Changes to how the adjustment to nodal positions is performed for lammpscac output
This commit is contained in:
Alex Selimov
parent
55fbe679e5
commit
849da1d24a
@ -9,7 +9,7 @@ module elements
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!Data structures used to represent the CAC elements. Each index represents an element
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character(len=100), allocatable :: type_ele(:) !Element type
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integer, allocatable :: size_ele(:), lat_ele(:) !Element siz
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integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:) !Element size
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real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
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integer, save :: ele_num !Number of elements
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@ -39,6 +39,7 @@ module elements
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!This can be easily increased with no change to efficiency
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integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type
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integer :: basis_type(10,10)
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real(kind=dp) :: lapa(10)
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public
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contains
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@ -140,7 +141,7 @@ module elements
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!Allocate element arrays
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if(n > 0) then
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allocate(type_ele(n), size_ele(n), lat_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
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allocate(type_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
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stat=allostat)
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if(allostat > 0) then
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print *, "Error allocating element arrays in elements.f90 because of: ", allostat
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@ -179,12 +180,17 @@ module elements
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allocate(temp_int(n+ele_num+buffer_size))
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temp_int(1:ele_size) = lat_ele
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temp_int(ele_size+1:) = 0
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call move_alloc(temp_int(1:ele_size), lat_ele)
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call move_alloc(temp_int, lat_ele)
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allocate(temp_int(n+ele_num+buffer_size))
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temp_int(1:ele_size) = size_ele
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temp_int(ele_size+1:) = 0
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call move_alloc(temp_int(1:ele_size), size_ele)
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call move_alloc(temp_int, size_ele)
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allocate(temp_int(n+ele_num+buffer_size))
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temp_int(1:ele_size) = lat_ele
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temp_int(ele_size+1:) = 0
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call move_alloc(temp_int, sbox_ele)
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allocate(char_temp(n+ele_num+buffer_size))
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char_temp(1:ele_size) = type_ele
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@ -210,9 +216,9 @@ module elements
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end if
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end subroutine
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subroutine add_element(type, size, lat, r)
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subroutine add_element(type, size, lat, sbox, r)
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!Subroutine which adds an element to the element arrays
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integer, intent(in) :: size, lat
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integer, intent(in) :: size, lat, sbox
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character(len=100), intent(in) :: type
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real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node)
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@ -220,6 +226,7 @@ module elements
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type_ele(ele_num) = type
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size_ele(ele_num) = size
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lat_ele(ele_num) = lat
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sbox_ele(ele_num) = sbox
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r_node(:,:,:,ele_num) = r(:,:,:)
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node_num = node_num + ng_node(lat)
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38
src/io.f90
38
src/io.f90
@ -204,7 +204,7 @@ module io
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!This subroutine writes out a .lmp style dump file
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character(len=100), intent(in) :: file
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integer :: write_num, i, inod, ibasis
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real(kind=dp) :: mass
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real(kind=dp) :: mass, fcc_adjust(3,8), local_adjust(3,8), rout(3)
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1 format(i16, ' Eight_Node', 4i16)
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2 format(i16, ' Atom', 4i16)
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@ -242,16 +242,32 @@ module io
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write(11, '(a)') 'CAC Elements'
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write(11, '(a)') ' '
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!Set up the nodal adjustment variables for all the different element types. This adjusts the node centers
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!from the center of the unit cell (as formulated in this code) to the corners of the unit cells
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do inod = 1, 8
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do i = 1,3
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if(is_equal(cubic_cell(i, inod),0.0_dp)) then
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fcc_adjust(i,inod) = -0.5_dp
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else
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fcc_adjust(i, inod) = 0.5_dp
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end if
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end do
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end do
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fcc_adjust = matmul(fcc_mat, fcc_adjust)
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!Write element nodal positions
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do i = 1, ele_num
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select case(trim(adjustl(type_ele(i))))
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case('fcc')
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!Now orient the current adjustment vector to the correct orientation
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local_adjust = matmul(sub_box_ori(:,:,sbox_ele(i)), fcc_adjust) * lapa(lat_ele(i))
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!The first entry is the element specifier
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write(11,1) i, basisnum(lat_ele(i)), size_ele(i), size_ele(i), size_ele(i)
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do ibasis = 1, basisnum(lat_ele(i))
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do inod = 1, 8
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!Nodal information for every node
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write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i)
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rout = r_node(:,ibasis,inod,i) + local_adjust(:,inod)
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write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), rout
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end do
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end do
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end select
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@ -486,6 +502,8 @@ module io
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write(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
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!Now for every lattice type write the basis atom types
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write(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
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!Now for every lattice type write the lattice parameters
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write(11,*) (lapa(i), i = 1, lattice_types)
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!Now write the numbers of elements and atoms
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write(11,*) atom_num, ele_num
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@ -498,7 +516,7 @@ module io
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!Write out the elements, this is written in two stages, one line for the element and then 1 line for
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!every basis at every node
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do i = 1, ele_num
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write(11, *) i, lat_ele(i), size_ele(i), type_ele(i)
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write(11, *) i, lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i)
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do inod = 1, ng_node(lat_ele(i))
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do ibasis =1, basisnum(lat_ele(i))
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write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
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@ -582,7 +600,7 @@ module io
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real(kind = dp), dimension(6), intent(out) :: temp_box_bd
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integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
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new_type_to_type(10), new_lattice_types
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new_type_to_type(10), new_lattice_types, sbox
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character(len=100) :: etype
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real(kind=dp) :: r(3), newdisplace(3)
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real(kind=dp), allocatable :: r_innode(:,:,:)
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@ -623,8 +641,6 @@ module io
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sub_box_array_bd(:,1,sub_box_num+1:) = sub_box_array_bd(:,1,sub_box_num+1:) + atom_num
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sub_box_array_bd(:,2,sub_box_num+1:) = sub_box_array_bd(:,2,sub_box_num+1:) + ele_num
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sub_box_num = sub_box_num + n
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!Read in the number of atom types and all their names
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read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)
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!Now fit these into the global list of atom types, after this new_type_to_type is the actual global
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@ -646,6 +662,8 @@ module io
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basis_type(i,j) = new_type_to_type(basis_type(i,j))
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end do
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end do
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!Read the lattice parameters for every lattice type
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read(11,*) (lapa(i), i = lattice_types+1, lattice_types+new_lattice_types)
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!Read number of elements and atoms and allocate arrays
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read(11, *) in_atoms, in_eles
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call grow_ele_arrays(in_eles, in_atoms)
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@ -659,7 +677,7 @@ module io
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!Read the elements
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do i = 1, in_eles
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read(11, *) n, type, size, etype
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read(11, *) n, type, size, sbox, etype
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do inod = 1, ng_node(type)
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do ibasis =1, basisnum(type)
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read(11,*) j, k, r_innode(:, ibasis, inod)
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@ -667,7 +685,7 @@ module io
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end do
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end do
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type = type + lattice_types
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call add_element(etype, size, type, r_innode)
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call add_element(etype, size, type, sbox+n, r_innode)
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end do
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!Close the file being read
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@ -676,5 +694,9 @@ module io
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!Only increment the lattice types if there are elements, if there are no elements then we
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!just overwrite the arrays
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if(in_eles > 0) lattice_types = lattice_types + new_lattice_types
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sub_box_num = sub_box_num + n
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end subroutine read_mb
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end module io
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11
src/main.f90
11
src/main.f90
@ -28,17 +28,6 @@ program main
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! Command line parsing
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arg_num = command_argument_count()
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!First check if we are writing out to lammpscac format by looping over all arguments
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do i = 1, arg_num
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call get_command_argument(i, argument)
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select case(argument(scan(argument,'.',.true.)+1:))
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case('cac')
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lmpcac = .true.
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case default
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continue
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end select
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end do
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!Determine if a mode is being used and what it is. The first argument has to be the mode
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!if a mode is being used
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call get_command_argument(1, argument)
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@ -12,7 +12,7 @@ module mode_create
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character(len=100) :: name, element_type
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real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
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orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3), adjustVar(3,8)
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orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
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integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
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basis_pos(3,10)
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logical :: dup_flag, dim_flag
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@ -105,7 +105,7 @@ module mode_create
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box_bd(2*i) = maxval(r_node_temp(i,:,:))
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box_bd(2*i-1) = origin(i)
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end do
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call add_element(element_type, esize, 1, r_node_temp)
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call add_element(element_type, esize, 1, 1, r_node_temp)
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end if
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!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
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@ -141,7 +141,7 @@ module mode_create
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r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis)
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end do
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end do
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call add_element(element_type, esize, 1, r_node_temp)
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call add_element(element_type, esize, 1, 1, r_node_temp)
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end do
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end if
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end if
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@ -199,7 +199,20 @@ module mode_create
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call get_command_argument(arg_pos, orient_string, arglen)
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if (arglen==0) STOP "Missing orientation in orient command of mode create"
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arg_pos = arg_pos+1
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call parse_ori_vec(orient_string, orient(i,:))
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ori_pos=2
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do j = 1,3
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if (orient_string(ori_pos:ori_pos) == '-') then
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ori_pos = ori_pos + 1
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read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
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if (stat>0) STOP "Error reading orient value"
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orient(i,j) = -orient(i,j)
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ori_pos = ori_pos + 1
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else
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read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
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if(stat>0) STOP "Error reading orient value"
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ori_pos=ori_pos + 1
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end if
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end do
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end do
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@ -234,6 +247,7 @@ module mode_create
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exit
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end select
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end do
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!Calculate the lattice periodicity length in lattice units
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do i = 1, 3
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lattice_space(i) = norm2(orient(i,:))
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@ -264,8 +278,9 @@ module mode_create
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!Now normalize the orientation matrix
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orient = matrix_normal(orient,3)
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!Set lattice_num to 1
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!Set lattice_num to 1 and add the lattice_parameter to the elements module lattice paramter variable
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lattice_types = 1
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lapa(1) = lattice_parameter
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!If we haven't defined a basis then define the basis and add the default basis atom type and position
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if (basisnum(1) == 0) then
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@ -286,7 +301,7 @@ module mode_create
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!Internal variables
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integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), &
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vlat(3), temp_lat(3,8), m, n, o
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real(kind=dp) :: v(3), temp_nodes(3,1,8), adjustVar(3,8)
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real(kind=dp) :: v(3), temp_nodes(3,1,8)
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real(kind=dp), allocatable :: resize_lat_array(:,:)
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logical, allocatable :: lat_points(:,:,:)
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logical :: node_in_bd(8)
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@ -294,23 +309,6 @@ module mode_create
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!Do some value initialization
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max_esize = esize
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!If we are writing out to lammpscac format then we have to adjust the nodal positions
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if(lmpcac) then
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do inod = 1, 8
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do i = 1,3
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if(is_equal(cubic_cell(i, inod),0.0_dp)) then
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adjustVar(i,inod) = -0.5_dp
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else
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adjustVar(i, inod) = 0.5_dp
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end if
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end do
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end do
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adjustVar(:,1:8) = matmul(orient,matmul(fcc_mat,adjustVar(:,1:8)))
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else
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adjustVar(:,:)=0.0_dp
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end if
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!First find the bounding lattice points (min and max points for the box in each dimension)
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numlatpoints = 1
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do i = 1, 3
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@ -328,6 +326,7 @@ module mode_create
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continue
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end select
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!Loop over all of lattice points within the boundary, we choose between two loops. One for the atomistic case
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!and one for the regular case
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if (esize==2) then
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@ -440,11 +439,9 @@ module mode_create
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end do
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if(all(node_in_bd)) then
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lat_ele_num = lat_ele_num+1
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do inod = 1, 8
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r_lat(:,inod,lat_ele_num) = temp_nodes(:,1,inod) + adjustVar(:,inod)
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end do
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lat_ele_num = lat_ele_num+1
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r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
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!Now set all the lattice points contained within an element to false
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do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
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do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))
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@ -510,4 +507,4 @@ module mode_create
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end subroutine error_message
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end module mode_create
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end module mode_create
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