Merge read-cac branch into main branch
This commit is contained in:
Alex Selimov
commit
2fda952d3f
@ -329,7 +329,6 @@ 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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@ -36,13 +36,13 @@ 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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@ -323,8 +323,6 @@ module elements
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integer :: i
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max_ng_node = 0
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do i=1, n
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select case(trim(adjustl(element_types(i))))
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case('fcc')
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@ -676,4 +674,39 @@ module elements
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end select
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end subroutine
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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 lat_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_type(:,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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lat_type = lattice_types
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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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162
src/io.f90
162
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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@ -196,7 +196,7 @@ module io
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do i = 1, ele_num
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call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
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select case(trim(adjustl(type_ele(i))))
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case('fcc')
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case('fcc','bcc')
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do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
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interp_num = interp_num+1
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call apply_periodic(r_interp(:,iatom))
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@ -591,7 +591,7 @@ module io
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end if
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select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
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case('restart', 'mb')
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case('restart', 'mb', 'cac')
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infilenum=infilenum+1
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infiles(infilenum) = temp_infile
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exit
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@ -618,6 +618,8 @@ module io
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call read_mb(infiles(i), displace, temp_box_bd)
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case('restart')
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call read_pycac(infiles(i), displace, temp_box_bd)
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case('cac')
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call read_lmpcac(infiles(i), displace, temp_box_bd)
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case default
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print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
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" is not accepted for writing. Please select from: mb and try again"
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@ -776,7 +778,7 @@ module io
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integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
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atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
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atom_type
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real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3)
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real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
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character(len=100) :: textholder, in_lattype_map(10)
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character(len=2) :: atomic_element
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!First open the file
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@ -949,4 +951,154 @@ module io
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call set_max_esize
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end if
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end subroutine read_pycac
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subroutine read_lmpcac(file, displace, temp_box_bd)
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!This subroutine is used to read .cac files which are used with the lammpsCAC format
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character(len=100), intent(in) :: file
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real(kind=dp), dimension(3), intent(in) :: displace
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real(kind = dp), dimension(6), intent(out) :: temp_box_bd
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character(len=100) :: textholder, element_type
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character(len=2) :: atom_species
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integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10), esize, &
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lat_type
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real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), newdisplace(3)
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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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!Now initialiaze some important variables if they aren't defined
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if (max_basisnum==0) max_basisnum = 10
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if (max_ng_node==0) max_ng_node=8
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!Read header information
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read(11, *) textholder
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!Read number of elements
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read(11, *) ele_in, textholder
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read(11, *) type_in, textholder
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!Read box_boundaries
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read(11,*) temp_box_bd(1:2), textholder
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read(11,*) temp_box_bd(3:4), textholder
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read(11,*) temp_box_bd(5:6), textholder
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!Shift the box boundaries if needed
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do i = 1, 3
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if (abs(displace(i)) > lim_zero) then
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newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
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else
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newdisplace(i)=displace(i)
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end if
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temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
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temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
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end do
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!Grow box boundaries
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call grow_box(temp_box_bd)
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!Allocate sub_box
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if (sub_box_num == 0) then
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call alloc_sub_box(1)
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else
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call grow_sub_box(1)
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end if
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!Because orientations and other needed sub_box information isn't really
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!present within the .cac file we just default a lot of it.
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sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
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sub_box_bd(:, sub_box_num+1) = temp_box_bd
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sub_box_num = sub_box_num + 1
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!Read useless information
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read(11,*) textholder
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!Read atomic masses
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do i = 1, type_in
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read(11,*) j, mass, textholder
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call ATOMMASSSPECIES(mass, atom_species)
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call add_atom_type(atom_species, type_map(i))
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end do
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!Read useless info
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read(11,*) textholder
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!Start the reading loop
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do i = 1, ele_in
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read(11,*) j, element_type, in_basis, esize
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!Check to see if we need to grow the max_basis_num
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select case(trim(adjustl(element_type)))
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case('Eight_Node')
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!Read in all the data
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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 lattice vectors and shift the nodal points from the corners to the center of the unit cell
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!Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
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!calculation
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lat_vec(:,1) = (r_in(:,1,2) - r_in(:,1,1))/(2*esize)
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lat_vec(:,2) = (r_in(:,1,4) - r_in(:,1,1))/(2*esize)
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lat_vec(:,3) = (r_in(:,1,5) - r_in(:,1,1))/(2*esize)
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!Now shift all the nodal positions
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select case(trim(adjustl(in_lattice_type)))
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case('fcc','FCC')
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do ibasis = 1, in_basis
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r_in(:,ibasis,1) = r_in(:,ibasis,1) + lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
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r_in(:,ibasis,2) = r_in(:,ibasis,2) - lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
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r_in(:,ibasis,3) = r_in(:,ibasis,3) - lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
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r_in(:,ibasis,4) = r_in(:,ibasis,4) + lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
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r_in(:,ibasis,5) = r_in(:,ibasis,5) + lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
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r_in(:,ibasis,6) = r_in(:,ibasis,6) - lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
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r_in(:,ibasis,7) = r_in(:,ibasis,7) - lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
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r_in(:,ibasis,8) = r_in(:,ibasis,8) + lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
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end do
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case default
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print *, in_lattice_type, " is not an accepted lattice type. Please select from: fcc"
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end select
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!Now map it to either an existing or new lattice type
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call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
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!Now add the element
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call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in(:,1:max_basisnum,1:max_ng_node))
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case('Atom')
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read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
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call add_atom(in_basis_types(ibasis), sub_box_num, r_in(:,1,1))
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end select
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end do
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end subroutine read_lmpcac
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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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character(len=100) :: textholder
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arg_pos = apos + 1
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call get_command_argument(arg_pos, textholder, 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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read(textholder,*) in_lapa
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print *, in_lapa
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, 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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read(textholder,*) in_lattice_type
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print *, in_lattice_type
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end subroutine set_cac
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end module io
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@ -60,6 +60,9 @@ 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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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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