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147 lines
4.6 KiB
147 lines
4.6 KiB
module opt_bubble
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!This module contains the bubble option which can be used to create voids with specific pressures of certain atoms
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use atoms
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use parameters
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use elements
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use box
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use opt_group
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implicit none
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real(kind=dp), private :: br, brat, c(3)
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character(len=2), private :: species
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public
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contains
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subroutine bubble(arg_pos)
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integer, intent(inout) :: arg_pos
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integer :: new_type, n, j, i, atom_num_pre
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real(kind = dp) :: p(3), rand, factor, per, vol, mass
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print *, '------------------------------------------------------------'
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print *, 'Option Bubble'
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print *, '------------------------------------------------------------'
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!First we parse the bubble command
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call parse_bubble(arg_pos)
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!Now we use the existing group code to delete a sphere which represents the bubble
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centroid=c
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radius = br
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type='all'
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gshape='sphere'
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group_nodes = .true.
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group_atom_types=0
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call get_group
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call refine_group
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call get_group
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atom_num_pre= atom_num
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call delete_group
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!Now we create a new atom type with the desired species
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call atommass(species, mass)
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call add_atom_type(mass, new_type)
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!Now we calculate the number of atoms we need to add for the desired pressure
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!print *, "Creating a bubble with pressure", bp, " at temperature ", bt, " with radius ", br
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!
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!factor = 1.0e24/6.02214e23
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!if (bp <= 10.0) then
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! per=factor*(3.29674113+4.51777872*bp**(-0.80473167))
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!else if (bp .le. 20.0) then
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! per=factor*(4.73419689-0.072919483*bp)
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!else
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! per=factor*(4.73419689-0.072919483*bp)
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! print *, 'warning: pressure is too high'
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! print *, 'equation of state is only valid for < 20 GPa'
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!endif
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!vol = 4.0*pi/3.0*br**3.0
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n = brat*(atom_num_pre-atom_num)
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print *, "Adding ", n, " atoms of species ", species
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!Now add n atoms randomly within the sphere
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do i = 1, n
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do while(.true.)
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do j = 1, 3
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call random_number(rand)
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p(j) = rand*(2*br) + c(j)-br
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end do
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if (norm2(p-c) < br) exit
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end do
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call add_atom(0, new_type, p)
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end do
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end subroutine bubble
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subroutine parse_bubble(arg_pos)
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integer, intent(inout) :: arg_pos
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integer :: i, arglen
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real(kind=dp) :: mass
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character(len=100) :: tmptxt
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!First read in the bubble centroid
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do i = 1, 3
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, tmptxt, arglen)
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print *, trim(adjustl(tmptxt))
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call parse_pos(i, tmptxt, c(i))
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end do
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!Now the bubble radius
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, tmptxt, arglen)
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print *, trim(adjustl(tmptxt))
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if(arglen == 0) stop "Missing bubble radius"
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read(tmptxt, *) br
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!Now bubble ratio
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, tmptxt, arglen)
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print *, trim(adjustl(tmptxt))
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if(arglen == 0) stop "Missing bubble ratio"
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read(tmptxt, *) brat
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!Now the bubble species
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, species, arglen)
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print *, species
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if(arglen == 0) stop "Missing bubble species"
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!OPtional arguments
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do while(.true.)
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if(arg_pos > command_argument_count()) exit
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arg_pos=arg_pos+1
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call get_command_argument(arg_pos, tmptxt)
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tmptxt=adjustl(tmptxt)
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select case(trim(tmptxt))
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case('excludetypes')
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arg_pos=arg_pos + 1
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call get_command_argument(arg_pos, tmptxt, arglen)
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if(arglen==0) stop "Missing number of atoms to exclude"
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read(tmptxt, *) exclude_num
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do i=1,exclude_num
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, tmptxt, arglen)
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if(arglen==0) stop "Missing exclude atom types"
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call atommass(tmptxt, mass)
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call add_atom_type(mass, exclude_types(i))
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end do
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case default
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exit
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end select
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end do
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return
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end subroutine parse_bubble
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end module opt_bubble
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