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This commit is contained in:
Alex Selimov 2020-10-24 09:13:16 -04:00
parent 22e250093b
commit f63335708b
5 changed files with 65 additions and 52 deletions
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13
src/Makefile
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@ -1,6 +1,13 @@
FC=ifort FC=gfortran
FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
#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 #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 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 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 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 .PHONY: clean
clean: clean:
$(RM) cacmb *.o $(RM) cacmb *.o *.mod
testfuncs: testfuncs.o functions.o subroutines.o testfuncs: testfuncs.o functions.o subroutines.o
$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@ $(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@

32
src/elements.f90
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@ -211,17 +211,17 @@ module elements
call move_alloc(temp_int, lat_ele) call move_alloc(temp_int, lat_ele)
allocate(temp_int(n+ele_num+buffer_size)) 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 temp_int(ele_size+1:) = 0
call move_alloc(temp_int, tag_ele) call move_alloc(temp_int, tag_ele)
allocate(temp_int(n+ele_num+buffer_size)) 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 temp_int(ele_size+1:) = 0
call move_alloc(temp_int, size_ele) call move_alloc(temp_int, size_ele)
allocate(temp_int(n+ele_num+buffer_size)) 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 temp_int(ele_size+1:) = 0
call move_alloc(temp_int, sbox_ele) call move_alloc(temp_int, sbox_ele)
@ -669,17 +669,17 @@ module elements
esize = size_ele(ie) esize = size_ele(ie)
select case(iface) select case(iface)
case(1) 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) 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) 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) 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) 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) 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 end select
!Now transform it to real space and adjust it to the position of the element in the first node. !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 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. !This returns the position of an interpolated basis from an element ie.
!i, j, k should be in natural coordinates !i, j, k should be in natural coordinates
integer, intent(in) :: i, j, k, r, s, t, ie, inod -= integer, intent(in) :: i, j, k
real(kind=dp), dimension(3,max_basisnum), intent(out) :: r 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) 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) 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) 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 ibasis = 1, basisnum(lat_ele(ie))
do inod = 1, ng_node(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
end do end do

2
src/mode_create.f90
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@ -135,7 +135,7 @@ module mode_create
case('bcc') case('bcc')
call build_with_rhomb(box_lat_vert, bcc_mat) call build_with_rhomb(box_lat_vert, bcc_mat)
case default 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" "element type"
stop 3 stop 3
end select end select

5
src/opt_group.f90
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@ -300,7 +300,7 @@ module opt_group
case('elements','element') case('elements','element')
if (group_ele_num > 0) then 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" "elements or include atoms identifier"
stop 3 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 !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. !from. In this case it is from the sbox of the first atom in the group.
new_ele = new_ele+1 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
end if end if

21
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 !Main calling function for the slip_plane option
integer, intent(inout) :: arg_pos 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), & 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, allocatable :: slip_eles(:), temp_int(:) 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) integer :: type_interp(max_basisnum*max_esize**3)
logical :: lat_points(max_esize,max_esize, max_esize) 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 !Now loop over all elements, find which ones intersect
do ie = 1, ele_num do ie = 1, ele_num
if( (spos < maxval(r_node(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie))).and. & 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 slip_enum = slip_enum + 1
if (slip_enum > size(slip_eles)) then if (slip_enum > size(slip_eles)) then
allocate(temp_int(size(slip_eles)+1024)) allocate(temp_int(size(slip_eles)+1024))
@ -70,7 +70,7 @@ module opt_slip_plane
!Now start trying to remesh the region, leaving the slip plane as a discontinuity !Now start trying to remesh the region, leaving the slip plane as a discontinuity
esize = size_ele(ie) - 2 esize = size_ele(ie) - 2
nump_ele = size_ele(ie)**3 nump_ele = size_ele(ie)**3
do while(esize > min_efillsize do while(esize > min_efillsize)
if(nump_ele < esize**3) then if(nump_ele < esize**3) then
esize = esize - 2 esize = esize - 2
else else
@ -78,21 +78,22 @@ module opt_slip_plane
do o = 1, size_ele(ie) - esize do o = 1, size_ele(ie) - esize
do n = 1, size_ele(ie) - esize do n = 1, size_ele(ie) - esize
do m = 1, size_ele(ie) - esize do m = 1, size_ele(ie) - esize
do inod = 1, ng_node(lat_ele(ie) do inod = 1, ng_node(lat_ele(ie))
vlat = ele(:,inod) + (/ m, n, o /) vlat = ele(:,inod) + (/ m, n, o /)
call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod)) call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
end do end do
!Check to see if the plane intersects this element if not then add it !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. & 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)),ie)))) then (spos > minval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)))))) then
nump_ele = nump_ele - esize**3 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 if
end do end do
end do end do
end do end do
end if end if
end do
end if end if
end if end if
end do end do