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Merge branch 'ft--read_pycac' into 'development'

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Ft  read pycac

See merge request aselimov/cacmb!1
master
Alex Selimov 4 years ago
parent 5b767038c2 a9b266d757
commit fa24b59028
7 changed files with 222 additions and 26 deletions
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8
README.md
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@ -277,6 +277,14 @@ Delete requires the usage of additional keywords to specify which delete action
This command will delete all overlapping atoms within a specific cutoff radius `rc_off`. This currently does not affect elements.
### Option sbox_ori
```
-sbox_ori sbox [hkl] [hkl] [hkl]
```
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

8
src/box.f90
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@ -11,7 +11,6 @@ module box
!command. Currently only mode_merge will require sub_boxes, for mode_create it will always
!allocate to only 1 sub_box
integer :: sub_box_num = 0
integer, allocatable :: sub_box_array_bd(:,:,:)!Boundaries in the atom and element arrays for each sub_box
real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes
real(kind=dp), allocatable :: sub_box_bd(:,:)!Boundaries for each of the sub_boxes
@ -38,11 +37,10 @@ module box
integer :: i
allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
allocate(sub_box_ori(3,3,n), sub_box_bd(6,n))
do i = 1, n
sub_box_ori(:,:,i) = identity_mat(3)
sub_box_bd(:,i) = 0.0_dp
sub_box_array_bd(:,:,i) = 1
end do
end subroutine alloc_sub_box
@ -65,10 +63,6 @@ module box
temp_bd(:, sub_box_num+1:) = 0.0_dp
call move_alloc(temp_bd, sub_box_bd)
temp_array_bd(:,:,1:sub_box_num) = sub_box_array_bd
temp_array_bd(:,:,sub_box_num+1:) = 1
call move_alloc(temp_array_bd, sub_box_array_bd)
return
end subroutine grow_sub_box

2
src/call_option.f90
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@ -29,6 +29,8 @@ subroutine call_option(option, arg_pos)
call get_command_argument(arg_pos, box_bc)
arg_pos=arg_pos+1
bound_called = .true.
case('-sbox_ori')
call sbox_ori(arg_pos)
case('-delete')
call run_delete(arg_pos)
case default

200
src/io.f90
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@ -389,7 +389,7 @@ module io
10 format('box matrix')
11 format(3f23.15)
12 format('coarse-grained domain')
13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis type x y z')
13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis x y z')
14 format('atomistic domain' / 'ia grain_atom type_atom x y z')
15 format('maximum lattice periodicity length' / 3f23.15)
16 format('Number of lattice types and atom types '/ 2i16)
@ -521,11 +521,10 @@ module io
write(11,*) box_bd(:)
!Write the number of sub_boxes in the system
write(11,*) sub_box_num
!For every subbox write the orientation, sub box boundary, and sub_box_array_bds
!For every subbox write the orientation, sub box boundar
do i = 1, sub_box_num
write(11,*) sub_box_ori(:,:,i)
write(11,*) sub_box_bd(:,i)
write(11,*) ((sub_box_array_bd(j,k,i), j = 1, 2), k = 1, 2)
end do
!Write the number of atom types in the current model and all of their names
@ -590,13 +589,13 @@ module io
end if
select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
case('xyz', 'lmp', 'vtk', 'mb')
case('restart', 'mb')
infilenum=infilenum+1
infiles(infilenum) = temp_infile
exit
case default
print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
"please input a filename with extension from following list: mb."
"please input a filename with extension from following list: mb, restart."
read(*,*) temp_infile
end select
@ -615,6 +614,8 @@ module io
select case(trim(adjustl(infiles(i)(scan(infiles(i),'.',.true.)+1:))))
case('mb')
call read_mb(infiles(i), displace, temp_box_bd)
case('restart')
call read_pycac(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"
@ -643,7 +644,6 @@ module io
!Read in the box boundary and grow the current active box bd
read(11, *) temp_box_bd(:)
print *, "displace", displace
do i = 1, 3
if (abs(displace(i)) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
@ -654,7 +654,6 @@ module io
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do
print *, "newdisplace", newdisplace
call grow_box(temp_box_bd)
!Read in the number of sub_boxes and allocate the variables
read(11, *) n
@ -676,14 +675,8 @@ module io
sub_box_bd(2*j-1,sub_box_num+i) = sub_box_bd(2*j-1, sub_box_num+i) + displace(j)
sub_box_bd(2*j,sub_box_num+i) = sub_box_bd(2*j, sub_box_num+i) + displace(j)
end do
!Read in sub_box_array_bd
read(11,*) ((sub_box_array_bd(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
end do
!Add the existing element boundaries
sub_box_array_bd(:,1,sub_box_num+1:) = sub_box_array_bd(:,1,sub_box_num+1:) + atom_num
sub_box_array_bd(:,2,sub_box_num+1:) = sub_box_array_bd(:,2,sub_box_num+1:) + ele_num
!Read in the number of atom types and all their names
read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)
!Now fit these into the global list of atom types, after this new_type_to_type is the actual global
@ -715,8 +708,8 @@ module io
new_loop:do i = 1, new_lattice_types
old_loop:do j = 1, lattice_types
!First check all the lattice level variables
if ((basisnum(i) == basisnum(j)).and. &
(ng_node(i) == ng_node(j))) then
if ((basisnum(lattice_types + i) == basisnum(j)).and. &
(ng_node(lattice_types + i) == ng_node(j))) then
!Now check the basis level variables
do ibasis =1, basisnum(i)
if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
@ -770,4 +763,181 @@ module io
call set_max_esize
end subroutine read_mb
subroutine read_pycac(file, displace, temp_box_bd)
!Add subroutine for reading in restart files from PyCAC. This code currently only
!works for 8 node elements.
character(len=100), intent(in) :: file
real(kind=dp), dimension(3), intent(in) :: displace
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
integer :: i, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
atom_type_map(10), etype_map(10), etype, lat_type, new_lattice_map(10), &
atom_type
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3)
character(len=100) :: textholder, in_lattype_map(10)
character(len=2) :: atomic_element
!First open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
!Disregard unneeded information
do i = 1, 3
read(11,*) textholder
end do
!Read element number
read(11,*) in_eles
!Discard info and read ng_max_node
do i = 1, 5
read(11,*) textholder
end do
read(11,*) max_ng_node
!Read element types (only needed inside this subroutine)
read(11,*) textholder
read(11,*) ele_types
!Read in atom num
read(11,*) textholder
read(11,*) in_atoms
!read in lattice_types and atom types
do i = 1,3
read(11,*) textholder
end do
read(11,*) in_lat_num, in_atom_types
!Read define atom_types by name
read(11,*) textholder
do i = 1, in_atom_types
read(11,*) j, atomic_element
call add_atom_type(atomic_element, atom_type_map(i))
end do
!Read in the boundary
read(11,*) textholder
read(11,*) box_bc
!Disregard useless info
do i = 1, 3
read(11,*) textholder
end do
!Read in lat_type map
do i = 1, in_lat_num
read(11,*) j, in_lattype_map(i)
ng_node(lattice_types+i) = 8 !Only cubic elements are currently supported in pyCAC
end do
!Disregard useless info
do i =1 , 3
read(11,*) textholder
end do
!Read box boundaries and displace them if necessary
read(11,*) temp_box_bd(:)
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
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 restart 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
!Read in more useless info
do i = 1, 10
read(11,*) textholder
end do
!Now read the ele_type to size and lat map
do i = 1, ele_types
read(11,*) j, etype_map(i)
etype_map(i) = etype_map(i) + 1
end do
!Now set up the lattice types. In this code it assumes that lattice_type 1 maps to
!atom type 1 because it only allows 1 atom per basis in pyCAC at the moment.
do i = 1, in_lat_num
basisnum(lattice_types+i) = 1
basis_type(1,lattice_types+i) = atom_type_map(i)
end do
!Figure out the lattice type maps in case we have repeated lattice_types
k = lattice_types + 1
new_lattice_map(:) = 0
new_loop:do i = 1, in_lat_num
old_loop:do j = 1, lattice_types
!First check all the lattice level variables
if ((basisnum(lattice_types+i) == basisnum(j)).and. &
(ng_node(lattice_types+i) == ng_node(j))) then
!Now check the basis level variables
do ibasis =1, basisnum(i)
if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
cycle old_loop
end if
end do
new_lattice_map(i) = j
cycle new_loop
end if
end do old_loop
new_lattice_map(i) = k
k = k+1
end do new_loop
!Read more useless data
read(11,*) textholder
read(11,*) textholder
!set max values and allocate variables
max_basisnum = maxval(basisnum)
max_ng_node = maxval(ng_node)
call grow_ele_arrays(in_eles, in_atoms)
!Now start reading the elements
do i = 1, in_eles
read(11,*) j, etype, k, lat_type
do inod = 1, 8
read(11, *) j, k, r_in(:,1,inod)
r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
end do
call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
end do
!Read useless data
read(11,*) textholder
read(11,*) textholder
do i = 1, in_atoms
read(11,*) j, k, atom_type, r_in_atom(:)
r_in_atom = r_in_atom + newdisplace
call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
end do
!Close file
close(11)
lattice_types = maxval(new_lattice_map)
sub_box_num = sub_box_num + 1
call set_max_esize
end subroutine read_pycac
end module io

3
src/mode_create.f90
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@ -158,9 +158,6 @@ module mode_create
sub_box_num = 1
sub_box_ori(:,:,1) = orient
sub_box_bd(:,1) = box_bd
sub_box_array_bd(1,:,1) = 1
sub_box_array_bd(2,1,1) = atom_num
sub_box_array_bd(2,2,1) = ele_num
end subroutine create
!This subroutine parses the command and pulls out information needed for mode_create
subroutine parse_command(arg_pos)

2
src/opt_group.f90
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@ -364,7 +364,7 @@ module opt_group
if (max_remesh) then
max_loops = (remesh_size-2)/2
max_loops = (remesh_size-3)/2
else
max_loops = 1
end if

25
src/opt_orient.f90
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@ -133,4 +133,29 @@ module opt_orient
box_bd = orig_box_bd
end subroutine unorient
subroutine sbox_ori(arg_pos)
integer, intent(inout) :: arg_pos
integer :: i, sbox_in, arg_len
real(kind = dp) :: new_orient(3,3)
character(len=100) :: textholder
character(len=8) :: ori_string
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder,arg_len)
if (arg_len== 0) stop 'Missing sbox in sbox_ori command'
read(textholder,*) sbox_in
do i = 1, 3
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, ori_string, arg_len)
if (arg_len == 0) print *, "Missing orientation vector in -orient option"
call parse_ori_vec(ori_string, new_orient(i,:))
new_orient(i,:) = new_orient(i,:) / norm2(new_orient(i,:))
end do
sub_box_ori(:,:,sbox_in) = new_orient
arg_pos = arg_pos + 1
end subroutine sbox_ori
end module opt_orient
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