Current working version of insert group
This commit is contained in:
Alex Selimov
parent
fe3cc92bc0
commit
f9ffd4ddb1
@ -37,7 +37,7 @@ program main
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!Call initialization functions
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call lattice_init
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call box_init
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call random_seed
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call init_random_seed
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force_overwrite=.false.
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wrap_flag = .false.
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@ -8,9 +8,12 @@ module opt_group
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use box
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implicit none
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integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num, group_type, notsize
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character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
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real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth, shell_thickness
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integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num, group_type, notsize, insert_type, &
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insert_site
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character(len=15) :: type, gshape!Type indicates what element type is selected and shape is the group shape
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real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth, shell_thickness, insert_conc, &
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insert_lattice
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logical :: displace, delete, max_remesh, refine, group_nodes, flip, efill, refinefill
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integer, allocatable :: element_index(:), atom_index(:)
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@ -29,6 +32,7 @@ module opt_group
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group_ele_num = 0
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group_atom_num = 0
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remesh_size=0
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insert_type = 0
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random_num=0
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group_type=0
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notsize=0
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@ -75,6 +79,11 @@ module opt_group
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call change_group_type
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end if
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if(insert_type > 0) then
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call get_group
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call insert_group
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end if
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end subroutine group
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subroutine parse_group(arg_pos)
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@ -98,11 +107,11 @@ module opt_group
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end select
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, shape, arglen)
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call get_command_argument(arg_pos, gshape, arglen)
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if (arglen==0) STOP "Missing group_shape in group command"
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!Now parse the arguments required by the user selected shape
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select case(trim(adjustl(shape)))
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select case(trim(adjustl(gshape)))
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case('block')
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do i= 1, 6
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arg_pos = arg_pos + 1
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@ -146,7 +155,7 @@ module opt_group
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vertices(i,2) = box_bd(2*i-1)
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vertices(i,3) = box_bd(2*i-1)
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else
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print *, "bwidth cannot be 0 in wedge shaped group"
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print *, "bwidth cannot be 0 in wedge gshaped group"
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stop 3
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end if
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else if (i == dim2) then
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@ -369,7 +378,7 @@ module opt_group
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continue
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case default
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print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
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print *, "Group shape ", trim(adjustl(gshape)), " is not currently accepted. Please check documentation ", &
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"for accepted group shapes."
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end select
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@ -426,8 +435,34 @@ module opt_group
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if(arglen ==0) stop "Missing notsize size"
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read(textholder, *) notsize
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print *, "Ignoring elements with size ", notsize
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case('insert')
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arg_pos=arg_pos+1
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call get_command_argument(arg_pos, textholder, arglen)
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if (arglen==0) stop "Missing element type for insert command"
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call add_atom_type(textholder, insert_type)
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arg_pos=arg_pos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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select case(trim(adjustl(textholder)))
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case('tetra')
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insert_site=1
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case('octa')
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insert_site=2
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case('mixed')
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insert_site=3
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case default
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!If it isn't an available option to opt_disl then we just exit
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print *, "site value must be tetra, octa, or mixed and not ", trim(adjustl(textholder))
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stop 3
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end select
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arg_pos=arg_pos+1
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call get_command_argument(arg_pos, textholder, arglen)
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if(arglen ==0) stop "Missing lattice_type in insert command"
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read(textholder, *) insert_lattice
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arg_pos=arg_pos+1
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call get_command_argument(arg_pos, textholder, arglen)
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if(arglen ==0) stop "Missing concentration in insert command"
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read(textholder, *) insert_conc
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case default
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!If it isn't an available option to opt_group then we just exit
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exit
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end select
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end do
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@ -440,7 +475,7 @@ module opt_group
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integer, allocatable :: resize_array(:)
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real(kind=dp) :: r_center(3), rand
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select case(trim(adjustl(shape)))
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select case(trim(adjustl(gshape)))
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case('block')
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print *, "Group has block shape with boundaries: ", block_bd
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case ('wedge')
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@ -1007,10 +1042,71 @@ module opt_group
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end subroutine change_group_type
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subroutine insert_group
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!This code inserts atoms into interstitial sites. This only works on atoms within the group due to the limitations with the
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!Coarse-graining methodology which doesn't allow for concentration fluctuations.
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real(kind=dp) interstitial_sites(3,14), rand, rinsert(3)
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integer :: add_num, i, j, rindex, sindex, ia, rlo, rhi, sbox
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integer, allocatable :: used_sites(:,:)
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subroutine split_group_elements
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!
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end subroutine split_group_elements
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!First save all of the displacement vectors from a lattice site to interstitial site
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!The first 6 are the octohedral sites and the next 8 are the tetrahedral sites
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interstitial_sites= reshape( (/ -0.5_dp, 0.0_dp, 0.0_dp, &
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0.5_dp, 0.0_dp, 0.0_dp, &
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0.0_dp,-0.5_dp, 0.0_dp, &
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0.0_dp, 0.5_dp, 0.0_dp, &
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0.0_dp, 0.0_dp,-0.5_dp, &
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0.0_dp, 0.0_dp, 0.5_dp, &
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-0.25_dp,-0.25_dp,-0.25_dp, &
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-0.25_dp,-0.25_dp, 0.25_dp, &
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-0.25_dp, 0.25_dp,-0.25_dp, &
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-0.25_dp, 0.25_dp, 0.25_dp, &
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0.25_dp,-0.25_dp,-0.25_dp, &
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0.25_dp,-0.25_dp, 0.25_dp, &
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0.25_dp, 0.25_dp,-0.25_dp, &
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0.25_dp, 0.25_dp, 0.25_dp /), &
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shape(interstitial_sites))
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!First we calculate the number of atoms needed based on the number of atoms in the group and the concentration
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interstitial_sites=interstitial_sites*insert_lattice
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add_num = (insert_conc*group_atom_num)/(1-insert_conc)
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allocate(used_sites(2,add_num))
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print *, "Inserting ", add_num, " atoms as atom type ", insert_type
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!Now set up the random number generator for the desired interstitial type
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select case(insert_site)
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case(1)
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rlo=1
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rhi=6
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case(2)
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rlo=7
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rhi = 14
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case(3)
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rlo=1
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rhi=14
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end select
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!Now add the atoms
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i = 1
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addloop:do while ( i < add_num)
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call random_number(rand)
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rindex = int(1+rand*(group_atom_num-1))
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ia=atom_index(rindex)
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call random_number(rand)
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sindex = int(rlo+rand*(rhi-rlo))
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do j = 1, i
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if((ia == used_sites(1,i)).and.(sindex == used_sites(2,i))) cycle addloop
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end do
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rinsert = r_atom(:,ia) + matmul(sub_box_ori(:,:,sbox_atom(ia)),interstitial_sites(:,sindex))
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sbox = sbox_atom(ia)
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call add_atom(0, insert_type, sbox, rinsert)
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used_sites(1,i) = ia
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used_sites(2,i) = sindex
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i = i + 1
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end do addloop
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end subroutine insert_group
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function in_group(r)
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!This subroutine determines if a point is within the group boundaries
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@ -1019,7 +1115,7 @@ module opt_group
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integer :: dim3, i
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logical :: in_group
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select case(trim(adjustl(shape)))
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select case(trim(adjustl(gshape)))
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case('block')
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in_group=in_block_bd(r,block_bd)
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case('wedge')
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@ -1068,7 +1164,7 @@ module opt_group
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in_group_ele=.false.
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if(trim(adjustl(shape)) == 'shell') then
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if(trim(adjustl(gshape)) == 'shell') then
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node_in_out(:) = -1
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!First calculate whether each element node is within the shell region, inside the shell sphere, or outside the
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!shell region
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@ -1083,13 +1179,13 @@ module opt_group
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exit nodeloop
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end if
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shape ='sphere'
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gshape ='sphere'
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if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(esize/=notsize)) then
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node_in_out(inod) = 1
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else
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node_in_out(inod) = 0
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end if
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shape='shell'
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gshape='shell'
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end do nodeloop
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!If any nodes are within the shell region, or if the shell region interescts an element then add it to the group
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@ -241,5 +241,52 @@ module subroutines
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return
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end subroutine check_right_ortho
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subroutine init_random_seed()
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implicit none
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integer, allocatable :: seed(:)
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integer :: i, n, un, istat, dt(8), pid, t(2), s
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integer(8) :: count, tms
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call random_seed(size = n)
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allocate(seed(n))
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! First try if the OS provides a random number generator
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open(newunit=un, file="/dev/urandom", access="stream", &
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form="unformatted", action="read", status="old", iostat=istat)
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if (istat == 0) then
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read(un) seed
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close(un)
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else
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! Fallback to XOR:ing the current time and pid. The PID is
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! useful in case one launches multiple instances of the same
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! program in parallel.
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call system_clock(count)
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if (count /= 0) then
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t = transfer(count, t)
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else
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call date_and_time(values=dt)
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tms = (dt(1) - 1970) * 365_8 * 24 * 60 * 60 * 1000 &
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+ dt(2) * 31_8 * 24 * 60 * 60 * 1000 &
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+ dt(3) * 24 * 60 * 60 * 60 * 1000 &
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+ dt(5) * 60 * 60 * 1000 &
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+ dt(6) * 60 * 1000 + dt(7) * 1000 &
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+ dt(8)
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t = transfer(tms, t)
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end if
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s = ieor(t(1), t(2))
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pid = getpid() + 1099279 ! Add a prime
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s = ieor(s, pid)
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if (n >= 3) then
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seed(1) = t(1) + 36269
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seed(2) = t(2) + 72551
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seed(3) = pid
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if (n > 3) then
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seed(4:) = s + 37 * (/ (i, i = 0, n - 4) /)
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end if
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else
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seed = s + 37 * (/ (i, i = 0, n - 1 ) /)
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end if
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end if
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call random_seed(put=seed)
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end subroutine init_random_seed
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end module subroutines
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