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Changes to how the adjustment to nodal positions is performed for lammpscac output

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This commit is contained in:
Alex Selimov 2020-01-15 09:39:30 -05:00
parent 55fbe679e5
commit 849da1d24a
4 changed files with 69 additions and 54 deletions
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38
src/io.f90
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@ -204,7 +204,7 @@ module io
!This subroutine writes out a .lmp style dump file
character(len=100), intent(in) :: file
integer :: write_num, i, inod, ibasis
real(kind=dp) :: mass
real(kind=dp) :: mass, fcc_adjust(3,8), local_adjust(3,8), rout(3)
1 format(i16, ' Eight_Node', 4i16)
2 format(i16, ' Atom', 4i16)
@ -242,16 +242,32 @@ module io
write(11, '(a)') 'CAC Elements'
write(11, '(a)') ' '
!Set up the nodal adjustment variables for all the different element types. This adjusts the node centers
!from the center of the unit cell (as formulated in this code) to the corners of the unit cells
do inod = 1, 8
do i = 1,3
if(is_equal(cubic_cell(i, inod),0.0_dp)) then
fcc_adjust(i,inod) = -0.5_dp
else
fcc_adjust(i, inod) = 0.5_dp
end if
end do
end do
fcc_adjust = matmul(fcc_mat, fcc_adjust)
!Write element nodal positions
do i = 1, ele_num
select case(trim(adjustl(type_ele(i))))
case('fcc')
!Now orient the current adjustment vector to the correct orientation
local_adjust = matmul(sub_box_ori(:,:,sbox_ele(i)), fcc_adjust) * lapa(lat_ele(i))
!The first entry is the element specifier
write(11,1) i, basisnum(lat_ele(i)), size_ele(i), size_ele(i), size_ele(i)
do ibasis = 1, basisnum(lat_ele(i))
do inod = 1, 8
!Nodal information for every node
write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i)
rout = r_node(:,ibasis,inod,i) + local_adjust(:,inod)
write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), rout
end do
end do
end select
@ -486,6 +502,8 @@ module io
write(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
!Now for every lattice type write the basis atom types
write(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
!Now for every lattice type write the lattice parameters
write(11,*) (lapa(i), i = 1, lattice_types)
!Now write the numbers of elements and atoms
write(11,*) atom_num, ele_num
@ -498,7 +516,7 @@ module io
!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
do i = 1, ele_num
write(11, *) i, lat_ele(i), size_ele(i), type_ele(i)
write(11, *) i, lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i)
do inod = 1, ng_node(lat_ele(i))
do ibasis =1, basisnum(lat_ele(i))
write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
@ -582,7 +600,7 @@ module io
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
new_type_to_type(10), new_lattice_types
new_type_to_type(10), new_lattice_types, sbox
character(len=100) :: etype
real(kind=dp) :: r(3), newdisplace(3)
real(kind=dp), allocatable :: r_innode(:,:,:)
@ -623,8 +641,6 @@ module io
sub_box_array_bd(:,1,sub_box_num+1:) = sub_box_array_bd(:,1,sub_box_num+1:) + atom_num
sub_box_array_bd(:,2,sub_box_num+1:) = sub_box_array_bd(:,2,sub_box_num+1:) + ele_num
sub_box_num = sub_box_num + n
!Read in the number of atom types and all their names
read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)
!Now fit these into the global list of atom types, after this new_type_to_type is the actual global
@ -646,6 +662,8 @@ module io
basis_type(i,j) = new_type_to_type(basis_type(i,j))
end do
end do
!Read the lattice parameters for every lattice type
read(11,*) (lapa(i), i = lattice_types+1, lattice_types+new_lattice_types)
!Read number of elements and atoms and allocate arrays
read(11, *) in_atoms, in_eles
call grow_ele_arrays(in_eles, in_atoms)
@ -659,7 +677,7 @@ module io
!Read the elements
do i = 1, in_eles
read(11, *) n, type, size, etype
read(11, *) n, type, size, sbox, etype
do inod = 1, ng_node(type)
do ibasis =1, basisnum(type)
read(11,*) j, k, r_innode(:, ibasis, inod)
@ -667,7 +685,7 @@ module io
end do
end do
type = type + lattice_types
call add_element(etype, size, type, r_innode)
call add_element(etype, size, type, sbox+n, r_innode)
end do
!Close the file being read
@ -676,5 +694,9 @@ module io
!Only increment the lattice types if there are elements, if there are no elements then we
!just overwrite the arrays
if(in_eles > 0) lattice_types = lattice_types + new_lattice_types
sub_box_num = sub_box_num + n
end subroutine read_mb
end module io