Working changes for reading .cac files
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Alex Selimov
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@ -191,7 +191,7 @@ This option creates a circular planar vacancy cluster of radius `radius` normal
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This option selects a group of either elements, nodes, atoms and applies some transformation to them.
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`select_type` - Either `nodes`, `atoms`, `elements`, `nodes/atoms`, `all`. When using the option `nodes` only nodes which are within the group are selected, `elements` selects elements based on whether the element center is within the group, `nodes/atoms` selects both nodes and atoms for the group. `all` selects elements based on the element center and atoms based on their position.
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`select_type` - Either `atoms`, `elements`,`both`. `elements` selects elements based on whether the element center is within the group, `nodes/atoms` selects both nodes and atoms for the group. `both` selects elements based on the element center and atoms based on their position.
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`group_shape` - Specifies what shape the group takes and dictates which options must be passed. Each shape requires different arguments and these arguments are represented by the placeholder `shape_arguments`. The accepted group shapes and arguments are below:
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@ -230,7 +230,7 @@ This command wraps atoms back into the simulation cell as though periodic bounda
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**Remesh**
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```
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remesh esize lattice_parameter lattice_type
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remesh esize
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```
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This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. When remeshing to atomistics the group can contain any orientations of elements but when remeshing to different finite elements, the group must contain all atoms/elements with the same orientation. `lattice_parameter` is the lattice parameter for the elements within the group and `lattice_type` is the lattice type (integer) that these new elements will be assigned to.
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@ -294,7 +294,6 @@ This command will delete all overlapping atoms within a specific cutoff radius `
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This option is primarily used when reading data from non .mb formats. This code simply sets the orientation variable for the specified sub box `sbox`.
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****
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## Position Specification
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Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below.
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@ -33,8 +33,10 @@ subroutine call_option(option, arg_pos)
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call sbox_ori(arg_pos)
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case('-delete')
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call run_delete(arg_pos)
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case('-set_cac')
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arg_pos = arg_pos+3
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case default
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print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
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stop 3
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end select
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end subroutine call_option
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end subroutine call_option
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@ -35,13 +35,13 @@ module elements
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integer :: lattice_types = 0
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integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type
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integer :: max_esize=0 !Maximum number of atoms per side of element
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real(kind=dp) :: lapa(10)
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!These variables contain information on the basis, for simplicities sake we limit
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!the user to the definition of 10 lattice types with 10 basis atoms at each lattice point.
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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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!Additional module level variables we need
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logical :: wrap_flag
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@ -632,4 +632,38 @@ module elements
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end select
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end subroutine
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end module elements
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subroutine lattice_map(in_bnum, in_btypes, in_ngnodes, in_lapa, lat_type)
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!This subroutine maps an input lattice type to either a new lattice type or an existing one depending on basis_type and
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!number of nodes at the atoms
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integer, intent(in) :: in_ngnodes, in_bnum, in_btypes(10) !Input variables
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real(kind=dp), intent(in) :: in_lapa
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integer, intent(out) :: lat_type
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integer j, ibasis
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lat_type = 0
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lat_loop:do j = 1, lattice_types
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!Check all the lattice level variables
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if ((basisnum(j) == in_bnum).and.(ng_node(j) == in_ngnodes).and.(is_equal(lapa(j),in_lapa))) then
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!Now check lattice level variables
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do ibasis = 1, basisnum(j)
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if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle old_loop
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end do
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lat_type = j
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exit lat_loop
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end if
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end do lat_loop
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!If it doesn't match an existing lattice type we add it
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if( lat_type == 0) then
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lattice_types = lattice_types + 1
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basisnum(lattice_types) = in_bnum
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basis_types(:,lattice_types) = in_btypes
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ng_node(lattice_types) = in_ngnodes
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lapa(lattice_types) = in_lapa
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end if
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end subroutine lattice_map
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end module elements
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47
src/io.f90
47
src/io.f90
@ -8,9 +8,9 @@ module io
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implicit none
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integer :: outfilenum = 0, infilenum = 0
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character(len=100) :: outfiles(100), infiles(100)
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character(len=100) :: outfiles(100), infiles(100), in_lattice_type=''
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logical :: force_overwrite
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real(kind=dp) :: in_lapa=0.0
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public
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contains
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@ -958,12 +958,15 @@ module io
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character(len=100) :: textholder, element_type, esize
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character(len=2) :: atom_species
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integer :: i, j, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
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real(kind=dp) :: mass, r_in(3,10,8)
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integer :: i, j, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
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real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3), in_ori(3,3)
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!First open the file
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!First check to make sure that we have set the needed variables
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if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then
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print *, "Please use set_cac to set needed parameters to read in .cac file"
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stop 3
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end if
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!Open the file
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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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!Read header information
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@ -978,8 +981,7 @@ module io
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read(11,*) textholder
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read(11,*) box_bd(1:2), texholder
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read(11,*) box_bd(3:4), texholder
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read(11,*) box_bd(5:6), texholder
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read(11,*) box_bd(5:6), texholder
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!Read useless information
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read(11,*) textholder
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read(11,*) textholder
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@ -1005,10 +1007,35 @@ module io
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do j = 1, 8*in_basis
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read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
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end do
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!Now calculate the orientation matrix based on the lattice type.
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lat_vec = r_in(:,1,2) - r_in(:,1,1)
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lat_vec = lat_vec / norm2(lat_vec)
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!Now figure out if is an existing lattice_type
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call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
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!
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end select
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end do
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end subroutine read_cac
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subroutine set_cac(apos)
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!This code parses input values
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integer, intent(in) :: apos
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integer :: arglen, arg_pos
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arg_pos = apos + 1
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call get_command_argument(arg_pos, in_lapa, arglen)
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if (arglen==0) then
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print *, "Missing lattice parameter for set_input_lat"
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end if
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, in_lattice_type, arglen)
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if (arglen==0) then
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print *, "Missing lattice type for set_input_lat"
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end if
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end subroutine set_input_lat(arg_pos)
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end module io
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@ -60,6 +60,11 @@ program main
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!This lets us know if we need to wrap atomic positions back into the cell
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case('-wrap')
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wrap_flag=.true.
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!This gives necessary information in order to correctly read .cac files
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case('-set_cac')
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call set_cac(i)
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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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