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Fixes to mode_create, moved basis_pos from elements to mode_create, added the mb file output style

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This commit is contained in:
Alex Selimov 2019-12-05 08:36:22 -05:00
parent 033b44dc40
commit fa1cb6ce58
3 changed files with 70 additions and 26 deletions
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12
src/elements.f90
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@ -30,19 +30,15 @@ module elements
!Below are lattice type arrays which provide information on the general form of the elements.
!We currently have a limit of 10 lattice types for simplicities sake but this can be easily increased.
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
!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), basis_type(10,10)!Max basis atom number, number of basis atoms in each lattice type
real(kind=dp) :: basis_pos(3,10,10) !Basis atom positions
!Simulation cell parameters
real(kind=dp) :: box_bd(6)
integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type
integer :: basis_type(10,10)
public
contains
@ -89,7 +85,6 @@ module elements
max_basisnum = 0
basisnum(:) = 0
basis_pos(:,:,:) = 0.0_dp
ng_node(:) = 0
end subroutine lattice_init
@ -304,4 +299,5 @@ module elements
return
end subroutine rhombshape
end module elements

62
src/io.f90
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@ -3,6 +3,7 @@ module io
use elements
use parameters
use atoms
use box
implicit none
@ -56,18 +57,10 @@ module io
cycle
end if
select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
case('xyz')
case('xyz', 'lmp', 'vtk', 'mb')
outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile
exit
case('lmp')
outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile
exit
case('vtk')
outfilenum=outfilenum+1
outfiles(outfilenum)=temp_outfile
exit
case default
print *, "File type: ", trim(temp_outfile(scan(temp_outfile,'.',.true.):)), "not currently accepted. ", &
"please input a filename with extension from following list: xyz, lmp, vtk."
@ -96,6 +89,8 @@ module io
call write_lmp(outfiles(i))
case('vtk')
call write_vtk(outfiles(i))
case('mb')
call write_mb(outfiles(i))
case default
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
" is not accepted for writing. Please select from: xyz and try again"
@ -276,4 +271,53 @@ module io
end do
close(11)
end subroutine
subroutine write_mb(file)
!This subroutine writes the cacmb formatted file which provides necessary information for building models
character(len=100), intent(in) :: file
integer :: i, j, inod, ibasis
!Open the .mb file for writing
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
!First write the box boundary information
!Write the global box boundaries
write(11,*) box_bd(:)
!Write the number of sub_boxes in the system
write(11,*) sub_box_num
!For every subbox write the orientation and sub box boundary
do i = 1, sub_box_num
write(11,*) sub_box_ori(:,:,i)
write(11,*) sub_box_bd(:,i)
end do
!Write the number of atom types in the current model and all of their names
write(11,*) atom_types, (type_to_name(i), i=1, atom_types)
!Write the number of lattice_types, basisnum and number of nodes for each lattice type
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
write(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
!Now write the numbers of elements and atoms
write(11,*) atom_num, ele_num
!Write out atoms first
do i = 1, atom_num
write(11,*) type_atom(i), r_atom(:,i)
end do
!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
do i = 1, ele_num
write(11, *) i, lat_ele(i), size_ele(i), type_ele(i)
do inod = 1, ng_node(lat_ele(i))
do ibasis =1, basisnum(lat_ele(i))
write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
end do
end do
end do
end subroutine write_mb
end module io

22
src/mode_create.f90
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@ -6,13 +6,15 @@ module mode_create
use io
use subroutines
use elements
use box
implicit none
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), &
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3)
integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6)
integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
basis_pos(3,10)
logical :: dup_flag, dim_flag
real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:)
@ -98,7 +100,7 @@ module mode_create
!Add the basis atoms to the unit cell
do inod = 1, max_ng_node
do ibasis = 1, basisnum(1)
r_node_temp(:,ibasis,inod) = cell_mat(:,inod) + basis_pos(:,ibasis,1) + origin(:)
r_node_temp(:,ibasis,inod) = cell_mat(:,inod) + basis_pos(:,ibasis) + origin(:)
end do
end do
do i = 1,3
@ -115,7 +117,7 @@ module mode_create
if(lat_atom_num > 0) then
do i = 1, lat_atom_num
do ibasis = 1, basisnum(1)
call add_atom(basis_type(ibasis,1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis,1))
call add_atom(basis_type(ibasis, 1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis))
end do
end do
deallocate(r_atom_lat)
@ -125,7 +127,7 @@ module mode_create
do i = 1, lat_ele_num
do inod= 1, ng_node(1)
do ibasis = 1, basisnum(1)
r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis,1)
r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis)
end do
end do
call add_element(element_type, esize, 1, r_node_temp)
@ -258,13 +260,17 @@ module mode_create
!Now normalize the orientation matrix
orient = matrix_normal(orient,3)
!Set lattice_num to 1
lattice_types = 1
!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
max_basisnum = 1
basisnum(1) = 1
call add_atom_type(name, basis_type(1,1)) !If basis command not defined then we use name as the atom_name
basis_pos(:,1,1) = 0.0_dp
basis_pos(:,1) = 0.0_dp
end if
!
end subroutine
subroutine build_with_rhomb(box_in_lat, transform_matrix)
@ -432,12 +438,11 @@ module mode_create
end do
!Now figure out how many lattice points could not be contained in elements
print *, count(lat_points)
allocate(r_atom_lat(3,count(lat_points)))
lat_atom_num = 0
do ix = 1, bd_in_array(3)
do iz = 1, bd_in_array(3)
do iy = 1, bd_in_array(2)
do iz = 1, bd_in_array(1)
do ix = 1, bd_in_array(1)
!If this point is a lattice point then save the lattice point as an atom
if (lat_points(ix,iy,iz)) then
v= (/ real(ix,dp), real(iy, dp), real(iz,dp) /)
@ -453,7 +458,6 @@ module mode_create
end do
end do
print *, lat_atom_num
end if
end subroutine build_with_rhomb