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Added tags to the element and atom arrays

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development
Alex Selimov 4 years ago
parent de15d0f8ae
commit a47c384a3f
5 changed files with 54 additions and 26 deletions
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4
src/Makefile
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@ -1,6 +1,6 @@
FC=ifort FC=ifort
#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays 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
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 OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.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

44
src/elements.f90
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@ -11,7 +11,7 @@ module elements
!Data structures used to represent the CAC elements. Each index represents an element !Data structures used to represent the CAC elements. Each index represents an element
character(len=100), allocatable :: type_ele(:) !Element type character(len=100), allocatable :: type_ele(:) !Element type
integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:) !Element size integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:), tag_ele(:) !Element size
real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
integer, save :: ele_num !Number of elements integer, save :: ele_num !Number of elements
@ -19,7 +19,7 @@ module elements
!Data structure used to represent atoms !Data structure used to represent atoms
integer, allocatable :: type_atom(:)!atom type integer, allocatable :: type_atom(:)!atom type
integer, allocatable :: sbox_atom(:) integer, allocatable :: sbox_atom(:), tag_atom(:)
real(kind =dp),allocatable :: r_atom(:,:) !atom position real(kind =dp),allocatable :: r_atom(:,:) !atom position
integer :: atom_num=0 !Number of atoms integer :: atom_num=0 !Number of atoms
@ -146,7 +146,7 @@ module elements
!Allocate element arrays !Allocate element arrays
if(n > 0) then if(n > 0) then
allocate(type_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), & allocate(type_ele(n), tag_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
stat=allostat) stat=allostat)
if(allostat > 0) then if(allostat > 0) then
print *, "Error allocating element arrays in elements.f90 because of: ", allostat print *, "Error allocating element arrays in elements.f90 because of: ", allostat
@ -156,7 +156,7 @@ module elements
if(m > 0) then if(m > 0) then
!Allocate atom arrays !Allocate atom arrays
allocate(type_atom(m), sbox_atom(m), r_atom(3,m), stat=allostat) allocate(type_atom(m), sbox_atom(m), tag_atom(m), r_atom(3,m), stat=allostat)
if(allostat > 0) then if(allostat > 0) then
print *, "Error allocating atom arrays in elements.f90 because of: ", allostat print *, "Error allocating atom arrays in elements.f90 because of: ", allostat
stop stop
@ -187,6 +187,11 @@ module elements
temp_int(ele_size+1:) = 0 temp_int(ele_size+1:) = 0
call move_alloc(temp_int, lat_ele) call move_alloc(temp_int, lat_ele)
allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = tag_ele
temp_int(ele_size+1:) = 0
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
temp_int(ele_size+1:) = 0 temp_int(ele_size+1:) = 0
@ -214,6 +219,11 @@ module elements
temp_int(atom_size+1:) = 0 temp_int(atom_size+1:) = 0
call move_alloc(temp_int, type_atom) call move_alloc(temp_int, type_atom)
allocate(temp_int(m+atom_num+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_num+buffer_size))
temp_int(1:atom_size) = sbox_atom temp_int(1:atom_size) = sbox_atom
temp_int(atom_size+1:) = 0 temp_int(atom_size+1:) = 0
@ -226,15 +236,25 @@ module elements
end if end if
end subroutine end subroutine
subroutine add_element(type, size, lat, sbox, r) subroutine add_element(tag, type, size, lat, sbox, r)
!Subroutine which adds an element to the element arrays !Subroutine which adds an element to the element arrays
integer, intent(in) :: size, lat, sbox integer, intent(in) :: size, lat, sbox, tag
character(len=100), intent(in) :: type character(len=100), intent(in) :: type
real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node) real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node)
integer :: newtag
ele_num = ele_num + 1 ele_num = ele_num + 1
if (tag==0) then
newtag = ele_num !If we don't assign a tag then pass the tag as the ele_num
else
newtag = tag
end if
!Check to see if we need to grow the arrays !Check to see if we need to grow the arrays
call grow_ele_arrays(1,0) call grow_ele_arrays(1,0)
tag_ele(ele_num) = newtag
type_ele(ele_num) = type type_ele(ele_num) = type
size_ele(ele_num) = size size_ele(ele_num) = size
lat_ele(ele_num) = lat lat_ele(ele_num) = lat
@ -245,14 +265,22 @@ module elements
end subroutine add_element end subroutine add_element
subroutine add_atom(type, sbox, r) subroutine add_atom(tag, type, sbox, r)
!Subroutine which adds an atom to the atom arrays !Subroutine which adds an atom to the atom arrays
integer, intent(in) :: type, sbox integer, intent(in) :: type, sbox, tag
real(kind=dp), intent(in), dimension(3) :: r real(kind=dp), intent(in), dimension(3) :: r
integer :: newtag
atom_num = atom_num+1 atom_num = atom_num+1
if(tag==0) then
newtag = atom_num !If we don't assign a tag then pass the tag as the atom_num
else
newtag = tag
end if
!Check to see if we need to grow the arrays !Check to see if we need to grow the arrays
call grow_ele_arrays(0,1) call grow_ele_arrays(0,1)
tag_atom(atom_num) = tag
type_atom(atom_num) = type type_atom(atom_num) = type
r_atom(:,atom_num) = r(:) r_atom(:,atom_num) = r(:)
sbox_atom(atom_num) = sbox sbox_atom(atom_num) = sbox

20
src/io.f90
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@ -543,13 +543,13 @@ module io
!Write out atoms first !Write out atoms first
do i = 1, atom_num do i = 1, atom_num
write(11,*) i, type_atom(i), sbox_atom(i), r_atom(:,i) write(11,*) tag_atom(i), type_atom(i), sbox_atom(i), r_atom(:,i)
end do end do
!Write out the elements, this is written in two stages, one line for the element and then 1 line for !Write out the elements, this is written in two stages, one line for the element and then 1 line for
!every basis at every node !every basis at every node
do i = 1, ele_num do i = 1, ele_num
write(11, *) i, lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i) write(11, *) tag_ele(i), lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i)
do inod = 1, ng_node(lat_ele(i)) do inod = 1, ng_node(lat_ele(i))
do ibasis =1, basisnum(lat_ele(i)) do ibasis =1, basisnum(lat_ele(i))
write(11,*) inod, ibasis, r_node(:, ibasis, inod, i) write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
@ -738,19 +738,19 @@ module io
do i = 1, in_atoms do i = 1, in_atoms
read(11,*) j, type, sbox, r(:) read(11,*) j, type, sbox, r(:)
r = r+newdisplace r = r+newdisplace
call add_atom(new_type_to_type(type), sbox+sub_box_num, r) call add_atom(j, new_type_to_type(type), sbox+sub_box_num, r)
end do end do
!Read the elements !Read the elements
do i = 1, in_eles do i = 1, in_eles
read(11, *) l, type, size, sbox, etype read(11, *) j, type, size, sbox, etype
do inod = 1, ng_node(type) do inod = 1, ng_node(type)
do ibasis =1, basisnum(type) do ibasis =1, basisnum(type)
read(11,*) j, k, r_innode(:, ibasis, inod) read(11,*) k, l, r_innode(:, ibasis, inod)
r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
end do end do
end do end do
call add_element(etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode) call add_element(j, etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode)
end do end do
!Close the file being read !Close the file being read
@ -773,7 +773,7 @@ module io
real(kind=dp), dimension(3), intent(in) :: displace real(kind=dp), dimension(3), intent(in) :: displace
real(kind = dp), dimension(6), intent(out) :: temp_box_bd real(kind = dp), dimension(6), intent(out) :: temp_box_bd
integer :: i, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, & integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), & atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
atom_type atom_type
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3) real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3)
@ -919,10 +919,10 @@ module io
do i = 1, in_eles do i = 1, in_eles
read(11,*) j, etype, k, lat_type read(11,*) j, etype, k, lat_type
do inod = 1, 8 do inod = 1, 8
read(11, *) j, k, r_in(:,1,inod) read(11, *) k, l, r_in(:,1,inod)
r_in(:,1,inod) = r_in(:,1,inod) + newdisplace r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
end do end do
call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in) call add_element(j, in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
end do end do
end if end if
@ -937,7 +937,7 @@ module io
do i = 1, in_atoms do i = 1, in_atoms
read(11,*) j, k, atom_type, r_in_atom(:) read(11,*) j, k, atom_type, r_in_atom(:)
r_in_atom = r_in_atom + newdisplace r_in_atom = r_in_atom + newdisplace
call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom) call add_atom(j,atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
end do end do
!Close file !Close file
close(11) close(11)

6
src/mode_create.f90
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@ -109,7 +109,7 @@ module mode_create
box_bd(2*i) = maxval(r_node_temp(i,:,:))+10.0_dp**-6.0_dp box_bd(2*i) = maxval(r_node_temp(i,:,:))+10.0_dp**-6.0_dp
box_bd(2*i-1) = minval(r_node_temp(i,:,:)) - 10.0_dp**-6.0_dp box_bd(2*i-1) = minval(r_node_temp(i,:,:)) - 10.0_dp**-6.0_dp
end do end do
call add_element(element_type, esize, 1, 1, r_node_temp) call add_element(0,element_type, esize, 1, 1, r_node_temp)
end if end if
!If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays !If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays
@ -136,7 +136,7 @@ module mode_create
if(lat_atom_num > 0) then if(lat_atom_num > 0) then
do i = 1, lat_atom_num do i = 1, lat_atom_num
do ibasis = 1, basisnum(1) do ibasis = 1, basisnum(1)
call add_atom(basis_type(ibasis, 1), 1, (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis)) call add_atom(0,basis_type(ibasis, 1), 1, (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis))
end do end do
end do end do
deallocate(r_atom_lat) deallocate(r_atom_lat)
@ -150,7 +150,7 @@ module mode_create
end do end do
end do end do
call add_element(element_type, elat(i), 1, 1, r_node_temp) call add_element(0,element_type, elat(i), 1, 1, r_node_temp)
end do end do
end if end if
end if end if

6
src/opt_group.f90
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@ -564,7 +564,7 @@ module opt_group
!here as well to make sure they are in the box !here as well to make sure they are in the box
do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3 do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
call apply_periodic(r_interp(:,j)) call apply_periodic(r_interp(:,j))
call add_atom(type_interp(j), sbox_ele(ie), r_interp(:,j)) call add_atom(0,type_interp(j), sbox_ele(ie), r_interp(:,j))
end do end do
end do end do
!Once all atoms are added we delete all of the elements !Once all atoms are added we delete all of the elements
@ -800,7 +800,7 @@ 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(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
@ -821,7 +821,7 @@ module opt_group
lat_points(ix,iy,iz) = .false. lat_points(ix,iy,iz) = .false.
r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat) r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat)
new_atom=new_atom+1 new_atom=new_atom+1
call add_atom(basis_type(1,ilat), is, r) call add_atom(0,basis_type(1,ilat), is, r)
end if end if
end do end do
end do end do

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