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Fixes to mode_create, moved basis_pos from elements to mode_create, added the mb file output style

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Alex Selimov 2019-12-05 08:36:22 -05:00
parent 033b44dc40
commit fa1cb6ce58
3 changed files with 70 additions and 26 deletions
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22
src/mode_create.f90
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@ -6,13 +6,15 @@ module mode_create
use io
use subroutines
use elements
use box
implicit none
character(len=100) :: name, element_type
real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3)
integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6)
integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
basis_pos(3,10)
logical :: dup_flag, dim_flag
real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:)
@ -98,7 +100,7 @@ module mode_create
!Add the basis atoms to the unit cell
do inod = 1, max_ng_node
do ibasis = 1, basisnum(1)
r_node_temp(:,ibasis,inod) = cell_mat(:,inod) + basis_pos(:,ibasis,1) + origin(:)
r_node_temp(:,ibasis,inod) = cell_mat(:,inod) + basis_pos(:,ibasis) + origin(:)
end do
end do
do i = 1,3
@ -115,7 +117,7 @@ module mode_create
if(lat_atom_num > 0) then
do i = 1, lat_atom_num
do ibasis = 1, basisnum(1)
call add_atom(basis_type(ibasis,1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis,1))
call add_atom(basis_type(ibasis, 1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis))
end do
end do
deallocate(r_atom_lat)
@ -125,7 +127,7 @@ module mode_create
do i = 1, lat_ele_num
do inod= 1, ng_node(1)
do ibasis = 1, basisnum(1)
r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis,1)
r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis)
end do
end do
call add_element(element_type, esize, 1, r_node_temp)
@ -258,13 +260,17 @@ module mode_create
!Now normalize the orientation matrix
orient = matrix_normal(orient,3)
!Set lattice_num to 1
lattice_types = 1
!If we haven't defined a basis then define the basis and add the default basis atom type and position
if (basisnum(1) == 0) then
max_basisnum = 1
basisnum(1) = 1
call add_atom_type(name, basis_type(1,1)) !If basis command not defined then we use name as the atom_name
basis_pos(:,1,1) = 0.0_dp
basis_pos(:,1) = 0.0_dp
end if
!
end subroutine
subroutine build_with_rhomb(box_in_lat, transform_matrix)
@ -432,12 +438,11 @@ module mode_create
end do
!Now figure out how many lattice points could not be contained in elements
print *, count(lat_points)
allocate(r_atom_lat(3,count(lat_points)))
lat_atom_num = 0
do ix = 1, bd_in_array(3)
do iz = 1, bd_in_array(3)
do iy = 1, bd_in_array(2)
do iz = 1, bd_in_array(1)
do ix = 1, bd_in_array(1)
!If this point is a lattice point then save the lattice point as an atom
if (lat_points(ix,iy,iz)) then
v= (/ real(ix,dp), real(iy, dp), real(iz,dp) /)
@ -453,7 +458,6 @@ module mode_create
end do
end do
print *, lat_atom_num
end if
end subroutine build_with_rhomb