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First attempts at figuring out the element format for lammpscac

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master
Alex Selimov 5 years ago
parent 54aa50b605
commit c1150ae4b1
2 changed files with 49 additions and 11 deletions
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14
src/io.f90
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@ -8,6 +8,7 @@ module io
integer :: outfilenum = 0, infilenum = 0
character(len=100) :: outfiles(10), infiles(10)
logical lmpcac
public
contains
@ -57,7 +58,12 @@ module io
cycle
end if
select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
case('xyz','lmp','vtk','cac')
case('xyz','lmp','vtk')
outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile
exit
case('cac')
lmpcac = .true.
outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile
exit
@ -98,18 +104,18 @@ module io
cycle
end if
if (scan(temp_outfile,'.',.true.) == 0) then
if (scan(temp_infile,'.',.true.) == 0) then
print *, "No extension included on filename, please type a full filename that includes an extension."
read(*,*) temp_infile
cycle
end if
select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
case('cac')
infilenum=infilenum+1
infiles(infilenum) = temp_infile
exit
case default
print *, "File type: ", trim(temp_infile(scan(temp_outfile,'.',.true.):)), " not currently accepted. ", &
print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), " not currently accepted. ", &
"please input a filename with extension from following list: cac."
read(*,*) temp_infile

46
src/mode_create.f90
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@ -11,7 +11,7 @@ module mode_create
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)
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), adjustVar(3,8)
integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6)
logical :: dup_flag, dim_flag
@ -91,14 +91,30 @@ module mode_create
continue
else
call cell_init(lattice_parameter, esize, element_type, orient, cell_mat)
if(lmpcac) then
do inod = 1, 8
do i = 1,3
if(is_equal(cubic_cell(i, inod),0.0_dp)) then
adjustVar(i,inod) = -0.5_dp*esize
else
adjustVar(i, inod) = 0.5_dp*esize
end if
end do
end do
else
adjustVar(:,:)=0.0_dp
end if
! call cell_init(lattice_parameter, esize, element_type, orient, cell_mat)
!If the user doesn't pass any build instructions than we just put the cell mat into the element_array
call alloc_ele_arrays(1,0)
!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) = lattice_parameter*matmul(orient, &
matmul(fcc_mat, esize*(cubic_cell(:,inod)+adjustVar(:,inod)))) &
+ basis_pos(:,ibasis,1)
end do
end do
do i = 1,3
@ -276,7 +292,7 @@ module mode_create
!Internal variables
integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, templatpoints, ele(3,8), rzero(3), ilat, &
type_interp(basisnum(1)*esize**3), vlat(3), temp_lat(3,8), m, n, o
real(kind=dp) :: v(3), temp_nodes(3,1,8), ele_atoms(3,esize**3), r_interp(3,basisnum(1)*esize**3)
real(kind=dp) :: v(3), temp_nodes(3,1,8), ele_atoms(3,esize**3), r_interp(3,basisnum(1)*esize**3), adjustVar(3,8)
real(kind=dp), allocatable :: resize_lat_array(:,:)
logical, allocatable :: lat_points(:,:,:)
logical :: node_in_bd(8)
@ -284,6 +300,21 @@ module mode_create
!Do some value initialization
max_esize = esize
!If we are writing out to lammpscac format then we have to adjust the nodal positions
if(lmpcac) then
do inod = 1, 8
do i = 1,3
if(is_equal(cubic_cell(i, inod),0.0_dp)) then
adjustVar(i,inod) = -0.25_dp
else
adjustVar(i, inod) = 0.25_dp
end if
end do
end do
else
adjustVar(:,:)=0.0_dp
end if
!First find the bounding lattice points (min and max points for the box in each dimension)
numlatpoints = 1
do i = 1, 3
@ -301,7 +332,6 @@ module mode_create
continue
end select
!Loop over all of lattice points within the boundary, we choose between two loops. One for the atomistic case
!and one for the regular case
if (esize==2) then
@ -415,8 +445,10 @@ module mode_create
if(all(node_in_bd)) then
lat_ele_num = lat_ele_num+1
r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
do inod = 1, 8
r_lat(:,inod,lat_ele_num) = temp_nodes(:,1,inod) + adjustVar(:,inod)
end do
!Now set all the lattice points contained within an element to false
do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))

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