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21
README.md
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@ -214,10 +214,10 @@ This command wraps atoms back into the simulation cell as though periodic bounda
**Remesh**
```
remesh esize
remesh esize lattice_parameter lattice_type
```
This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. When remeshing to atomistics the group can contain any orientations of elements but when remeshing to different finite elements, the group must contain all atoms/elements with the same orientation.
This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. When remeshing to atomistics the group can contain any orientations of elements but when remeshing to different finite elements, the group must contain all atoms/elements with the same orientation. `lattice_parameter` is the lattice parameter for the elements within the group and `lattice_type` is the lattice type (integer) that these new elements will be assigned to.
**Max**
@ -291,3 +291,20 @@ Specifying positions in cacmb can be done through a variety of ways. Examples of
`rand[val1:val2]` - returns a random position that lies within the range
`rande[facenum]` - Returns a random position in an interelement boundary which is offset of the element face `facenum`. Face numbers are based on the which vertices comprise the face. Vertex numbers are shown in the figure below for the primitive fcc unit cell which is what the fcc rhombohedral element is based from. The face numbers are:
Face 1: [1,2,3,4]
Face 2: [1,2,6,5]
Face 3: [2,3,7,6]
Face 4: [3,4,8,7]
Face 5: [1,4,8,5]
Face 6: [5,6,7,8]
Image for vertex numbers is:
![](/home/alexselimov/Documents/CACmb/Numbered_element.png)

148
src/elements.f90
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@ -64,11 +64,11 @@ module elements
shape(fcc_cell))
!Now we create a list containing the list of vertices needed to describe the 6 cube faces
cubic_faces(:,1) = (/ 1, 4, 8, 5 /)
cubic_faces(:,2) = (/ 2, 3, 7, 6 /)
cubic_faces(:,3) = (/ 1, 2, 6, 5 /)
cubic_faces(:,1) = (/ 1, 2, 3, 4 /)
cubic_faces(:,2) = (/ 1, 2, 6, 5 /)
cubic_faces(:,3) = (/ 2, 3, 7, 6 /)
cubic_faces(:,4) = (/ 3, 4, 8, 7 /)
cubic_faces(:,5) = (/ 1, 2, 3, 4 /)
cubic_faces(:,5) = (/ 1, 4, 8, 5 /)
cubic_faces(:,6) = (/ 5, 6, 7, 8 /)
!!Now initialize the fcc primitive cell
@ -491,4 +491,144 @@ module elements
end do
end subroutine
recursive subroutine parse_pos(i, pos_string, pos)
!This subroutine parses the pos command allowing for command which include inf
integer, intent(in) :: i !The dimension of the position
character(len=100), intent(in) :: pos_string !The position string
real(kind=dp), intent(out) :: pos !The output parsed position value
integer :: iospara, face, ele, randsize
real(kind=dp) :: rand, rone, rtwo, rand_ele_pos(3)
character(len=100) :: cone, ctwo
iospara = 0
if(trim(adjustl(pos_string)) == 'inf') then
pos=box_bd(2*i)
else if(trim(adjustl(pos_string)) == '-inf') then
pos=box_bd(2*i-1)
else if (trim(adjustl(pos_string)) == 'rand') then
call random_number(rand)
pos = (box_bd(2*i)-box_bd(2*i-1))*rand + box_bd(2*i-1)
else if (index(pos_string,'rande')>0) then
!First select a random element
call random_number(rand)
ele= 1 + floor(ele_num*rand)
!Now read the rest of the command which specifies the face we need and check
!to make sure it's an accepted face number
cone = pos_string(index(pos_string, '[')+1:index(pos_string, '[')+1)
!Check to see if we also pass an element size, if it was passed then make sure our
!random element is the right size
if(index(pos_string,':') > 0) then
ctwo = pos_string(index(pos_string, ':')+1:index(pos_string,']')-1)
read(ctwo, *) randsize
do while(randsize /= size_ele(ele))
call random_number(rand)
ele= 1 + floor(ele_num*rand)
end do
end if
read(cone, *) face
if ((face < 1).or.(face > 6)) stop "Current face number must be 1,2,3,4,5,6. Please check documentation"
!Now get the position
call offset_pos(ele, face, rand_ele_pos)
pos = rand_ele_pos(i)
else if (index(pos_string,'rand')>0) then
call random_number(rand)
cone = pos_string(index(pos_string, '[')+1:index(pos_string,':')-1)
call parse_pos(i, cone, rone)
ctwo = pos_string(index(pos_string, ':')+1:index(pos_string,']')-1)
call parse_pos(i, ctwo, rtwo)
pos = (rtwo - rone)*rand + rone
else if ((index(pos_string,'-') > 0).and.(index(pos_string,'inf')>0)) then
!Now extract the number we are reducing from infinity
if(index(pos_string,'inf') < index(pos_string,'-')) then
read(pos_string(index(pos_string,'-')+1:), *, iostat=iospara) pos
else
read(pos_string(1:index(pos_string,'-')-1), *, iostat=iospara) pos
end if
pos = box_bd(2*i) - pos
else if ((index(pos_string,'+') > 0).and.(index(pos_string,'inf')>0)) then
!Now extract the number we are reducing from infinity
if(index(pos_string,'inf') < index(pos_string,'+')) then
read(pos_string(index(pos_string,'+')+1:), *, iostat=iospara) pos
else
read(pos_string(1:index(pos_string,'+')-1), *, iostat=iospara) pos
end if
pos = box_bd(2*i-1) + pos
else if ((index(pos_string,'*') > 0).and.(index(pos_string,'inf')>0)) then
!Now extract the number we are reducing from infinity
if(index(pos_string,'inf') < index(pos_string,'*')) then
read(pos_string(index(pos_string,'*')+1:), *, iostat=iospara) pos
else
read(pos_string(1:index(pos_string,'*')-1), *, iostat=iospara) pos
end if
pos = (box_bd(2*i)-box_bd(2*i-1))*pos + box_bd(2*i-1)
else
read(pos_string, *, iostat=iospara) pos
end if
if (iospara > 0) then
print *, "Error reading position argument ", trim(adjustl(pos_string)), ". Please reformat and try again."
end if
end subroutine parse_pos
subroutine offset_pos(ie, iface, pos)
!This returns a position slightly offset from the center of an element face
!This is used to return a random position within an element discontinuity
integer, intent(in) :: ie !Element index
integer, intent(in) :: iface !Face number between 1 and 6
real(kind=dp), dimension(3), intent(out) :: pos !Position vector
!Other variables we need
integer :: esize
real(kind=dp) :: orient(3,3), ori_inv(3,3), lp, r_cubic_node(3,8)
!First find the offset vector for the face in the untransformed cubic cell
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 /)
case(2)
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 /)
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 /)
case(5)
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 /)
end select
!Now transform it to real space and adjust it to the position of the element in the first node.
select case (trim(adjustl(type_ele(ie))))
case('fcc')
!First we have to extract the element lattice parameter
call matrix_inverse(sub_box_ori(:,:,sbox_ele(ie)),3,ori_inv)
r_cubic_node = r_node(:,1,:,ie)
r_cubic_node = matmul(fcc_inv,matmul(ori_inv,r_cubic_node))
lp = (maxval(r_cubic_node(1,:))-minval(r_cubic_node(1,:)))/(esize-1)
pos = matmul(sub_box_ori(:,:,sbox_ele(ie)),matmul(fcc_mat,pos))*lp
pos = pos + r_node(:,1, 1, ie)
case default
print *, trim(adjustl(type_ele(ie))), " is not a currently accepted element type for random element positions"
stop 3
end select
end subroutine
end module elements

57
src/io.f90
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@ -373,7 +373,8 @@ module io
!NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the
!each element has only 1 atom type at the node.
character(len=100), intent(in) :: file
integer :: interp_max, i, j, inod, ibasis, ip, unique_index(10), unique_num
integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_num, &
etype
real(kind=dp) :: box_vec(3)
1 format('time' / i16, f23.15)
@ -405,6 +406,22 @@ module io
!Below writes the header information for the restart file
!First figure out all of the unique element types
unique_num = 0
unique_index(:) = 0
eleloop:do i = 1, ele_num
do j =1 , unique_num
if ( ( size_ele(i) == size_ele( unique_index(j) ) ).and. &
( lat_ele(i) == lat_ele(unique_index(j)) ) ) then
cycle eleloop
end if
end do
unique_num = unique_num + 1
unique_index(unique_num) = i
unique_size(unique_num) = size_ele(i)
end do eleloop
!Calculate the max number of atoms per element
select case(max_ng_node)
case(8)
@ -415,7 +432,7 @@ module io
write(11,20) interp_max
write(11,3) node_num
write(11,19) max_ng_node
write(11,4) lattice_types
write(11,4) unique_num
write(11,5) atom_num
write(11,6) 1 !Grain_num is ignored
write(11,16) lattice_types, atom_types
@ -454,26 +471,21 @@ module io
!write the element information
if(ele_num > 0) then
write(11,12)
!First figure out all of the unique element types
unique_num = 0
unique_index(:) = 0
eleloop:do i = 1, ele_num
do j =1 , unique_num
if ( ( size_ele(i) == size_ele( unique_index(j) ) ).and. &
( lat_ele(i) == lat_ele(unique_index(j)) ) ) then
cycle eleloop
end if
end do
unique_num = unique_num + 1
unique_index(unique_num) = i
end do eleloop
do i = 1, unique_num
write(11,'(3i16)') i, size_ele(i)-1, basis_type(1,i)
write(11,'(3i16)') i, size_ele(unique_index(i))-1, basis_type(1,lat_ele(unique_index(i)))
end do
ip = 0
write(11,13)
do i = 1, ele_num
write(11, '(4i16)') i, lat_ele(i), 1, basis_type(1,lat_ele(i))
!Figure out the ele type
do j = 1, unique_num
if ( unique_size(j) == size_ele(i)) then
etype = j
exit
endif
end do
write(11, '(4i16)') i, etype, 1, basis_type(1,lat_ele(i))
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
ip = ip + 1
@ -633,15 +645,16 @@ module io
print *, "displace", displace
do i = 1, 3
if (displace(i) > lim_zero) then
if (abs(displace(i)) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
else
newdisplace=displace(i)
newdisplace(i)=displace(i)
end if
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do
print *, "newdisplace", newdisplace
call grow_box(temp_box_bd)
!Read in the number of sub_boxes and allocate the variables
read(11, *) n
@ -730,7 +743,7 @@ module io
do i = 1, in_atoms
read(11,*) j, type, sbox, r(:)
r = r+newdisplace
call add_atom(new_type_to_type(type), sbox, r)
call add_atom(new_type_to_type(type), sbox+sub_box_num, r)
end do
!Read the elements
@ -742,7 +755,7 @@ module io
r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
end do
end do
call add_element(etype, size, new_lattice_map(type), sbox+n, r_innode)
call add_element(etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode)
end do
!Close the file being read

11
src/opt_orient.f90
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@ -20,6 +20,7 @@ module opt_orient
integer, intent(inout) :: arg_pos
integer :: i, ibasis, inod
logical :: isortho, isrighthanded
real(kind=dp) :: inv_sub_box_ori(3,3,sub_box_num)
!First parse the orient command
@ -70,6 +71,7 @@ module opt_orient
integer, intent(inout) :: arg_pos
integer :: i, arg_len
logical :: isortho, isrighthanded
character(len=8) :: ori_string
!Pull out the new user orientation
@ -82,6 +84,15 @@ module opt_orient
!Normalize the orientation matrix
new_orient = matrix_normal(new_orient,3)
!Check right hand rule and orthogonality
call check_right_ortho(new_orient, isortho, isrighthanded)
if (.not.isortho) then
stop "Directions in orient are not orthogonal"
else if (.not.isrighthanded) then
stop "Directions in orient are not righthanded"
end if
arg_pos = arg_pos + 1
end subroutine parse_orient

62
src/subroutines.f90
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@ -171,67 +171,7 @@ module subroutines
return
end subroutine parse_ori_vec
recursive subroutine parse_pos(i, pos_string, pos)
!This subroutine parses the pos command allowing for command which include inf
integer, intent(in) :: i !The dimension of the position
character(len=100), intent(in) :: pos_string !The position string
real(kind=dp), intent(out) :: pos !The output parsed position value
integer :: iospara
real(kind=dp) :: rand, rone, rtwo
character(len=100) :: cone, ctwo
iospara = 0
if(trim(adjustl(pos_string)) == 'inf') then
pos=box_bd(2*i)
else if(trim(adjustl(pos_string)) == '-inf') then
pos=box_bd(2*i-1)
else if (trim(adjustl(pos_string)) == 'rand') then
call random_number(rand)
pos = (box_bd(2*i)-box_bd(2*i-1))*rand + box_bd(2*i-1)
else if (index(pos_string,'rand')>0) then
call random_number(rand)
cone = pos_string(index(pos_string, '[')+1:index(pos_string,':')-1)
call parse_pos(i, cone, rone)
ctwo = pos_string(index(pos_string, ':')+1:index(pos_string,']')-1)
call parse_pos(i, ctwo, rtwo)
pos = (rtwo - rone)*rand + rone
else if ((index(pos_string,'-') > 0).and.(index(pos_string,'inf')>0)) then
!Now extract the number we are reducing from infinity
if(index(pos_string,'inf') < index(pos_string,'-')) then
read(pos_string(index(pos_string,'-')+1:), *, iostat=iospara) pos
else
read(pos_string(1:index(pos_string,'-')-1), *, iostat=iospara) pos
end if
pos = box_bd(2*i) - pos
else if ((index(pos_string,'+') > 0).and.(index(pos_string,'inf')>0)) then
!Now extract the number we are reducing from infinity
if(index(pos_string,'inf') < index(pos_string,'+')) then
read(pos_string(index(pos_string,'+')+1:), *, iostat=iospara) pos
else
read(pos_string(1:index(pos_string,'+')-1), *, iostat=iospara) pos
end if
pos = box_bd(2*i-1) + pos
else if ((index(pos_string,'*') > 0).and.(index(pos_string,'inf')>0)) then
!Now extract the number we are reducing from infinity
if(index(pos_string,'inf') < index(pos_string,'*')) then
read(pos_string(index(pos_string,'*')+1:), *, iostat=iospara) pos
else
read(pos_string(1:index(pos_string,'*')-1), *, iostat=iospara) pos
end if
pos = (box_bd(2*i)-box_bd(2*i-1))*pos + box_bd(2*i-1)
else
read(pos_string, *, iostat=iospara) pos
end if
if (iospara > 0) then
print *, "Error reading position argument ", trim(adjustl(pos_string)), ". Please reformat and try again."
end if
end subroutine parse_pos
subroutine heapsort(a)

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