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Latest working changes to read-CAC

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This commit is contained in:
Alex Selimov 2020-04-23 12:17:04 -04:00
parent b3e05da6a4
commit 4038cab76f
2 changed files with 76 additions and 21 deletions
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2
src/elements.f90
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@ -294,8 +294,6 @@ module elements
integer :: i
max_ng_node = 0
do i=1, n
select case(trim(adjustl(element_types(i))))
case('fcc')

95
src/io.f90
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@ -776,7 +776,7 @@ module io
integer :: i, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
atom_type_map(10), etype_map(10), etype, lat_type, new_lattice_map(10), &
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)
character(len=100) :: textholder, in_lattype_map(10)
character(len=2) :: atomic_element
!First open the file
@ -950,7 +950,7 @@ module io
end if
end subroutine read_pycac
subroutine read_cac(file, displace, temp_box_bd)
subroutine read_lmpcac(file, displace, temp_box_bd)
!This subroutine is used to read .cac files which are used with the lammpsCAC format
character(len=100), intent(in) :: file
real(kind=dp), dimension(3), intent(in) :: displace
@ -958,8 +958,8 @@ module io
character(len=100) :: textholder, element_type, esize
character(len=2) :: atom_species
integer :: i, j, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3), in_ori(3,3)
integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), temp_box_bd(6), newdisplace(3)
!First check to make sure that we have set the needed variables
if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then
@ -968,6 +968,9 @@ module io
end if
!Open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
!Now initialiaze some important variables
max_basis_num = 10
!Read header information
read(11, *) textholder
@ -979,9 +982,38 @@ module io
!Read box_boundaries
read(11,*) textholder
read(11,*) box_bd(1:2), texholder
read(11,*) box_bd(3:4), texholder
read(11,*) box_bd(5:6), texholder
read(11,*) temp_box_bd(1:2), texholder
read(11,*) temp_box_bd(3:4), texholder
read(11,*) temp_box_bd(5:6), texholder
!Shift the box boundaries if needed
do i = 1, 3
if (abs(displace(i)) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
else
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
!Grow box boundaries
call grow_box(temp_box_bd)
!Allocate sub_box
if (sub_box_num == 0) then
call alloc_sub_box(1)
else
call grow_sub_box(1)
end if
!Because orientations and other needed sub_box information isn't really
!present within the .cac file we just default a lot of it.
sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
sub_box_bd(:, sub_box_num+1) = temp_box_bd
sub_box_num = sub_box_num + 1
!Read useless information
read(11,*) textholder
read(11,*) textholder
@ -1001,25 +1033,50 @@ module io
!Start the reading loop
do i = 1, ele_in
read(11,*) j, ele, element_type, in_basis, esize
!Check to see if we need to grow the max_basis_num
select case(trim(adjustl(element_type)))
case('Eight_Node')
!Read in all the data
do j = 1, 8*in_basis
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
!Read in all the data
do j = 1, 8*in_basis
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
end do
!Now calculate the lattice vectors and shift the nodal points from the corners to the center of the unit cell
!Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
!calculation
lat_vec(:,1) = (r_node(:,1,2) - r_node(:,1,1))/esize
lat_vec(:,2) = (r_node(:,1,4) - r_node(:,1,1))/esize
lat_vec(:,3) = (r_node(:,1,5) - r_node(:,1,1))/esize
!Now shift all the nodal positions
select case(trim(adjustl(in_lattice_type)))
case('fcc','FCC')
do ibasis = 1, in_basis
r_in(:,ibasis,1) = r_in(:,ibasis,1) + lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,2) = r_in(:,ibasis,2) - lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,3) = r_in(:,ibasis,3) - lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,4) = r_in(:,ibasis,4) + lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,5) = r_in(:,ibasis,5) + lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,6) = r_in(:,ibasis,6) - lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,7) = r_in(:,ibasis,7) - lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,8) = r_in(:,ibasis,8) + lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
end do
!Now calculate the orientation matrix based on the lattice type.
lat_vec = r_in(:,1,2) - r_in(:,1,1)
lat_vec = lat_vec / norm2(lat_vec)
!Now figure out if is an existing lattice_type
call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
case default
print *, in_lattice_type, " is not an accepted lattice type. Please select from: fcc"
end select
!Now map it to either an existing or new lattice type
call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
!Now add the element
call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in)
case('Atom')
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
call add_atom(in_basis_types(ibasis), sub_box_num, r_in(:,1,1))
end select
end do
end subroutine read_cac
end subroutine read_lmpcac
subroutine set_cac(apos)
!This code parses input values