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Merge branch 'ft--option-slip-plane' into development

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This commit is contained in:
Alex Selimov 2020-10-28 17:53:28 -04:00
commit 0929400d19
6 changed files with 236 additions and 25 deletions
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16
src/Makefile
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@ -1,9 +1,15 @@
FC=gfortran
#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
FC=ifort
#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 -O3 -g
#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
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
.SUFFIXES:
@ -17,7 +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 $@

3
src/call_option.f90
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@ -6,6 +6,7 @@ subroutine call_option(option, arg_pos)
use opt_deform
use opt_delete
use opt_redef_box
use opt_slip_plane
use box
implicit none
@ -41,6 +42,8 @@ subroutine call_option(option, arg_pos)
arg_pos=arg_pos +3
case('-redef_box')
call redef_box(arg_pos)
case('-slip_plane')
call run_slip_plane(arg_pos)
case default
print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
stop 3

59
src/elements.f90
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@ -201,38 +201,39 @@ module elements
!First check to make sure if it is allocated
if (allocated(size_ele)) then
!Figure out the size of the atom and element arrays
ele_size = size(size_ele)
!Check if we need to grow the ele_size, if so grow all the variables
if ( n+ele_num > size(size_ele)) then
allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = lat_ele
allocate(temp_int(n+ele_size+buffer_size))
temp_int(1:ele_size) = lat_ele(1:ele_size)
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, lat_ele)
allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = tag_ele
allocate(temp_int(n+ele_size+buffer_size))
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
allocate(temp_int(n+ele_size+buffer_size))
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
allocate(temp_int(n+ele_size+buffer_size))
temp_int(1:ele_size) = sbox_ele(1:ele_size)
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, sbox_ele)
allocate(char_temp(n+ele_num+buffer_size))
char_temp(1:ele_size) = type_ele
allocate(char_temp(n+ele_size+buffer_size))
char_temp(1:ele_size) = type_ele(1:ele_size)
call move_alloc(char_temp, type_ele)
allocate(temp_ele_real(3, max_basisnum, max_ng_node, n+ele_num+buffer_size))
temp_ele_real(:,:,:,1:ele_size) = r_node
allocate(temp_ele_real(3, max_basisnum, max_ng_node, n+ele_size+buffer_size))
temp_ele_real(:,:,:,1:ele_size) = r_node(:,:,:,1:ele_size)
temp_ele_real(:,:,:,ele_size+1:) = 0.0_dp
call move_alloc(temp_ele_real, r_node)
end if
@ -244,22 +245,22 @@ module elements
if (allocated(type_atom)) then
atom_size = size(type_atom)
if (m+atom_num > atom_size) then
allocate(temp_int(m+atom_num+buffer_size))
allocate(temp_int(m+atom_size+buffer_size))
temp_int(1:atom_size) = type_atom
temp_int(atom_size+1:) = 0
call move_alloc(temp_int, type_atom)
allocate(temp_int(m+atom_num+buffer_size))
allocate(temp_int(m+atom_size+buffer_size))
temp_int(1:atom_size) = tag_atom
temp_int(atom_size+1:) = 0
call move_alloc(temp_int, tag_atom)
allocate(temp_int(m+atom_num+buffer_size))
allocate(temp_int(m+atom_size+buffer_size))
temp_int(1:atom_size) = sbox_atom
temp_int(atom_size+1:) = 0
call move_alloc(temp_int, sbox_atom)
allocate(temp_real(3,m+atom_num+buffer_size))
allocate(temp_real(3,m+atom_size+buffer_size))
temp_real(:,1:atom_size) = r_atom
temp_real(:, atom_size+1:) = 0.0_dp
call move_alloc(temp_real, r_atom)
@ -278,6 +279,7 @@ module elements
integer :: newtag
ele_num = ele_num + 1
node_num = node_num + ng_node(lat)
if (tag==0) then
newtag = ele_num !If we don't assign a tag then pass the tag as the ele_num
@ -293,7 +295,6 @@ module elements
lat_ele(ele_num) = lat
sbox_ele(ele_num) = sbox
r_node(:,:,:,ele_num) = r(:,:,:)
node_num = node_num + ng_node(lat)
end subroutine add_element
@ -750,4 +751,28 @@ module elements
end subroutine lattice_map
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
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)
rout(:,:) = 0
do ibasis = 1, basisnum(lat_ele(ie))
do inod = 1, ng_node(lat_ele(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 subroutine
end module elements

2
src/mode_create.f90
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@ -528,7 +528,7 @@ module mode_create
do i = 1, 3
filzero(i) = bd_ele_lat(2*i-1) -1
end do
do while(efill_size>9)
do while(efill_size>min_efillsize)
!First check whether there are enough lattice points to house the current element size
efill_ele=cubic_cell*(efill_size-1)
if (nump_ele < efill_size**3) then

176
src/opt_slip_plane.f90 Normal file
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@ -0,0 +1,176 @@
module opt_slip_plane
use parameters
use elements
use functions
use subroutines
implicit none
integer :: sdim
real(kind=dp) :: spos
logical :: efill
public
contains
subroutine run_slip_plane(arg_pos)
!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, 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
integer :: type_interp(max_basisnum*max_esize**3)
logical :: lat_points(max_esize,max_esize, max_esize)
print *, '---------------------Option Slip_Plane----------------------'
!Initialize variables
efill = .false.
slip_enum = 0
old_atom_num = atom_num
!!Parse the argument
call parse(arg_pos)
!If we are running the efill code then we have to initiate some variables
if(efill) then
new_ele_num = 0
end if
allocate(slip_eles(1024))
!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
slip_enum = slip_enum + 1
if (slip_enum > size(slip_eles)) then
allocate(temp_int(size(slip_eles)+1024))
temp_int(1:size(slip_eles)) = slip_eles
temp_int(size(slip_eles)+1:) = 0
call move_alloc(temp_int, slip_eles)
end if
slip_eles(slip_enum) = ie
!If we aren't efilling then just refine the element
if(.not.efill) then
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), sbox_ele(ie), r_interp(:,ia))
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
latloop:do m = 1, size_ele(ie) - esize
do inod = 1, ng_node(lat_ele(ie))
vlat = ele(:,inod) + (/ m, n, o /)
if (.not.lat_points(vlat(1), vlat(2),vlat(3))) cycle latloop
call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
end do
!Check to make sure all lattice points exist for the current element
if(any(.not.lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1))) cycle latloop
!Check to see if the plane intersects this element if not then add it
maxp = maxval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie))))
minp = minval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie))))
if(.not.(spos < maxp).and.(spos > minp))then
nump_ele = nump_ele - esize**3
lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1) = .false.
call add_element(0, type_ele(ie), esize, lat_ele(ie), sbox_ele(ie), rfill)
new_ele_num = new_ele_num + 1
end if
end do latloop
end do
end do
end if
esize= esize-2
end do
! Now add the leftover lattice points as atoms
do o = 1, size_ele(ie)
do n = 1, size_ele(ie)
do m = 1, size_ele(ie)
if(lat_points(m,n,o)) then
call get_interp_pos(m,n,o, ie, ratom(:,:))
do ibasis = 1, basisnum(lat_ele(ie))
call apply_periodic(r_atom(:,ibasis))
call add_atom(0, basis_type(ibasis,lat_ele(ie)), sbox_ele(ie), ratom(:,ibasis))
end do
end if
end do
end do
end do
end if
end if
end do
!Once we finish adding elements delete the old ones
call delete_elements(slip_enum, slip_eles(1:slip_enum))
!Output data
if(.not.efill) then
print *, "We refine ", slip_enum, " elements into ", atom_num - old_atom_num , " atoms"
else
print *, "We refine ", slip_enum, " elements into ", atom_num - old_atom_num , " atoms and ", new_ele_num, " elements"
end if
end subroutine run_slip_plane
subroutine parse(arg_pos)
!This subroutine parses the input arguments to the mode
integer, intent(inout) :: arg_pos
integer :: arglen
character(len = 100) :: textholder
!First read the dimension
arg_pos = arg_pos +1
call get_command_argument(arg_pos,textholder, arglen)
if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
!Check to make sure that the dimension is correct
select case(trim(adjustl(textholder)))
case('x','X')
sdim = 1
case('y','Y')
sdim = 2
case('z','Z')
sdim = 3
case default
print *, "Error: dimension ", trim(adjustl(textholder)), " is not accepted. Please select from x, y, or z"
end select
!Now parse the position of the slip plane
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
call parse_pos(sdim, textholder, spos)
!Now check to see if efill was passed
arg_pos = arg_pos + 1
if(.not.(arg_pos > command_argument_count())) then
call get_command_argument(arg_pos, textholder, arglen)
if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
if(trim(adjustl(textholder)) == "efill") then
arg_pos = arg_pos +1
efill = .true.
end if
end if
end subroutine parse
end module opt_slip_plane

3
src/parameters.f90
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@ -3,7 +3,8 @@ module parameters
implicit none
!Default precision
integer, parameter :: dp= selected_real_kind(15,307)
integer, parameter :: dp= selected_real_kind(15,307), &
min_efillsize = 11
!Parameters for floating point tolerance
real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), &
lim_large = huge(1.0_dp), &