Merge branch 'ft--read_pycac' into 'development'
Ft read pycac See merge request aselimov/cacmb!1
This commit is contained in:
Alex Selimov
commit
fa24b59028
@ -277,6 +277,14 @@ Delete requires the usage of additional keywords to specify which delete action
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This command will delete all overlapping atoms within a specific cutoff radius `rc_off`. This currently does not affect elements.
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### Option sbox_ori
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```
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-sbox_ori sbox [hkl] [hkl] [hkl]
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```
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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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@ -11,7 +11,6 @@ module box
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!command. Currently only mode_merge will require sub_boxes, for mode_create it will always
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!allocate to only 1 sub_box
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integer :: sub_box_num = 0
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integer, allocatable :: sub_box_array_bd(:,:,:)!Boundaries in the atom and element arrays for each sub_box
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real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes
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real(kind=dp), allocatable :: sub_box_bd(:,:)!Boundaries for each of the sub_boxes
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@ -38,11 +37,10 @@ module box
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integer :: i
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allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
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allocate(sub_box_ori(3,3,n), sub_box_bd(6,n))
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do i = 1, n
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sub_box_ori(:,:,i) = identity_mat(3)
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sub_box_bd(:,i) = 0.0_dp
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sub_box_array_bd(:,:,i) = 1
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end do
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end subroutine alloc_sub_box
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@ -65,10 +63,6 @@ module box
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temp_bd(:, sub_box_num+1:) = 0.0_dp
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call move_alloc(temp_bd, sub_box_bd)
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temp_array_bd(:,:,1:sub_box_num) = sub_box_array_bd
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temp_array_bd(:,:,sub_box_num+1:) = 1
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call move_alloc(temp_array_bd, sub_box_array_bd)
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return
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end subroutine grow_sub_box
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@ -29,6 +29,8 @@ subroutine call_option(option, arg_pos)
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call get_command_argument(arg_pos, box_bc)
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arg_pos=arg_pos+1
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bound_called = .true.
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case('-sbox_ori')
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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 default
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200
src/io.f90
200
src/io.f90
@ -389,7 +389,7 @@ module io
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10 format('box matrix')
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11 format(3f23.15)
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12 format('coarse-grained domain')
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13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis type x y z')
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13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis x y z')
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14 format('atomistic domain' / 'ia grain_atom type_atom x y z')
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15 format('maximum lattice periodicity length' / 3f23.15)
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16 format('Number of lattice types and atom types '/ 2i16)
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@ -521,11 +521,10 @@ module io
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write(11,*) box_bd(:)
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!Write the number of sub_boxes in the system
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write(11,*) sub_box_num
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!For every subbox write the orientation, sub box boundary, and sub_box_array_bds
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!For every subbox write the orientation, sub box boundar
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do i = 1, sub_box_num
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write(11,*) sub_box_ori(:,:,i)
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write(11,*) sub_box_bd(:,i)
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write(11,*) ((sub_box_array_bd(j,k,i), j = 1, 2), k = 1, 2)
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end do
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!Write the number of atom types in the current model and all of their names
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@ -590,13 +589,13 @@ 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('xyz', 'lmp', 'vtk', 'mb')
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case('restart', 'mb')
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infilenum=infilenum+1
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infiles(infilenum) = temp_infile
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exit
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case default
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print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
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"please input a filename with extension from following list: mb."
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"please input a filename with extension from following list: mb, restart."
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read(*,*) temp_infile
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end select
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@ -615,6 +614,8 @@ module io
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select case(trim(adjustl(infiles(i)(scan(infiles(i),'.',.true.)+1:))))
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case('mb')
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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 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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@ -643,7 +644,6 @@ module io
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!Read in the box boundary and grow the current active box bd
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read(11, *) temp_box_bd(:)
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print *, "displace", displace
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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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@ -654,7 +654,6 @@ module io
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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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print *, "newdisplace", newdisplace
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call grow_box(temp_box_bd)
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!Read in the number of sub_boxes and allocate the variables
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read(11, *) n
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@ -676,14 +675,8 @@ module io
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sub_box_bd(2*j-1,sub_box_num+i) = sub_box_bd(2*j-1, sub_box_num+i) + displace(j)
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sub_box_bd(2*j,sub_box_num+i) = sub_box_bd(2*j, sub_box_num+i) + displace(j)
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end do
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!Read in sub_box_array_bd
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read(11,*) ((sub_box_array_bd(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
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end do
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!Add the existing element boundaries
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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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!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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@ -715,8 +708,8 @@ module io
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new_loop:do i = 1, new_lattice_types
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old_loop:do j = 1, lattice_types
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!First check all the lattice level variables
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if ((basisnum(i) == basisnum(j)).and. &
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(ng_node(i) == ng_node(j))) then
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if ((basisnum(lattice_types + i) == basisnum(j)).and. &
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(ng_node(lattice_types + i) == ng_node(j))) then
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!Now check the basis level variables
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do ibasis =1, basisnum(i)
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if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
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@ -770,4 +763,181 @@ module io
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call set_max_esize
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end subroutine read_mb
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subroutine read_pycac(file, displace, temp_box_bd)
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!Add subroutine for reading in restart files from PyCAC. This code currently only
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!works for 8 node elements.
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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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integer :: i, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
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atom_type_map(10), etype_map(10), etype, lat_type, new_lattice_map(10), &
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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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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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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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!Disregard unneeded information
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do i = 1, 3
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read(11,*) textholder
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end do
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!Read element number
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read(11,*) in_eles
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!Discard info and read ng_max_node
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do i = 1, 5
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read(11,*) textholder
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end do
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read(11,*) max_ng_node
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!Read element types (only needed inside this subroutine)
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read(11,*) textholder
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read(11,*) ele_types
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!Read in atom num
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read(11,*) textholder
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read(11,*) in_atoms
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!read in lattice_types and atom types
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do i = 1,3
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read(11,*) textholder
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end do
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read(11,*) in_lat_num, in_atom_types
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!Read define atom_types by name
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read(11,*) textholder
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do i = 1, in_atom_types
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read(11,*) j, atomic_element
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call add_atom_type(atomic_element, atom_type_map(i))
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end do
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!Read in the boundary
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read(11,*) textholder
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read(11,*) box_bc
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!Disregard useless info
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do i = 1, 3
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read(11,*) textholder
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end do
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!Read in lat_type map
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do i = 1, in_lat_num
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read(11,*) j, in_lattype_map(i)
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ng_node(lattice_types+i) = 8 !Only cubic elements are currently supported in pyCAC
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end do
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!Disregard useless info
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do i =1 , 3
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read(11,*) textholder
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end do
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!Read box boundaries and displace them if necessary
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read(11,*) temp_box_bd(:)
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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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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 restart 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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!Read in more useless info
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do i = 1, 10
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read(11,*) textholder
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end do
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!Now read the ele_type to size and lat map
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do i = 1, ele_types
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read(11,*) j, etype_map(i)
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etype_map(i) = etype_map(i) + 1
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end do
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!Now set up the lattice types. In this code it assumes that lattice_type 1 maps to
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!atom type 1 because it only allows 1 atom per basis in pyCAC at the moment.
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do i = 1, in_lat_num
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basisnum(lattice_types+i) = 1
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basis_type(1,lattice_types+i) = atom_type_map(i)
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end do
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!Figure out the lattice type maps in case we have repeated lattice_types
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k = lattice_types + 1
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new_lattice_map(:) = 0
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new_loop:do i = 1, in_lat_num
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old_loop:do j = 1, lattice_types
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!First check all the lattice level variables
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if ((basisnum(lattice_types+i) == basisnum(j)).and. &
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(ng_node(lattice_types+i) == ng_node(j))) then
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!Now check the basis level variables
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do ibasis =1, basisnum(i)
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if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
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cycle old_loop
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end if
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end do
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new_lattice_map(i) = j
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cycle new_loop
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end if
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end do old_loop
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new_lattice_map(i) = k
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k = k+1
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end do new_loop
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!Read more useless data
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read(11,*) textholder
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read(11,*) textholder
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!set max values and allocate variables
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max_basisnum = maxval(basisnum)
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max_ng_node = maxval(ng_node)
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call grow_ele_arrays(in_eles, in_atoms)
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!Now start reading the elements
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do i = 1, in_eles
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read(11,*) j, etype, k, lat_type
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do inod = 1, 8
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read(11, *) j, k, r_in(:,1,inod)
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r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
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end do
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call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
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end do
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!Read useless data
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read(11,*) textholder
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read(11,*) textholder
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do i = 1, in_atoms
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read(11,*) j, k, atom_type, r_in_atom(:)
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r_in_atom = r_in_atom + newdisplace
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call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
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end do
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!Close file
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close(11)
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lattice_types = maxval(new_lattice_map)
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sub_box_num = sub_box_num + 1
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call set_max_esize
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end subroutine read_pycac
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end module io
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@ -158,9 +158,6 @@ module mode_create
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sub_box_num = 1
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sub_box_ori(:,:,1) = orient
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sub_box_bd(:,1) = box_bd
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sub_box_array_bd(1,:,1) = 1
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sub_box_array_bd(2,1,1) = atom_num
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sub_box_array_bd(2,2,1) = ele_num
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end subroutine create
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!This subroutine parses the command and pulls out information needed for mode_create
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subroutine parse_command(arg_pos)
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@ -364,7 +364,7 @@ module opt_group
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if (max_remesh) then
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max_loops = (remesh_size-2)/2
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max_loops = (remesh_size-3)/2
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else
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max_loops = 1
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end if
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@ -133,4 +133,29 @@ module opt_orient
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box_bd = orig_box_bd
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end subroutine unorient
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subroutine sbox_ori(arg_pos)
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integer, intent(inout) :: arg_pos
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integer :: i, sbox_in, arg_len
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real(kind = dp) :: new_orient(3,3)
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character(len=100) :: textholder
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character(len=8) :: ori_string
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder,arg_len)
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if (arg_len== 0) stop 'Missing sbox in sbox_ori command'
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read(textholder,*) sbox_in
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do i = 1, 3
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, ori_string, arg_len)
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if (arg_len == 0) print *, "Missing orientation vector in -orient option"
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call parse_ori_vec(ori_string, new_orient(i,:))
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new_orient(i,:) = new_orient(i,:) / norm2(new_orient(i,:))
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end do
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sub_box_ori(:,:,sbox_in) = new_orient
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arg_pos = arg_pos + 1
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end subroutine sbox_ori
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end module opt_orient
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