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Current working version of insert group

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development
Alex Selimov 4 years ago
parent fe3cc92bc0
commit f9ffd4ddb1
3 changed files with 160 additions and 17 deletions
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2
src/main.f90
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@ -37,7 +37,7 @@ program main
!Call initialization functions
call lattice_init
call box_init
call random_seed
call init_random_seed
force_overwrite=.false.
wrap_flag = .false.

128
src/opt_group.f90
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@ -8,9 +8,12 @@ module opt_group
use box
implicit none
integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num, group_type, notsize
character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth, shell_thickness
integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num, group_type, notsize, insert_type, &
insert_site
character(len=15) :: type, gshape!Type indicates what element type is selected and shape is the group shape
real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth, shell_thickness, insert_conc, &
insert_lattice
logical :: displace, delete, max_remesh, refine, group_nodes, flip, efill, refinefill
integer, allocatable :: element_index(:), atom_index(:)
@ -29,6 +32,7 @@ module opt_group
group_ele_num = 0
group_atom_num = 0
remesh_size=0
insert_type = 0
random_num=0
group_type=0
notsize=0
@ -75,6 +79,11 @@ module opt_group
call change_group_type
end if
if(insert_type > 0) then
call get_group
call insert_group
end if
end subroutine group
subroutine parse_group(arg_pos)
@ -98,11 +107,11 @@ module opt_group
end select
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, shape, arglen)
call get_command_argument(arg_pos, gshape, arglen)
if (arglen==0) STOP "Missing group_shape in group command"
!Now parse the arguments required by the user selected shape
select case(trim(adjustl(shape)))
select case(trim(adjustl(gshape)))
case('block')
do i= 1, 6
arg_pos = arg_pos + 1
@ -146,7 +155,7 @@ module opt_group
vertices(i,2) = box_bd(2*i-1)
vertices(i,3) = box_bd(2*i-1)
else
print *, "bwidth cannot be 0 in wedge shaped group"
print *, "bwidth cannot be 0 in wedge gshaped group"
stop 3
end if
else if (i == dim2) then
@ -369,7 +378,7 @@ module opt_group
continue
case default
print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
print *, "Group shape ", trim(adjustl(gshape)), " is not currently accepted. Please check documentation ", &
"for accepted group shapes."
end select
@ -426,8 +435,34 @@ module opt_group
if(arglen ==0) stop "Missing notsize size"
read(textholder, *) notsize
print *, "Ignoring elements with size ", notsize
case('insert')
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing element type for insert command"
call add_atom_type(textholder, insert_type)
arg_pos=arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
select case(trim(adjustl(textholder)))
case('tetra')
insert_site=1
case('octa')
insert_site=2
case('mixed')
insert_site=3
case default
!If it isn't an available option to opt_disl then we just exit
print *, "site value must be tetra, octa, or mixed and not ", trim(adjustl(textholder))
stop 3
end select
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen ==0) stop "Missing lattice_type in insert command"
read(textholder, *) insert_lattice
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen ==0) stop "Missing concentration in insert command"
read(textholder, *) insert_conc
case default
!If it isn't an available option to opt_group then we just exit
exit
end select
end do
@ -440,7 +475,7 @@ module opt_group
integer, allocatable :: resize_array(:)
real(kind=dp) :: r_center(3), rand
select case(trim(adjustl(shape)))
select case(trim(adjustl(gshape)))
case('block')
print *, "Group has block shape with boundaries: ", block_bd
case ('wedge')
@ -1007,10 +1042,71 @@ module opt_group
end subroutine change_group_type
subroutine insert_group
!This code inserts atoms into interstitial sites. This only works on atoms within the group due to the limitations with the
!Coarse-graining methodology which doesn't allow for concentration fluctuations.
real(kind=dp) interstitial_sites(3,14), rand, rinsert(3)
integer :: add_num, i, j, rindex, sindex, ia, rlo, rhi, sbox
integer, allocatable :: used_sites(:,:)
!First save all of the displacement vectors from a lattice site to interstitial site
!The first 6 are the octohedral sites and the next 8 are the tetrahedral sites
interstitial_sites= reshape( (/ -0.5_dp, 0.0_dp, 0.0_dp, &
0.5_dp, 0.0_dp, 0.0_dp, &
0.0_dp,-0.5_dp, 0.0_dp, &
0.0_dp, 0.5_dp, 0.0_dp, &
0.0_dp, 0.0_dp,-0.5_dp, &
0.0_dp, 0.0_dp, 0.5_dp, &
-0.25_dp,-0.25_dp,-0.25_dp, &
-0.25_dp,-0.25_dp, 0.25_dp, &
-0.25_dp, 0.25_dp,-0.25_dp, &
-0.25_dp, 0.25_dp, 0.25_dp, &
0.25_dp,-0.25_dp,-0.25_dp, &
0.25_dp,-0.25_dp, 0.25_dp, &
0.25_dp, 0.25_dp,-0.25_dp, &
0.25_dp, 0.25_dp, 0.25_dp /), &
shape(interstitial_sites))
!First we calculate the number of atoms needed based on the number of atoms in the group and the concentration
interstitial_sites=interstitial_sites*insert_lattice
add_num = (insert_conc*group_atom_num)/(1-insert_conc)
allocate(used_sites(2,add_num))
print *, "Inserting ", add_num, " atoms as atom type ", insert_type
!Now set up the random number generator for the desired interstitial type
select case(insert_site)
case(1)
rlo=1
rhi=6
case(2)
rlo=7
rhi = 14
case(3)
rlo=1
rhi=14
end select
subroutine split_group_elements
!
end subroutine split_group_elements
!Now add the atoms
i = 1
addloop:do while ( i < add_num)
call random_number(rand)
rindex = int(1+rand*(group_atom_num-1))
ia=atom_index(rindex)
call random_number(rand)
sindex = int(rlo+rand*(rhi-rlo))
do j = 1, i
if((ia == used_sites(1,i)).and.(sindex == used_sites(2,i))) cycle addloop
end do
rinsert = r_atom(:,ia) + matmul(sub_box_ori(:,:,sbox_atom(ia)),interstitial_sites(:,sindex))
sbox = sbox_atom(ia)
call add_atom(0, insert_type, sbox, rinsert)
used_sites(1,i) = ia
used_sites(2,i) = sindex
i = i + 1
end do addloop
end subroutine insert_group
function in_group(r)
!This subroutine determines if a point is within the group boundaries
@ -1019,7 +1115,7 @@ module opt_group
integer :: dim3, i
logical :: in_group
select case(trim(adjustl(shape)))
select case(trim(adjustl(gshape)))
case('block')
in_group=in_block_bd(r,block_bd)
case('wedge')
@ -1068,7 +1164,7 @@ module opt_group
in_group_ele=.false.
if(trim(adjustl(shape)) == 'shell') then
if(trim(adjustl(gshape)) == 'shell') then
node_in_out(:) = -1
!First calculate whether each element node is within the shell region, inside the shell sphere, or outside the
!shell region
@ -1083,13 +1179,13 @@ module opt_group
exit nodeloop
end if
shape ='sphere'
gshape ='sphere'
if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(esize/=notsize)) then
node_in_out(inod) = 1
else
node_in_out(inod) = 0
end if
shape='shell'
gshape='shell'
end do nodeloop
!If any nodes are within the shell region, or if the shell region interescts an element then add it to the group

47
src/subroutines.f90
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@ -241,5 +241,52 @@ module subroutines
return
end subroutine check_right_ortho
subroutine init_random_seed()
implicit none
integer, allocatable :: seed(:)
integer :: i, n, un, istat, dt(8), pid, t(2), s
integer(8) :: count, tms
call random_seed(size = n)
allocate(seed(n))
! First try if the OS provides a random number generator
open(newunit=un, file="/dev/urandom", access="stream", &
form="unformatted", action="read", status="old", iostat=istat)
if (istat == 0) then
read(un) seed
close(un)
else
! Fallback to XOR:ing the current time and pid. The PID is
! useful in case one launches multiple instances of the same
! program in parallel.
call system_clock(count)
if (count /= 0) then
t = transfer(count, t)
else
call date_and_time(values=dt)
tms = (dt(1) - 1970) * 365_8 * 24 * 60 * 60 * 1000 &
+ dt(2) * 31_8 * 24 * 60 * 60 * 1000 &
+ dt(3) * 24 * 60 * 60 * 60 * 1000 &
+ dt(5) * 60 * 60 * 1000 &
+ dt(6) * 60 * 1000 + dt(7) * 1000 &
+ dt(8)
t = transfer(tms, t)
end if
s = ieor(t(1), t(2))
pid = getpid() + 1099279 ! Add a prime
s = ieor(s, pid)
if (n >= 3) then
seed(1) = t(1) + 36269
seed(2) = t(2) + 72551
seed(3) = pid
if (n > 3) then
seed(4:) = s + 37 * (/ (i, i = 0, n - 4) /)
end if
else
seed = s + 37 * (/ (i, i = 0, n - 1 ) /)
end if
end if
call random_seed(put=seed)
end subroutine init_random_seed
end module subroutines

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