get EPOT_IND 11]



exitmd



#----------------------------------------------------------------
# Command to get volume data
# cut -b 244-264 prop.out | more
