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CACmb
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Merge read-cac branch into main branch

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development
Alex Selimov 4 years ago
parent a47c384a3f b52d7761e0
commit 2fda952d3f
5 changed files with 199 additions and 10 deletions
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1
README.md
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@ -329,7 +329,6 @@ This command will delete all overlapping atoms within a specific cutoff radius `
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`.
****
## Position Specification
Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below.

4
src/call_option.f90
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@ -33,8 +33,10 @@ subroutine call_option(option, arg_pos)
call sbox_ori(arg_pos)
case('-delete')
call run_delete(arg_pos)
case('-set_cac')
arg_pos=arg_pos +3
case default
print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
stop 3
end select
end subroutine call_option
end subroutine call_option

39
src/elements.f90
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@ -36,13 +36,13 @@ module elements
integer :: lattice_types = 0
integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type
integer :: max_esize=0 !Maximum number of atoms per side of element
real(kind=dp) :: lapa(10)
!These variables contain information on the basis, for simplicities sake we limit
!the user to the definition of 10 lattice types with 10 basis atoms at each lattice point.
!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 :: basis_type(10,10)
real(kind=dp) :: lapa(10)
!Additional module level variables we need
logical :: wrap_flag
@ -323,8 +323,6 @@ module elements
integer :: i
max_ng_node = 0
do i=1, n
select case(trim(adjustl(element_types(i))))
case('fcc')
@ -676,4 +674,39 @@ module elements
end select
end subroutine
subroutine lattice_map(in_bnum, in_btypes, in_ngnodes, in_lapa, lat_type)
!This subroutine maps an input lattice type to either a new lattice type or an existing one depending on basis_type and
!number of nodes at the atoms
integer, intent(in) :: in_ngnodes, in_bnum, in_btypes(10) !Input variables
real(kind=dp), intent(in) :: in_lapa
integer, intent(out) :: lat_type
integer j, ibasis
lat_type = 0
lat_loop:do j = 1, lattice_types
!Check all the lattice level variables
if ((basisnum(j) == in_bnum).and.(ng_node(j) == in_ngnodes).and.(is_equal(lapa(j),in_lapa))) then
!Now check lattice level variables
do ibasis = 1, basisnum(j)
if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle lat_loop
end do
lat_type = j
exit lat_loop
end if
end do lat_loop
!If it doesn't match an existing lattice type we add it
if( lat_type == 0) then
lattice_types = lattice_types + 1
basisnum(lattice_types) = in_bnum
basis_type(:,lattice_types) = in_btypes
ng_node(lattice_types) = in_ngnodes
lapa(lattice_types) = in_lapa
lat_type = lattice_types
end if
end subroutine lattice_map
end module elements

162
src/io.f90
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@ -8,9 +8,9 @@ module io
implicit none
integer :: outfilenum = 0, infilenum = 0
character(len=100) :: outfiles(100), infiles(100)
character(len=100) :: outfiles(100), infiles(100), in_lattice_type=''
logical :: force_overwrite
real(kind=dp) :: in_lapa=0.0
public
contains
@ -196,7 +196,7 @@ module io
do i = 1, ele_num
call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
select case(trim(adjustl(type_ele(i))))
case('fcc')
case('fcc','bcc')
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
interp_num = interp_num+1
call apply_periodic(r_interp(:,iatom))
@ -591,7 +591,7 @@ module io
end if
select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
case('restart', 'mb')
case('restart', 'mb', 'cac')
infilenum=infilenum+1
infiles(infilenum) = temp_infile
exit
@ -618,6 +618,8 @@ module io
call read_mb(infiles(i), displace, temp_box_bd)
case('restart')
call read_pycac(infiles(i), displace, temp_box_bd)
case('cac')
call read_lmpcac(infiles(i), displace, temp_box_bd)
case default
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
" is not accepted for writing. Please select from: mb and try again"
@ -776,7 +778,7 @@ module io
integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
atom_type
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3)
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
character(len=100) :: textholder, in_lattype_map(10)
character(len=2) :: atomic_element
!First open the file
@ -949,4 +951,154 @@ module io
call set_max_esize
end if
end subroutine read_pycac
subroutine read_lmpcac(file, displace, temp_box_bd)
!This subroutine is used to read .cac files which are used with the lammpsCAC format
character(len=100), intent(in) :: file
real(kind=dp), dimension(3), intent(in) :: displace
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
character(len=100) :: textholder, element_type
character(len=2) :: atom_species
integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10), esize, &
lat_type
real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), newdisplace(3)
!First check to make sure that we have set the needed variables
if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then
print *, "Please use set_cac to set needed parameters to read in .cac file"
stop 3
end if
!Open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
!Now initialiaze some important variables if they aren't defined
if (max_basisnum==0) max_basisnum = 10
if (max_ng_node==0) max_ng_node=8
!Read header information
read(11, *) textholder
!Read number of elements
read(11, *) ele_in, textholder
read(11, *) type_in, textholder
!Read box_boundaries
read(11,*) temp_box_bd(1:2), textholder
read(11,*) temp_box_bd(3:4), textholder
read(11,*) temp_box_bd(5:6), textholder
!Shift the box boundaries if needed
do i = 1, 3
if (abs(displace(i)) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
else
newdisplace(i)=displace(i)
end if
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do
!Grow box boundaries
call grow_box(temp_box_bd)
!Allocate sub_box
if (sub_box_num == 0) then
call alloc_sub_box(1)
else
call grow_sub_box(1)
end if
!Because orientations and other needed sub_box information isn't really
!present within the .cac file we just default a lot of it.
sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
sub_box_bd(:, sub_box_num+1) = temp_box_bd
sub_box_num = sub_box_num + 1
!Read useless information
read(11,*) textholder
!Read atomic masses
do i = 1, type_in
read(11,*) j, mass, textholder
call ATOMMASSSPECIES(mass, atom_species)
call add_atom_type(atom_species, type_map(i))
end do
!Read useless info
read(11,*) textholder
!Start the reading loop
do i = 1, ele_in
read(11,*) j, element_type, in_basis, esize
!Check to see if we need to grow the max_basis_num
select case(trim(adjustl(element_type)))
case('Eight_Node')
!Read in all the data
do j = 1, 8*in_basis
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
end do
!Now calculate the lattice vectors and shift the nodal points from the corners to the center of the unit cell
!Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
!calculation
lat_vec(:,1) = (r_in(:,1,2) - r_in(:,1,1))/(2*esize)
lat_vec(:,2) = (r_in(:,1,4) - r_in(:,1,1))/(2*esize)
lat_vec(:,3) = (r_in(:,1,5) - r_in(:,1,1))/(2*esize)
!Now shift all the nodal positions
select case(trim(adjustl(in_lattice_type)))
case('fcc','FCC')
do ibasis = 1, in_basis
r_in(:,ibasis,1) = r_in(:,ibasis,1) + lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,2) = r_in(:,ibasis,2) - lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,3) = r_in(:,ibasis,3) - lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,4) = r_in(:,ibasis,4) + lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,5) = r_in(:,ibasis,5) + lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,6) = r_in(:,ibasis,6) - lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,7) = r_in(:,ibasis,7) - lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,8) = r_in(:,ibasis,8) + lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
end do
case default
print *, in_lattice_type, " is not an accepted lattice type. Please select from: fcc"
end select
!Now map it to either an existing or new lattice type
call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
!Now add the element
call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in(:,1:max_basisnum,1:max_ng_node))
case('Atom')
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
call add_atom(in_basis_types(ibasis), sub_box_num, r_in(:,1,1))
end select
end do
end subroutine read_lmpcac
subroutine set_cac(apos)
!This code parses input values
integer, intent(in) :: apos
integer :: arglen, arg_pos
character(len=100) :: textholder
arg_pos = apos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) then
print *, "Missing lattice parameter for set_input_lat"
end if
read(textholder,*) in_lapa
print *, in_lapa
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) then
print *, "Missing lattice type for set_input_lat"
end if
read(textholder,*) in_lattice_type
print *, in_lattice_type
end subroutine set_cac
end module io

3
src/main.f90
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@ -60,6 +60,9 @@ program main
!This lets us know if we need to wrap atomic positions back into the cell
case('-wrap')
wrap_flag=.true.
case('-set_cac')
call set_cac(i)
end select
end do
!Determine if a mode is being used and what it is. The first argument has to be the mode

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