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Alex Selimov 1 year ago
parent d6f11590f3
commit 8e924e1658
13 changed files with 338 additions and 109 deletions
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2
src/Makefile
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@ -33,7 +33,7 @@ $(OBJDIR)/%.o: %.f90
deps:
@fortdepend -o Makefile.dep -i mpi -b obj -w
@makedepf90 -b obj *.f90 > Makefile.dep
#----------------- CLEAN UP -----------------#

2
src/caller.f90
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@ -60,6 +60,8 @@ module caller
call group(arg_pos)
case('-ow')
arg_pos = arg_pos + 1
case('-novel')
arg_pos = arg_pos+1
case('-wrap')
arg_pos = arg_pos + 1
case('-norefine')

92
src/elements.f90
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@ -437,7 +437,7 @@ module elements
real(kind=dp), dimension(3, max_basisnum*max_esize**3), intent(out) :: r_interp !Interpolated atomic positions
real(kind = dp), optional, intent(in) :: eng(:,:), f(:,:,:), &
v(:,:,:)
real(kind=dp), dimension(10, max_basisnum*max_esize**3), optional,intent(out) :: data_interp !Interpolated atomic positions
real(kind=dp), dimension(:,:), optional,intent(out) :: data_interp !Interpolated atomic positions
!Internal variables
integer :: it, is, ir, ibasis, inod, ia, bnum, lat_type_temp, adjust
@ -528,6 +528,68 @@ module elements
return
end subroutine interpolate_atoms
subroutine interpolate_vel(type, esize, lat_type, vel_in, vel_interp)
!This subroutine returns the interpolated atoms from the elements.
!Arguments
character(len=*), intent(in) :: type !The type of element that it is
integer, intent(in) :: esize !The number of atoms per side
integer, intent(in) :: lat_type !The integer lattice type of the element
real(kind=dp), dimension(:,:,:), intent(in) :: vel_in !Nodal positions
real(kind=dp), dimension(3, max_basisnum*max_esize**3), intent(out) :: vel_interp !Interpolated atomic positions
!Internal variables
integer :: it, is, ir, ibasis, inod, ia, bnum, lat_type_temp, adjust
real(kind=dp) :: a_shape(max_ng_node)
real(kind=dp) :: t, s, r
!Initialize some variables
vel_interp(:,:) = 0.0_dp
ia = 0
!Define bnum based on the input lattice type. If lat_type=0 then we are interpolating lattice points which means
!the basis is 0,0,0, and the type doesn't matter
select case(lat_type)
case(0)
bnum=1
lat_type_temp = 1
case default
bnum = basisnum(lat_type)
lat_type_temp = lat_type
end select
select case(type)
case('fcc','bcc')
!Now loop over all the possible sites
do it = 1, esize
t=-1.0_dp +(it-1)*(2.0_dp/(esize-1))
do is =1, esize
s=-1.0_dp +(is-1)*(2.0_dp/(esize-1))
do ir = 1, esize
r=-1.0_dp +(ir-1)*(2.0_dp/(esize-1))
call rhombshape(r,s,t,a_shape)
do ibasis = 1, bnum
ia = ia + 1
do inod = 1, 8
vel_interp(:,ia) = vel_interp(:,ia) + a_shape(inod) * vel_in(:,ibasis,inod)
end do
end do
end do
end do
end do
end select
if (ia /= bnum*esize**3) then
print *, "Incorrect interpolation"
stop 3
end if
return
end subroutine interpolate_vel
subroutine rhombshape(r,s,t, shape_fun)
!Shape function for rhombohedral elements
real(kind=8), intent(in) :: r, s, t
@ -661,6 +723,7 @@ module elements
end do
end subroutine wrap_atoms
subroutine wrap_elements
integer :: i, inod, ibasis, j, node_in_bd(3,max_ng_node)
real(kind =dp) :: box_len(3)
@ -1018,11 +1081,36 @@ do i = 1, atom_num
subroutine add_atom_data(ia, eng, force, virial)
!Function which sets the atom data arrays
integer, intent(in) :: ia
real(kind=dp), intent(in) :: eng, force(3), virial(6)
real(kind=dp), intent(in) :: eng, force(:), virial(:)
integer :: size_atom_array
real(kind=dp), allocatable :: tmp_eng(:), tmp_force(:,:), tmp_virial(:,:)
size_atom_array=size(tag_atom)
if(ia > atom_num) then
stop "ia in add_atom_dat shouldn't be larger than atom_num"
else if(ia > size(energy_atom)) then
allocate(tmp_eng(size(energy_atom)+1024))
allocate(tmp_force(3, size(energy_atom)+1024))
allocate(tmp_virial(6, size(energy_atom)+1024))
tmp_eng=0.0_dp
tmp_eng(1:size(energy_atom)) = energy_atom
call move_alloc(tmp_eng, energy_atom)
tmp_force=0.0_dp
tmp_force(:, 1:size(force_atom, 2)) = force_atom
call move_alloc(tmp_force, force_atom)
tmp_virial=0.0_dp
tmp_virial(:, 1:size(virial_atom,2)) = virial_atom
call move_alloc(tmp_virial, virial_atom)
end if
energy_atom(ia) = eng
force_atom(:,ia) = force(:)
virial_atom(:,ia) = virial(:)
vflag = .true.
return
end subroutine add_atom_data

4
src/functions.f90
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@ -168,11 +168,11 @@ END FUNCTION StrDnCase
do i =1 ,3
!Check upper bound
if(v(i) > (box_bd(2*i)+10.0_dp**(-10)) ) then
if(v(i) > (box_bd(2*i))) then
in_block_bd =.false.
exit
!Check lower bound
else if (v(i) < (box_bd(2*i-1)-10.0_dp**(-10))) then
else if (v(i) < (box_bd(2*i-1))+1d-6) then
in_block_bd = .false.
exit
end if

28
src/io.f90
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@ -139,7 +139,7 @@ module io
do i = 1, ele_num
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
write(11, '(2i16, 3f23.15)') basis_type(ibasis,lat_ele(i)), 1, r_node(:,ibasis,inod,i)
write(11, *) basis_type(ibasis,lat_ele(i)), 1, r_node(:,ibasis,inod,i)
outn = outn + 1
end do
end do
@ -151,7 +151,7 @@ module io
!Write atom positions
do i = 1, atom_num
write(11, '(2i16, 3f23.15)') type_atom(i), 0, r_atom(:,i)
write(11, *) type_atom(i), 0, r_atom(:,i)
outn = outn + 1
end do
@ -207,7 +207,7 @@ module io
write(11, '(a)') 'Atoms'
write(11, '(a)') ' '
do i = 1, atom_num
write(11, '(2i16, 3f23.15)') tag_atom(i), type_atom(i), r_atom(:,i)
write(11, *) tag_atom(i), type_atom(i), r_atom(:,i)
end do
!Write refined element atomic positions
@ -219,7 +219,7 @@ module io
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
interp_num = interp_num+1
call apply_periodic(r_interp(:,iatom))
write(11, '(2i16, 3f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
write(11, *) atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
end do
end select
end do
@ -277,12 +277,12 @@ module io
if (write_dat) then
do i = 1, atom_num
write(11, '(2i16, 13f23.15)') tag_atom(i), type_atom(i), r_atom(:,i), energy_atom(i), &
write(11, *) tag_atom(i), type_atom(i), r_atom(:,i), energy_atom(i), &
force_atom(:,i), virial_atom(:,i)
end do
else
do i = 1, atom_num
write(11, '(2i16, 3f23.15)') tag_atom(i), type_atom(i), r_atom(:,i)
write(11, *) tag_atom(i), type_atom(i), r_atom(:,i)
end do
end if
@ -294,12 +294,12 @@ module io
do inod =1, ng_node(lat_ele(i))
do ibasis=1, basisnum(lat_ele(i))
if(write_dat) then
write(11, '(2i16, 13f23.15)') atom_num+interp_num, basis_type(ibasis,lat_ele(i)), &
write(11, *) atom_num+interp_num, basis_type(ibasis,lat_ele(i)), &
r_node(:, ibasis, inod, i), energy_node(ibasis,inod,i), force_node(:, ibasis, inod, i), &
virial_node(:, ibasis, inod, i)
else
write(11, '(2i16, 3f23.15)') atom_num+interp_num, basis_type(ibasis,lat_ele(i)), &
write(11, *) atom_num+interp_num, basis_type(ibasis,lat_ele(i)), &
r_node(:, ibasis, inod, i)
end if
interp_num = interp_num +1
@ -321,14 +321,14 @@ module io
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
interp_num = interp_num+1
call apply_periodic(r_interp(:,iatom))
write(11, '(2i16, 13f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom), &
write(11, *) atom_num+interp_num, type_interp(iatom), r_interp(:,iatom), &
data_interp(:,iatom)
end do
else
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
interp_num = interp_num+1
call apply_periodic(r_interp(:,iatom))
write(11, '(2i16, 3f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
write(11, *) atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
end do
end if
end select
@ -998,7 +998,7 @@ module io
!Internal Variables
integer :: i, j, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip, atom_type_map(100)
id, type_node, ilat, esize, tag, atype, bnum, n, ibasis, ip, atom_type_map(100)
real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), vela(3),&
ee(10,20), fe(3,10,20), ve(6,10,20), re(3,10,20), vele(3,10,20), atomic_masses(10)
character(len=100) :: textholder, fcc
@ -1064,11 +1064,11 @@ module io
do ia = 1, in_atoms
read(11,'(a)') line(:)
if(read_vel) then
read(line,*) tag, type, ra(:), ea, fa(:), va(:), vela(:)
read(line,*) tag, atype, ra(:), ea, fa(:), va(:), vela(:)
else
read(line,*) tag, type, ra(:), ea, fa(:), va(:)
read(line,*) tag, atype, ra(:), ea, fa(:), va(:)
end if
call add_atom(tag, atom_type_map(type), ra)
call add_atom(tag, atom_type_map(atype), ra)
call add_atom_data(atom_num, ea, fa, va)
if(read_vel) vel_atom(:,atom_num) = vela
end do

26
src/mode_calc.f90
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@ -25,6 +25,9 @@ module mode_calc
case('tot_virial')
allocate(calculated(6))
call calc_tot_virial
case('tot_energy')
allocate(calculated(1))
call calc_tot_energy
case default
print *, trim(adjustl(calc_opt)), " is not accepted as a calc option in mode_calc"
stop 3
@ -87,5 +90,26 @@ module mode_calc
print *, "Total virial is calculated as : (v11, v22, v33, v32, v31, v21)"
print *, calculated
end subroutine
end subroutine calc_tot_virial
subroutine calc_tot_energy
integer :: i, inod, ibasis, j
calculated=0
!Sum atom energies
do i = 1, atom_num
calculated(1) = calculated(1) + energy_atom(i)
end do
!Sum element energies
do i =1, ele_num
do inod=1, ng_node(lat_ele(i))
do ibasis=1, basisnum(lat_ele(i))
calculated(1) = calculated(1) + energy_node(ibasis, inod, i)*(size_ele(i)**3)/ng_node(lat_ele(i))
end do
end do
end do
print *, 'Total energy in eV is:'
print *, calculated(1)
end subroutine calc_tot_energy
end module mode_calc

4
src/mode_create.f90
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@ -12,9 +12,9 @@ module mode_create
character(len=100) :: name, element_type
real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3), basis_pos(3,10)
integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
basis_pos(3,10), esize_nums, esize_index(10)
esize_nums, esize_index(10)
logical :: dup_flag, dim_flag, efill, crossb(3)
real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:)

4
src/neighbors.f90
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@ -82,7 +82,7 @@ module neighbors
real(kind=dp), intent(in) :: rc_off
integer, intent(in) :: n
real(kind=dp), dimension(3,n) :: r_list
real(kind=dp), dimension(:, :), intent(in) :: r_list
integer :: i, j, c(3),cn(3), ci, cj, ck, num_nei, nei, v(3), period_dir(3)
!Variables for cell list code
@ -92,7 +92,7 @@ module neighbors
real(kind=dp) :: r(3), box_len(3)
logical :: period_bd(3)
!First reallocate the neighbor list codes
!First reallocate the neighbor list variables
if (allocated(nei_list)) then
deallocate(nei_list,nei_num, periodvec)
end if

32
src/opt_bubble.f90
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@ -32,7 +32,7 @@ module opt_bubble
type='all'
gshape='sphere'
group_nodes = .true.
group_atom_types=0
call get_group
call refine_group
call get_group
@ -80,6 +80,7 @@ module opt_bubble
integer, intent(inout) :: arg_pos
integer :: i, arglen
real(kind=dp) :: mass
character(len=100) :: tmptxt
@ -111,7 +112,34 @@ module opt_bubble
print *, species
if(arglen == 0) stop "Missing bubble species"
arg_pos = arg_pos +1
!OPtional arguments
do while(.true.)
if(arg_pos > command_argument_count()) exit
arg_pos=arg_pos+1
call get_command_argument(arg_pos, tmptxt)
tmptxt=adjustl(tmptxt)
select case(trim(tmptxt))
case('excludetypes')
arg_pos=arg_pos + 1
call get_command_argument(arg_pos, tmptxt, arglen)
if(arglen==0) stop "Missing number of atoms to exclude"
read(tmptxt, *) exclude_num
do i=1,exclude_num
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, tmptxt, arglen)
if(arglen==0) stop "Missing exclude atom types"
call atommass(tmptxt, mass)
call add_atom_type(mass, exclude_types(i))
end do
case default
exit
end select
end do
return
end subroutine parse_bubble
end module opt_bubble

2
src/opt_delete.f90
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@ -87,7 +87,7 @@ module opt_delete
allocate(which_cell(3,atom_num))
!First pass the atom list and atom num to the algorithm which builds the cell list
call build_cell_list(atom_num, r_atom, rc_off, cell_num, num_in_cell, cell_list, which_cell)
call build_cell_list(atom_num, r_atom, 5*rc_off, cell_num, num_in_cell, cell_list, which_cell)
!Now loop over every atom and figure out if it has neighbors within the rc_off
delete_num = 0

2
src/opt_disl.f90
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@ -520,7 +520,7 @@ module opt_disl
end do
return
end subroutine
end subroutine disloop
!********************************************************
! SOLIDANGLE

229
src/opt_group.f90
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@ -12,7 +12,7 @@ module opt_group
implicit none
integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num, group_type, notsize, insert_type, &
insert_site, num_species
insert_site, num_species, group_atom_types, exclude_num, exclude_types(10)
character(len=15) :: type, gshape!Type indicates what element type is selected and shape is the group shape
character(len=2) :: species_type(10)
real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth, shell_thickness, insert_conc, &
@ -39,6 +39,7 @@ module opt_group
insert_type = 0
random_num=0
group_type=0
group_atom_types=0
notsize=0
displace=.false.
delete=.false.
@ -47,6 +48,7 @@ module opt_group
flip = .false.
group_nodes=.false.
num_species = 0
exclude_num = 0
if(allocated(element_index)) deallocate(element_index)
if(allocated(atom_index)) deallocate(atom_index)
@ -87,10 +89,10 @@ module opt_group
call displace_group
end if
if(insert_type > 0) then
print *, "Insert command has been dropped"
stop 1
!print *, "Insert command has been dropped"
!stop 1
call get_group
! call insert_group
call insert_group
end if
if(num_species > 0) then
@ -470,6 +472,24 @@ module opt_group
refine=.true.
case('refinefill')
refinefill=.true.
case('selecttype')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing select type"
call atommass(textholder, mass)
call add_atom_type(mass, group_atom_types)
case('excludetypes')
arg_pos=arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen==0) stop "Missing number of atoms to exclude"
read(textholder, *) exclude_num
do i=1,exclude_num
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen==0) stop "Missing exclude atom types"
call atommass(textholder, mass)
call add_atom_type(mass, exclude_types(i))
end do
case('remesh')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
@ -619,7 +639,7 @@ module opt_group
select case(trim(adjustl(type)))
case('atoms','all')
do i = 1, atom_num
if(in_group(r_atom(:,i)).neqv.flip) then
if(in_group(type_atom(i), r_atom(:,i)).neqv.flip) then
group_atom_num = group_atom_num + 1
if (group_atom_num > size(atom_index)) then
allocate(resize_array(size(atom_index) + 1024))
@ -687,8 +707,19 @@ module opt_group
!This command is used to refine the group to full atomistics
integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), data_interp(10, max_basisnum*max_esize**3), &
vel_interp(3, max_basisnum*max_esize**3)
real(kind=dp), allocatable :: vel_tmp(:,:)
logical :: refine_dat
if (allocated(force_node)) then
refine_dat=.true.
else
refine_dat=.false.
end if
print *, size(data_interp)
!Refining to atoms
if(group_ele_num > 0) then
orig_atom_num = atom_num
@ -698,17 +729,38 @@ module opt_group
do i = 1, group_ele_num
ie = element_index(i)
!Get the interpolated atom positions
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
if (refine_dat) then
call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp, &
energy_node(:,:,i), force_node(:,:,:,i), virial_node(:,:,:,i), data_interp)
else
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
end if
if(allocated(vel_atom)) then
call interpolate_vel(type_ele(i), size_ele(i), lat_ele(i), vel_node(:,:,:,i), vel_interp)
end if
!Loop over all interpolated atoms and add them to the system, we apply periodic boundaries
!here as well to make sure they are in the box
do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
call apply_periodic(r_interp(:,j))
call add_atom(0,type_interp(j), r_interp(:,j))
if(refine_dat) then
call add_atom_data(atom_num, data_interp(1, j), data_interp(2:4, j), data_interp(5:10, j))
end if
if(allocated(vel_atom)) then
if(size(vel_atom, 2) < size(type_atom)) then
allocate(vel_tmp(3, size(type_atom)))
vel_tmp=0.0_dp
vel_tmp(:, 1:size(vel_atom,2)) = vel_atom
call move_alloc(vel_tmp, vel_atom)
end if
vel_atom(:, atom_num) = vel_interp(:,j)
end if
end do
end do
!Once all atoms are added we delete all of the elements
call delete_elements(group_ele_num, element_index)
print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms."
end if
end subroutine refine_group
@ -745,7 +797,7 @@ module opt_group
ravg = ravg + rfill(:,ibasis, 1)/basisnum(lat_ele(ie))
end do
if( in_group(ravg)) then
if( in_group(0,ravg)) then
nump_ele = nump_ele - 1
end if
end do
@ -1118,77 +1170,79 @@ 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
! 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
!
! !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
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
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
!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
if ((insert_conc > 1).or.(insert_conc < 0)) stop "Insert concentration should be between 0 and 1"
add_num = (insert_conc*group_atom_num)
allocate(used_sites(2,add_num))
print *, "Inserting ", add_num, " atoms as atom type ", insert_type
!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(box_ori,interstitial_sites(:,sindex))
call add_atom(0, insert_type, rinsert)
used_sites(1,i) = ia
used_sites(2,i) = sindex
i = i + 1
end do addloop
end subroutine insert_group
subroutine alloy_group
!This subroutine randomizes the atom types to reach desired concentrations, this only operates on atoms
integer :: i, j, ia, type_map(10), added_types(num_species)
real(kind=dp) :: rand, mass, old_fractions(num_species)
character(len=2) :: sorted_species_type(10)
logical :: species_mapped(10)
print *, "Alloying group with desired fractions", s_fractions(1:num_species)
@ -1196,10 +1250,13 @@ module opt_group
!First we sort the fractions
call quicksort(s_fractions(1:num_species))
species_mapped = .false.
do i = 1,num_species
do j=1, num_species
if (is_equal(s_fractions(i), old_fractions(j))) then
if (is_equal(s_fractions(i), old_fractions(j)) .and. .not. species_mapped(j)) then
sorted_species_type(i)=species_type(j)
species_mapped(j) = .true.
exit
end if
end do
end do
@ -1230,8 +1287,9 @@ module opt_group
return
end subroutine alloy_group
function in_group(r)
function in_group(atype, r)
!This subroutine determines if a point is within the group boundaries
integer, intent(in) :: atype
real(kind=dp), intent(in) :: r(3)
real(kind=dp) :: rnorm
@ -1276,6 +1334,19 @@ module opt_group
case('all')
in_group = .true.
end select
if(group_atom_types> 0) then
in_group = in_group.and.(atype== group_atom_types)
elseif(exclude_num > 0) then
if(in_group) then
do i=1,exclude_num
if (atype == exclude_types(i)) then
in_group=.false.
exit
end if
end do
end if
end if
end function in_group
function in_group_ele(esize, elat, rn)
@ -1299,13 +1370,13 @@ module opt_group
r_center(:)= r_center(:) + rn(:,ibasis,inod)/basisnum(elat)
end do
if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(size_ele(i)/=notsize)) then
if((in_group(0,rn(:, ibasis, inod)).neqv.flip).and.(size_ele(i)/=notsize)) then
node_in_out(inod) = 2
exit nodeloop
end if
gshape ='sphere'
if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(esize/=notsize)) then
if((in_group(0,rn(:, ibasis, inod)).neqv.flip).and.(esize/=notsize)) then
node_in_out(inod) = 1
else
node_in_out(inod) = 0
@ -1327,7 +1398,7 @@ module opt_group
end do
end do
if ((in_group(r_center).neqv.flip).and.(esize/= notsize)) then
if ((in_group(0,r_center).neqv.flip).and.(esize/= notsize)) then
in_group_ele=.true.
return
end if
@ -1336,7 +1407,7 @@ module opt_group
r_center(:) = 0.0_dp
do inod = 1, ng_node(elat)
do ibasis = 1, basisnum(elat)
if ((in_group(rn(:,ibasis,inod)).neqv.flip).and.(esize/=notsize)) then
if ((in_group(0,rn(:,ibasis,inod)).neqv.flip).and.(esize/=notsize)) then
in_group_ele=.true.
return
end if

20
src/opt_slip_plane.f90
Unescape View File

@ -17,11 +17,13 @@ module opt_slip_plane
!Main calling function for the slip_plane option
integer, intent(inout) :: arg_pos
integer :: ie, ia, slip_enum, old_atom_num, esize, new_ele_num, n, m, o, ele(3,8), nump_ele, inod, vlat(3), ibasis
integer :: ie, ia, slip_enum, old_atom_num, esize, new_ele_num, n, m, o, ele(3,8), nump_ele, inod, vlat(3), ibasis,&
starting_anum
integer, allocatable :: slip_eles(:), temp_int(:)
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), rfill(3,max_basisnum, max_ng_node), ratom(3,max_basisnum), &
maxp, minp
maxp, minp, vel_interp(3, max_basisnum*max_esize**3)
real(kind=dp), allocatable :: vel_tmp(:,:)
integer :: type_interp(max_basisnum*max_esize**3)
logical :: lat_points(max_esize,max_esize, max_esize)
@ -58,11 +60,25 @@ module opt_slip_plane
!If we aren't efilling then just refine the element
if(.not.efill) then
starting_anum=atom_num
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
do ia = 1, basisnum(lat_ele(ie)) * size_ele(ie)**3
call apply_periodic(r_interp(:,ia))
call add_atom(0, type_interp(ia), r_interp(:,ia))
end do
if(allocated(vel_atom)) then
call interpolate_vel(type_ele(ie), size_ele(ie), lat_ele(ie), vel_node(:,:,:,ie), vel_interp)
if(size(vel_atom,2) < size(type_atom)) then
allocate(vel_tmp(3, size(type_atom)))
vel_tmp=0.0_dp
vel_tmp(:, 1:size(vel_atom,2)) = vel_atom
call move_alloc(vel_tmp, vel_atom)
end if
do ia = 1, basisnum(lat_ele(ie)) * size_ele(ie)**3
vel_atom(:, starting_anum+ia) = vel_interp(:, ia)
end do
end if
!If we are efilling then the code is slightly more complex
else
!First populate the lat points array

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