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Alex Selimov 4 years ago
parent 22e250093b
commit f63335708b
5 changed files with 66 additions and 53 deletions
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13
src/Makefile
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@ -1,6 +1,13 @@
FC=ifort
FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
FC=gfortran
#Ifort flags
#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
#gfortran flags
#FFLAGS=-mcmodel=large -O3 -g
FFLAGS=-mcmodel=large -O0 -g -fbacktrace -fcheck=all
MODES=mode_create.o mode_merge.o mode_convert.o
OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o opt_deform.o opt_redef_box.o opt_slip_plane.o
OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES) $(OPTIONS) call_option.o sorts.o
@ -16,7 +23,7 @@ cacmb: $(OBJECTS)
.PHONY: clean
clean:
$(RM) cacmb *.o
$(RM) cacmb *.o *.mod
testfuncs: testfuncs.o functions.o subroutines.o
$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@

36
src/elements.f90
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@ -211,17 +211,17 @@ module elements
call move_alloc(temp_int, lat_ele)
allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = tag_ele
temp_int(1:ele_size) = tag_ele(1:ele_size)
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, tag_ele)
allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = size_ele
temp_int(1:ele_size) = size_ele(1:ele_size)
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, size_ele)
allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = lat_ele
temp_int(1:ele_size) = lat_ele(1:ele_size)
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, sbox_ele)
@ -282,8 +282,8 @@ module elements
size_ele(ele_num) = size
lat_ele(ele_num) = lat
sbox_ele(ele_num) = sbox
r_node(:,:,:,ele_num) = r(:,:,:)
node_num = node_num + ng_node(lat)
r_node(:,:,:,ele_num) = r(:,:,:)
node_num = node_num + ng_node(lat)
end subroutine add_element
@ -669,17 +669,17 @@ module elements
esize = size_ele(ie)
select case(iface)
case(1)
pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, -10.0_dp**-2.0_dp /)
pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, -10.0_dp**(-2.0_dp) /)
case(2)
pos = (/ real(esize-1,dp)/2.0_dp, -10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp /)
pos = (/ real(esize-1,dp)/2.0_dp, -10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp /)
case(3)
pos = (/ (esize-1)+10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
pos = (/ (esize-1)+10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
case(4)
pos = (/ real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp /)
pos = (/ real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp /)
case(5)
pos = (/ -10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
pos = (/ -10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
case(6)
pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**-2.0_dp /)
pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**(-2.0_dp) /)
end select
!Now transform it to real space and adjust it to the position of the element in the first node.
@ -736,20 +736,24 @@ module elements
end subroutine lattice_map
subroutine get_interp_pos(i,j,k, ie, r)
subroutine get_interp_pos(i,j,k, ie, rout)
!This returns the position of an interpolated basis from an element ie.
!i, j, k should be in natural coordinates
integer, intent(in) :: i, j, k, r, s, t, ie, inod -=
real(kind=dp), dimension(3,max_basisnum), intent(out) :: r
integer, intent(in) :: i, j, k
real(kind=dp), dimension(3,max_basisnum), intent(out) :: rout
integer :: ie, ibasis, inod
real(kind=dp) :: a_shape(8), r, s, t
r = (1.0_dp*(i-1)-(size_ele(ie)-1)/2)/(1.0_dp*(size_ele(ie)-1)/2)
s = (1.0_dp*(j-1)-(size_ele(ie)-1)/2)/(1.0_dp*(size_ele(ie)-1)/2)
t = (1.0_dp*(k-1)-(size_ele(ie)-1)/2)/(1.0_dp*(size_ele(ie)-1)/2)
r(:) = 0
rout(:,:) = 0
do ibasis = 1, basisnum(lat_ele(ie))
do inod = 1, ng_node(lat_ele(ie))
r(:,ibasis) = r(:,ibasis) + a_shape(inod) * r_node(:,ibasis,inod,ie)
call rhombshape(r,s,t,a_shape)
rout(:,ibasis) = rout(:,ibasis) + a_shape(inod) * r_node(:,ibasis,inod,ie)
end do
end do

2
src/mode_create.f90
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@ -135,7 +135,7 @@ module mode_create
case('bcc')
call build_with_rhomb(box_lat_vert, bcc_mat)
case default
print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ", &
print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ",&
"element type"
stop 3
end select

5
src/opt_group.f90
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@ -300,7 +300,7 @@ module opt_group
case('elements','element')
if (group_ele_num > 0) then
print *, "Elements specifier used more than once in group id command with type both, either use type ", &
print *, "Elements specifier used more than once in group id command with type both, either use type ",&
"elements or include atoms identifier"
stop 3
@ -824,7 +824,8 @@ module opt_group
!Add the element, for the sbox we just set it to the same sbox that we get the orientation
!from. In this case it is from the sbox of the first atom in the group.
new_ele = new_ele+1
call add_element(0,remesh_ele_type, working_esize, ilat, sbox_atom(atom_index(1)),r_new_node)
call add_element(0,remesh_ele_type, working_esize, ilat, &
sbox_atom(atom_index(1)),r_new_node)
end if
end if

63
src/opt_slip_plane.f90
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@ -17,11 +17,11 @@ 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), &
rfill(3,max_basisnum, max_ng_node)
integer :: ie, ia, slip_enum, old_atom_num, esize, new_ele_num, n, m, o, ele(3,8), nump_ele, inod, vlat(3)
integer, allocatable :: slip_eles(:), temp_int(:)
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), rfill(3,max_basisnum, max_ng_node)
integer :: type_interp(max_basisnum*max_esize**3)
logical :: lat_points(max_esize,max_esize, max_esize)
@ -45,7 +45,7 @@ module opt_slip_plane
!Now loop over all elements, find which ones intersect
do ie = 1, ele_num
if( (spos < maxval(r_node(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie))).and. &
(spos > minval(r_node(sdim,1:basisnum(lat_ele(ie),1:ng_node(lat_ele(ie)),ie)))) then
(spos > minval(r_node(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie)))) then
slip_enum = slip_enum + 1
if (slip_enum > size(slip_eles)) then
allocate(temp_int(size(slip_eles)+1024))
@ -64,35 +64,36 @@ module opt_slip_plane
end do
!If we are efilling then the code is slightly more complex
else
!First populate the lat points array
lat_points(1:size_ele(ie),1:size_ele(ie), 1:size_ele(ie)) = .true.
!Now start trying to remesh the region, leaving the slip plane as a discontinuity
esize = size_ele(ie) - 2
nump_ele = size_ele(ie)**3
do while(esize > min_efillsize
if(nump_ele < esize**3) then
esize = esize - 2
else
ele = cubic_cell*(esize -1)
do o = 1, size_ele(ie) - esize
do n = 1, size_ele(ie) - esize
do m = 1, size_ele(ie) - esize
do inod = 1, ng_node(lat_ele(ie)
vlat = ele(:,inod) + (/ m, n, o /)
call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
!First populate the lat points array
lat_points(1:size_ele(ie),1:size_ele(ie), 1:size_ele(ie)) = .true.
!Now start trying to remesh the region, leaving the slip plane as a discontinuity
esize = size_ele(ie) - 2
nump_ele = size_ele(ie)**3
do while(esize > min_efillsize)
if(nump_ele < esize**3) then
esize = esize - 2
else
ele = cubic_cell*(esize -1)
do o = 1, size_ele(ie) - esize
do n = 1, size_ele(ie) - esize
do m = 1, size_ele(ie) - esize
do inod = 1, ng_node(lat_ele(ie))
vlat = ele(:,inod) + (/ m, n, o /)
call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
end do
!Check to see if the plane intersects this element if not then add it
if((spos < maxval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie))))).and. &
(spos > minval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)))))) then
nump_ele = nump_ele - esize**3
lat_points(m:m+esize, n:n+esize, o:o+esize) = .false.
call add_element(0, type_ele(ie), esize, lat_ele(ie), sbox_ele(ie), rfill)
end if
end do
!Check to see if the plane intersects this element if not then add it
if((spos < maxval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie))).and. &
(spos > minval(rfill(sdim,1:basisnum(lat_ele(ie),1:ng_node(lat_ele(ie)),ie)))) then
nump_ele = nump_ele - esize**3
end if
end do
end do
end do
end if
end if
end do
end if
end if
end do

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