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Merge pull request #7 from aselimov/redo-lammpscac

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Changes to how the adjustment to nodal positions is performed for lam…
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aselimov 5 years ago committed by GitHub
parent 55fbe679e5 849da1d24a
commit fe6101167f
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4 changed files with 69 additions and 54 deletions
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19
src/elements.f90
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@ -9,7 +9,7 @@ module elements
!Data structures used to represent the CAC elements. Each index represents an element !Data structures used to represent the CAC elements. Each index represents an element
character(len=100), allocatable :: type_ele(:) !Element type character(len=100), allocatable :: type_ele(:) !Element type
integer, allocatable :: size_ele(:), lat_ele(:) !Element siz integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:) !Element size
real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
integer, save :: ele_num !Number of elements integer, save :: ele_num !Number of elements
@ -39,6 +39,7 @@ module elements
!This can be easily increased with no change to efficiency !This can be easily increased with no change to efficiency
integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type
integer :: basis_type(10,10) integer :: basis_type(10,10)
real(kind=dp) :: lapa(10)
public public
contains contains
@ -140,7 +141,7 @@ module elements
!Allocate element arrays !Allocate element arrays
if(n > 0) then if(n > 0) then
allocate(type_ele(n), size_ele(n), lat_ele(n), r_node(3,max_basisnum, max_ng_node,n), & allocate(type_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
stat=allostat) stat=allostat)
if(allostat > 0) then if(allostat > 0) then
print *, "Error allocating element arrays in elements.f90 because of: ", allostat print *, "Error allocating element arrays in elements.f90 because of: ", allostat
@ -179,12 +180,17 @@ module elements
allocate(temp_int(n+ele_num+buffer_size)) allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = lat_ele temp_int(1:ele_size) = lat_ele
temp_int(ele_size+1:) = 0 temp_int(ele_size+1:) = 0
call move_alloc(temp_int(1:ele_size), lat_ele) call move_alloc(temp_int, lat_ele)
allocate(temp_int(n+ele_num+buffer_size)) allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = size_ele temp_int(1:ele_size) = size_ele
temp_int(ele_size+1:) = 0 temp_int(ele_size+1:) = 0
call move_alloc(temp_int(1:ele_size), size_ele) call move_alloc(temp_int, size_ele)
allocate(temp_int(n+ele_num+buffer_size))
temp_int(1:ele_size) = lat_ele
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, sbox_ele)
allocate(char_temp(n+ele_num+buffer_size)) allocate(char_temp(n+ele_num+buffer_size))
char_temp(1:ele_size) = type_ele char_temp(1:ele_size) = type_ele
@ -210,9 +216,9 @@ module elements
end if end if
end subroutine end subroutine
subroutine add_element(type, size, lat, r) subroutine add_element(type, size, lat, sbox, r)
!Subroutine which adds an element to the element arrays !Subroutine which adds an element to the element arrays
integer, intent(in) :: size, lat integer, intent(in) :: size, lat, sbox
character(len=100), intent(in) :: type character(len=100), intent(in) :: type
real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node) real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node)
@ -220,6 +226,7 @@ module elements
type_ele(ele_num) = type type_ele(ele_num) = type
size_ele(ele_num) = size size_ele(ele_num) = size
lat_ele(ele_num) = lat lat_ele(ele_num) = lat
sbox_ele(ele_num) = sbox
r_node(:,:,:,ele_num) = r(:,:,:) r_node(:,:,:,ele_num) = r(:,:,:)
node_num = node_num + ng_node(lat) node_num = node_num + ng_node(lat)

38
src/io.f90
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@ -204,7 +204,7 @@ module io
!This subroutine writes out a .lmp style dump file !This subroutine writes out a .lmp style dump file
character(len=100), intent(in) :: file character(len=100), intent(in) :: file
integer :: write_num, i, inod, ibasis 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) 1 format(i16, ' Eight_Node', 4i16)
2 format(i16, ' Atom', 4i16) 2 format(i16, ' Atom', 4i16)
@ -242,16 +242,32 @@ module io
write(11, '(a)') 'CAC Elements' write(11, '(a)') 'CAC Elements'
write(11, '(a)') ' ' 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 !Write element nodal positions
do i = 1, ele_num do i = 1, ele_num
select case(trim(adjustl(type_ele(i)))) select case(trim(adjustl(type_ele(i))))
case('fcc') 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 !The first entry is the element specifier
write(11,1) i, basisnum(lat_ele(i)), size_ele(i), size_ele(i), size_ele(i) 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 ibasis = 1, basisnum(lat_ele(i))
do inod = 1, 8 do inod = 1, 8
!Nodal information for every node !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 do end do
end select 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) 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 !Now for every lattice type write the basis atom types
write(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_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 !Now write the numbers of elements and atoms
write(11,*) atom_num, ele_num 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 !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 !every basis at every node
do i = 1, ele_num 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 inod = 1, ng_node(lat_ele(i))
do ibasis =1, basisnum(lat_ele(i)) do ibasis =1, basisnum(lat_ele(i))
write(11,*) inod, ibasis, r_node(:, ibasis, inod, 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 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, & 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 character(len=100) :: etype
real(kind=dp) :: r(3), newdisplace(3) real(kind=dp) :: r(3), newdisplace(3)
real(kind=dp), allocatable :: r_innode(:,:,:) 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(:,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_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 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) 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 !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)) basis_type(i,j) = new_type_to_type(basis_type(i,j))
end do end do
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 number of elements and atoms and allocate arrays
read(11, *) in_atoms, in_eles read(11, *) in_atoms, in_eles
call grow_ele_arrays(in_eles, in_atoms) call grow_ele_arrays(in_eles, in_atoms)
@ -659,7 +677,7 @@ module io
!Read the elements !Read the elements
do i = 1, in_eles 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 inod = 1, ng_node(type)
do ibasis =1, basisnum(type) do ibasis =1, basisnum(type)
read(11,*) j, k, r_innode(:, ibasis, inod) read(11,*) j, k, r_innode(:, ibasis, inod)
@ -667,7 +685,7 @@ module io
end do end do
end do end do
type = type + lattice_types type = type + lattice_types
call add_element(etype, size, type, r_innode) call add_element(etype, size, type, sbox+n, r_innode)
end do end do
!Close the file being read !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 !Only increment the lattice types if there are elements, if there are no elements then we
!just overwrite the arrays !just overwrite the arrays
if(in_eles > 0) lattice_types = lattice_types + new_lattice_types if(in_eles > 0) lattice_types = lattice_types + new_lattice_types
sub_box_num = sub_box_num + n
end subroutine read_mb end subroutine read_mb
end module io end module io

11
src/main.f90
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@ -28,17 +28,6 @@ program main
! Command line parsing ! Command line parsing
arg_num = command_argument_count() arg_num = command_argument_count()
!First check if we are writing out to lammpscac format by looping over all arguments
do i = 1, arg_num
call get_command_argument(i, argument)
select case(argument(scan(argument,'.',.true.)+1:))
case('cac')
lmpcac = .true.
case default
continue
end select
end do
!Determine if a mode is being used and what it is. The first argument has to be the mode !Determine if a mode is being used and what it is. The first argument has to be the mode
!if a mode is being used !if a mode is being used
call get_command_argument(1, argument) call get_command_argument(1, argument)

49
src/mode_create.f90
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@ -12,7 +12,7 @@ module mode_create
character(len=100) :: name, element_type 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), & 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), duplicate(3), adjustVar(3,8) orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), & integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
basis_pos(3,10) basis_pos(3,10)
logical :: dup_flag, dim_flag logical :: dup_flag, dim_flag
@ -105,7 +105,7 @@ module mode_create
box_bd(2*i) = maxval(r_node_temp(i,:,:)) box_bd(2*i) = maxval(r_node_temp(i,:,:))
box_bd(2*i-1) = origin(i) box_bd(2*i-1) = origin(i)
end do end do
call add_element(element_type, esize, 1, r_node_temp) call add_element(element_type, esize, 1, 1, r_node_temp)
end if end if
!If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays !If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays
@ -141,7 +141,7 @@ module mode_create
r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis) r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis)
end do end do
end do end do
call add_element(element_type, esize, 1, r_node_temp) call add_element(element_type, esize, 1, 1, r_node_temp)
end do end do
end if end if
end if end if
@ -199,7 +199,20 @@ module mode_create
call get_command_argument(arg_pos, orient_string, arglen) call get_command_argument(arg_pos, orient_string, arglen)
if (arglen==0) STOP "Missing orientation in orient command of mode create" if (arglen==0) STOP "Missing orientation in orient command of mode create"
arg_pos = arg_pos+1 arg_pos = arg_pos+1
call parse_ori_vec(orient_string, orient(i,:)) ori_pos=2
do j = 1,3
if (orient_string(ori_pos:ori_pos) == '-') then
ori_pos = ori_pos + 1
read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
if (stat>0) STOP "Error reading orient value"
orient(i,j) = -orient(i,j)
ori_pos = ori_pos + 1
else
read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
if(stat>0) STOP "Error reading orient value"
ori_pos=ori_pos + 1
end if
end do
end do end do
@ -234,6 +247,7 @@ module mode_create
exit exit
end select end select
end do end do
!Calculate the lattice periodicity length in lattice units !Calculate the lattice periodicity length in lattice units
do i = 1, 3 do i = 1, 3
lattice_space(i) = norm2(orient(i,:)) lattice_space(i) = norm2(orient(i,:))
@ -264,8 +278,9 @@ module mode_create
!Now normalize the orientation matrix !Now normalize the orientation matrix
orient = matrix_normal(orient,3) orient = matrix_normal(orient,3)
!Set lattice_num to 1 !Set lattice_num to 1 and add the lattice_parameter to the elements module lattice paramter variable
lattice_types = 1 lattice_types = 1
lapa(1) = lattice_parameter
!If we haven't defined a basis then define the basis and add the default basis atom type and position !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 if (basisnum(1) == 0) then
@ -286,7 +301,7 @@ module mode_create
!Internal variables !Internal variables
integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), & integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), &
vlat(3), temp_lat(3,8), m, n, o vlat(3), temp_lat(3,8), m, n, o
real(kind=dp) :: v(3), temp_nodes(3,1,8), adjustVar(3,8) real(kind=dp) :: v(3), temp_nodes(3,1,8)
real(kind=dp), allocatable :: resize_lat_array(:,:) real(kind=dp), allocatable :: resize_lat_array(:,:)
logical, allocatable :: lat_points(:,:,:) logical, allocatable :: lat_points(:,:,:)
logical :: node_in_bd(8) logical :: node_in_bd(8)
@ -294,23 +309,6 @@ module mode_create
!Do some value initialization !Do some value initialization
max_esize = esize 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) = -0.5_dp
else
adjustVar(i, inod) = 0.5_dp
end if
end do
end do
adjustVar(:,1:8) = matmul(orient,matmul(fcc_mat,adjustVar(:,1:8)))
else
adjustVar(:,:)=0.0_dp
end if
!First find the bounding lattice points (min and max points for the box in each dimension) !First find the bounding lattice points (min and max points for the box in each dimension)
numlatpoints = 1 numlatpoints = 1
do i = 1, 3 do i = 1, 3
@ -328,6 +326,7 @@ module mode_create
continue continue
end select end select
!Loop over all of lattice points within the boundary, we choose between two loops. One for the atomistic case !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 !and one for the regular case
if (esize==2) then if (esize==2) then
@ -441,9 +440,7 @@ module mode_create
if(all(node_in_bd)) then if(all(node_in_bd)) then
lat_ele_num = lat_ele_num+1 lat_ele_num = lat_ele_num+1
do inod = 1, 8 r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
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 !Now set all the lattice points contained within an element to false
do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:)) do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))

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